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DOE OSTI2020

Advanced Laboratory and Field Arrays: Evaluating Sampling Techniques for MHK Biological Monitoring (Task 6)

The overall goal of the task was to identify cost effective biological sampling techniques for MHK environmental monitoring. Protected, demersal, and pelagic fish and selected nektonic invertebrates were surveyed using capture and remote sensing techniques at the PacWave sites. The performance of capture and remote sensing monitoring techniques were evaluated and generic nekton monitoring indices were developed for MHK technologies and sites. In parallel to data collections at the PacWave site, the ability of regression models to characterize, detect, and predict change in acoustic data was evaluated using acoustic data collected in Admiralty Inlet, WA, during a biological monitoring study of the proposed SnoPud tidal turbine project site. Expected outcomes of these efforts included an evaluation of instrumentation and techniques used to monitor biological variability; identification of data streams that can be used to detect and quantify change; and sampling requirements to ensure detection of change in monitored variables.

13 HYDRO ENERGY↗

DOE OSTI2025

East Tennessee Technology Park Biological Monitoring and Abatement Program 2024 Calendar Year Report

The East Tennessee Technology Park (ETTP) Biological Monitoring and Abatement Program (BMAP) consists of three tasks that reflect different but complementary approaches to evaluating the ecological integrity of waters near ETTP. These tasks include (1) bioaccumulation monitoring of fish and clams, (2) benthic macroinvertebrate species richness and density monitoring, and (3) fish community monitoring. The sampling and analysis requirements for the ETTP BMAP in calendar year 2024, covering in part both FY 2024 and FY 2025, are outlined in the respective FY sampling and analysis plans (UCOR 2023, 2024). Sampled water bodies and locations for the ETTP BMAP are shown in Figures 1 and 2. This ETTP BMAP report presents the CY 2024 results and provides context with results from previous years. The report also includes Oak Ridge National Laboratory (ORNL)–generated biological monitoring data collected for other US Department of Energy programs, including the UCOR Water Resources Restoration Program (WRRP) off-site fish bioaccumulation data (UCOR 2023) and select Y-12 National Security Complex (Y-12) BMAP fish bioaccumulation data. Historical data collected for the ETTP BMAP and other programs in the nearby Poplar Creek and Clinch River are provided where appropriate. This progress report provides an update on the biological monitoring activities supporting the ETTP UCOR Environmental Compliance organization, which sponsors the ETTP BMAP. In addition to this internal reporting, ETTP BMAP results are provided in the annual remediation effectiveness reports and the annual site environmental reports, both of which are publicly available. BMAP data are also available to the public via the Oak Ridge Environmental Information System (https://ucor.com/oak-ridge-environmental-information-system-oreis/).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Distinct Clinical Impact and Biological Function of Angiopoietin and Angiopoietin-like Proteins in Human Breast Cancer

Secreted angiopoietin/angiopoietin-like (ANGPT/ANGPTL) proteins are involved in many biological processes. However, the role of these proteins in human breast cancers (BCs) remains largely unclear. Here, we conducted integrated omics analyses to evaluate the clinical impact of ANGPT/ANGPTL proteins and to elucidate their biological functions. In BCs, we identified rare mutations in ANGPT/ANGPTL genes, frequent gains of ANGPT1, ANGPT4, and ANGPTL1, and frequent losses of ANGPT2, ANGPTL5, and ANGPTL7, but observed that ANGPTL1, 2, and 4 were robustly downregulated in multiple datasets. The expression levels of ANGPTL1, 5, and 8 were positively correlated with overall survival (OS), while the expression levels of ANGPTL4 were negatively correlated with OS. Additionally, the expression levels of ANGPTL1 and 7 were positively correlated with distant metastasis-free survival (DMFS), while the expression levels of ANGPT2 and ANGPTL4 were negatively correlated with DMFS. The prognostic impacts of ANGPT/ANGPTL genes depended on the molecular subtypes and on clinical factors. We discovered that various ANGPT/ANGPTL genes were co-expressed with various genes involved in different pathways. Finally, with the exception of ANGPTL3, the remaining genes showed significant correlations with cancer-associated fibroblasts, endothelial cells, and microenvironment score, whereas only ANGPTL6 was significantly correlated with immune score. Our findings provide strong evidence for the distinct clinical impact and biological function of ANGPT/ANGPTL proteins, but the question of whether some of them could be potential therapeutic targets still needs further investigation in BCs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Methods, systems, and compositions for studying solvent accessibility and three-dimensional structure of biological molecules

