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DOE OSTI2023

Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments

‘Cell Painting’ is an imaging-based high-throughput phenotypic profiling (HTPP) method in which cultured cells are fluorescently labeled to visualize subcellular structures (i.e., nucleus, nucleoli, endoplasmic reticulum, cytoskeleton, Golgi apparatus / plasma membrane and mitochondria) and to quantify morphological changes in response to chemicals or other perturbagens. HTPP is a high-throughput and cost-effective bioactivity screening method that detects effects associated with many different molecular mechanisms in an untargeted manner, enabling rapid in vitro hazard assessment for thousands of chemicals. Here, 1201 chemicals from the ToxCast library were screened in concentration-response up to ~100 μM in human U-2 OS cells using HTPP. A phenotype altering concentration (PAC) was estimated for chemicals active in the tested range. PACs tended to be higher than lower bound potency values estimated from a broad collection of targeted high-throughput assays, but lower than the threshold for cytotoxicity. In vitro to in vivo extrapolation (IVIVE) was used to estimate administered equivalent doses (AEDs) based on PACs for comparison to human exposure predictions. AEDs for 18/412 chemicals overlapped with predicted human exposures. Phenotypic profile information was also leveraged to identify putative mechanisms of action and group chemicals. Of 58 known nuclear receptor modulators, only glucocorticoids and retinoids produced characteristic profiles; and both receptor types are expressed in U-2 OS cells. Thirteen chemicals with profile similarity to glucocorticoids were tested in a secondary screen and one chemical, pyrene, was confirmed by an orthogonal gene expression assay as a novel putative GR modulating chemical. Most active chemicals demonstrated profiles not associated with a known mechanism-of-action. However, many structurally related chemicals produced similar profiles, with exceptions such as diniconazole, whose profile differed from other active conazoles. Overall, the present study demonstrates how HTPP can be applied in screening-level chemical assessments through a series of examples and brief case studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Observation of two cascading screening processes in an iron-based superconductor

Understanding how renormalized quasiparticles emerge in strongly correlated electron materials provides a challenge for both experiment and theory. It has been predicted that distinctive spin and orbital screening mechanisms drive this process in multiorbital materials with strong Coulomb and Hund’s interactions. Here, we provide the experimental evidence of both mechanisms from angle- resolved photoemission spectroscopy on RbFe 2 As 2 . We observe that the emergence of low-energy Fe 3d xy quasiparticles below 90K coincides with spin screening. A second process changes the spectral weight at high energies up to room temperature. Supported by theoretical calculations we attribute it to orbital screening of Fe 3d atomic excitations. These two cascading screening processes drive the temperature evolution from a bad metal to a correlated Fermi liquid.

Condensed-matter physics↗

DOE OSTI2022

Cordon screen: A cordon-based congestion pricing policy evaluation method for U.S. cities

Global trends toward urbanization will exacerbate traffic congestion, delays in economic productivity, and air pollution issues for growing cities. Traffic congestion pricing is one method available to help ameliorate these concerns. New York City is on the verge of implementing a cordon-based traffic congestion pricing policy around its central business district. For budget-constrained municipalities, evaluating implementation of such policy could be costly. This article proposes a sketch-planning methodology, called Cordon Screen, for major U.S. cities to evaluate the net income, traffic mitigation, and avoided pollution emissions from cordon-based traffic congestion pricing. This method relies on national datasets and limited user-specific data inputs, along with a range of user-selectable assumptions informed by academic literature to deliver order-of-magnitude results. The numerous limitations of