This disclosure provides methods, systems, and compositions of matter for studying solvent accessibility and three-dimensional structure of biological molecules. A plasma can be used to generate marker radicals, which can interact with a biological molecule and mark the solvent-accessible portions of the biological molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Better Living Through Biology: Studying Enzymes to Make Industrial Processes More Efficient

In biology, enzymes are the molecular machinery needed to speed up slow chemical reactions for life to occur. These molecular machines enhance chemical processes to a large degree, allowing for improbable and challenging chemical reactions to efficiently happen in water at room temperature. Many microorganisms have specialized enzymes used to tackle particularly challenging chemistry that they experience in their own environment. Our group is studying a specific enzyme using a reaction called "electron bifurcation" that energetically pairs electrons and is analogous to a trampoline, using one person's jump to propel another person higher than they could by themselves. We have learned that certain metal- and vitamin-containing pathways in this protein funnel electrons in specific directions. Our investigation into this enzyme is the foundation for future industrial applications, ranging from biological production of sustainable aviation fuel from CO2, production of nitrogen-based fertilizers, and biologically remediating environmental contamination.

BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Engineering the Future through Synthetic Biology

The last two decades have witnessed tremendous progress in synthetic biology. Despite the technological advances, the maturing field has yet to transition from fundamental study to translational practice. In this perspective article, I discuss my vision to enable this transition. Here, with this vision, our next generation will solve global problems through synthetic biology.

42 ENGINEERING↗

DOE OSTI2024

Refinement of the “ Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration

Members of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Assessment of the Biological Impact of Engineered Nanomaterials Using Mass Spectrometry-based MultiOmics Approaches

The widespread use of engineered nanomaterials (ENMs) has expanded further than our understanding of their toxicity, prompting research into the biological responses against exposure to such materials. Genomics and transcriptomics have been extensively used to evaluate the biological effects of exposure to various ENMs. By determining gene activities, these studies provided valuable information to infer how cells respond to the toxicological effects of many ENMs. The application of mass spectrometry (MS)-based omics tools, such as proteomics, lipidomics, and metabolomics, offer post-genomic perspectives of what cellular processes are altered. Individually, these technologies have revealed the proteome, lipidome, and metabolome landscape upon exposure to ENMs. Together, these approaches demonstrate the ENM-induced adaptation in a broad range of cellular processes at multiple levels and the complexity of ENM-cell interactions. As a result, integrating multiple layers of MS-based omics data is trending to complement genomics data. In this review chapter, we discuss the applications of these tools for a comprehensive systems-level characterization of the biological responses induced by engineered nanomaterials.

Engineered nanomaterials, Proteomics, Metabolomics↗

DOE OSTI2020

Systems with greater perenniality and crop diversity enhance soil biological health

Abstract Soil health has received heightened interest because of its association with long‐term agricultural sustainability and ecological benefits, including soil carbon (C) accumulation. We examined the effects of crop diversity and perenniality on soil biological health and assessed impacts on mineralization and C stabilization processes across 10 systems including four no‐till annual row crops, two monoculture perennials, and four polyculture perennials. Crop diversity increased soil biological health in both annual and perennial systems. Rotated annuals with a cover crop increased permanganate oxidizable C (POXC) and soil organic matter relative to continuous corn ( Zea mays L.). Perennial polycultures also had 88% and 23% greater mineralizable C relative to the annual and monoculture perennial systems, respectively. All polyculture perennials had significantly greater POXC relative to switchgrass ( Panicum virgatum L.) and annual systems, with the exception of restored prairie. Of the systems assessed in this study, incorporating perennial polycultures into rotations is the most effective way to increase soil biological health and enhance C stabilization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

A Step-by-Step Protocol from METASPACE to Biological Interpretation

Mass spectrometry imaging (MSI) represents an exceptional tool for exploring complex biological systems spatially at the molecular level. However, due to its multidimensional nature and large-scale data output, it presents considerable challenges when it comes to extracting meaningful biological insights. Recent advancements, such as the METASPACE platform, have enabled researchers to efficiently process, annotate, and interpret MSI datasets by leveraging machine learning and cloud-based infrastructure. In this tutorial, we present a detailed and user-friendly R-pipeline designed to help METASPACE users navigate untargeted metabolomic annotations and transform them into practical insights about their biological systems. By combining METASPACE annotations with rapid R-based screening, this workflow not only streamlined the analytical process but also enhanced the understanding of spatial molecular distribution, especially for complex systems. Here, this easy-to-follow approach has the potential for applications in diagnostics, drug discovery, environmental and ecological processes, and more. We envision this pipeline to be particularly useful for newcomers to the field of MSI and

Moreno Pedraza, Abigail↗

DOE OSTI2024

Dosimetric and biological impact of activity extravasation of radiopharmaceuticals in PET imaging

The increasing use of nuclear medicine and PET imaging has intensified scrutiny of radiotracer extravasation. To our knowledge, this topic is understudied but holds great potential for enhancing our understanding of extravasation in clinical PET imaging. This work aims to (1) quantify the absorbed doses from radiotracer extravasation in PET imaging, both locally at the site of extravasation and with the extravasation location as a source of exposure to bodily organs and (2) assess the biological ramifications within the injection site at the cellular level. A radiation dosimetry simulation was performed using a whole-body 4D Extended Cardiac-Torso (XCAT) phantom embedded in the GATE Monte Carlo platform. A 10-mCi dose of 18 F-FDG was chosen to simulate a typical clinical PET scan scenario, with 10% of the activity extravasated in the antecubital fossa of the right arm of the phantom. The extravasation volume was modeled as a 5.5 mL rectangle in the hypodermal layer of skin. Absorbed dose contributions were calculated for the first two half-lives, assuming biological clearance thereafter. Dose calculations were performed as absorbed doses at the organ and skin levels. Energy deposition was simulated both at the local extravasation site and in multiple organs of interest and converted to absorbed doses based on their respective masses. Each simulation was repeated ten times to estimate Monte Carlo uncertainties. Biological impacts on cells within the extravasated volume were evaluated by randomizing cells and exposing them to a uniform radiation source of 18 F and 68 Ga. Particle types, their energies, and direction cosines were recorded in phase space files using a separate Geant4 simulation to characterize their entry into the nucleus of the cellular volume. Subsequently, the phase space files were imported into the TOPAS-nBio simulation to assess the extent of DNA damage, including double-strand breaks (DSBs) and single-strand breaks (SSBs). Organ-level dosimetric estimations are presented for 18 F and 68 Ga radionuclides in various organs of interest. With 10% extravasation, the hypodermal layer of the skin received the highest absorbed dose of 1.32 ± 0.01 Gy for 18 F and 0.99 ± 0.01 Gy for 68 Ga. The epidermal and dermal layers received absorbed doses of 0.07 ± 0.01 Gy and 0.13 ± 0.01 Gy for 18 F, and 0.14 ± 0.01 Gy and 0.29 ± 0.01 Gy for 68 Ga, respectively. In the extravasated volume, 18 F caused an average absorbed dose per nucleus of 0.17 ± 0.01 Gy, estimated to result in 10.58 ± 0.50 DSBs and 268.11 ± 12.43 SSBs per nucleus. For 68 Ga, the absorbed dose per nucleus was 0.11 ± 0.01 Gy, leading to an estimated 6.49 ± 0.34 DSBs and 161.24 ± 8.12 SSBs per nucleus. Absorbed doses in other organs were on the order of micro-gray (µGy). The likelihood of epidermal erythema resulting from extravasation during PET imaging is low, as the simulated absorbed doses to the epidermis remain below the thresholds that trigger such effects. Moreover, the organ-level absorbed doses were found to be clinically insignificant across various simulated organs. The minimal DNA damage at the extravasation site suggests that long-term harm, such as radiation-induced carcinogenesis, is highly unlikely.

DNA strand breaks↗

DOE OSTI2024

Density estimation via measure transport: Outlook for applications in the biological sciences

Abstract One among several advantages of measure transport methods is that they allow or a unified framework for processing and analysis of data distributed according to a wide class of probability measures. Within this context, we present results from computational studies aimed at assessing the potential of measure transport techniques, specifically, the use of triangular transport maps, as part of a workflow intended to support research in the biological sciences. Scenarios characterized by the availability of limited amount of sample data, which are common in domains such as radiation biology, are of particular interest. We find that when estimating a distribution density function given limited amount of sample data, adaptive transport maps are advantageous. In particular, statistics gathered from computing series of adaptive transport maps, trained on a series of randomly chosen subsets of the set of available data samples, leads to uncovering information hidden in the data. As a result, in the radiation biology application considered here, this approach provides a tool for generating hypotheses about gene relationships and their dynamics under radiation exposure.

gene expression data↗

DOE OSTI2025

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Computational studies of hydraulic stressors for biological performance assessment in a hydropower plant with Kaplan turbine

We report Hydropower is currently one of the preeminent sources of renewable energy in the United States and globally. Hydropower plants also have detrimental impacts on the environment and ecology, including direct impacts to anadromous fish populations. The computational fluid dynamics (CFD) – based Biological Performance Assessment (BioPA) toolset is used for biological evaluations of fish passage through hydropower plants. The hydraulic environment of a hydropower plant was evaluated using CFD coupled with discrete element method (DEM) simulations. The predicted flow field and particle collision rate were validated against the experimental data in a water flume that has an idealized hydroturbine distributor geometry. Flow simulations were conducted to evaluate the hydraulic stressors, such as nadir pressure, fluid shear, runner collision, in a physical scale in a hydropower plant with Kaplan turbine which are responsible for injury and mortality of fish in a downstream migration. The cumulative exposure probability for the nadir pressure and collision with turbine runner was found to decrease with increased discharge rate. The lowest discharge rate shows the higher value of cumulative shear exposure probability. The maximum value of collision velocity increases with increased discharge rate. We offer the conclusions that will help in understanding various hydraulic stressors for biological assessment for environmentally sustainable hydroturbine passage.

13 HYDRO ENERGY↗

DOE OSTI2022

Current nature-based biological practices for rare earth elements extraction and recovery: Bioleaching and biosorption

There is a growing demand for advancing products and renewable technologies worldwide that rely on rare earth elements (REEs), including those directly necessary for a low-carbon energy transition, national security applications, and consumer electronics. This study focuses on current nature-based biological methods (i.e., bioleaching and biosorption) for REEs extraction from electronic wastes (e-wastes) and ore deposits. Herein, comprehensive narrative and systematic reviews of bioleaching and biosorption extraction methods are performed to identify their sustainability challenges and benefits, and highlight the potential pathways that would address the existing gaps. From the narrative review, it is evident that biological methods for REEs extraction are more environmentally friendly than conventional methods currently used in the REE mining industry (e.g., acid leaching and solvent extraction). From the systematic review, it is clear that bioleaching and biosorption research has been a rapidly growing field of interest over the last 10 years, particularly for precious metals extraction (e.g., copper and gold). From both reviews, it is apparent that REEs extraction from domestic ore deposits alone is inadequate, and sustainable REEs recovery from e-wastes is also necessary to meet the growing REEs demand. It is concluded that targeted mixed REEs extraction for specific products can be a potential pathway for sustainable REEs extraction from both ore and e-wastes that would reduce separation costs and emissions from the associated use of harsh chemicals. It is further concluded that nature-based biological REE extraction solutions offer an opportunity to generate significant socio-economic and environmental benefits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Designed and biologically active protein lattices

Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Development and flight-testing of modular autonomous cultivation systems for biological plastics upcycling aboard the ISS

Cultivation of microorganisms in space has enormous potential to enable in-situ resource utilization (ISRU) Here, we develop an autonomous payload with fully programmable serial passaging and sample preservation, termed the Modular Open Biological Platform (MOBP), and flight-test the MOBP aboard the International Space Station (ISS) by conducting enzymatic and microbial plastics upcycling experiments. The MOBP is a compact, modular bioreactor system that allows for sustained microbial growth via automated media transfers, such as those for sample collection and storage for terrestrial analyses, and precise data monitoring from integrated sensors. The MOBP was flight-tested with two experiments designed to evaluate biological upcycling of the plastic poly(ethylene terephthalate) (PET). The bioproduct βKA can be polymerized into a nylon-6,6 analog with improved properties for use in the production of a variety of materials. We posit the MOBP will aid in democratizing the execution of synthetic biology in spaceflight towards enabling ISRU.

09 BIOMASS FUELS↗

DOE OSTI2023

The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes

The OSU/PNNL Superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 10 zebrafish-specific phenotypes. Our portal provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov.

Gosline, Sara JC↗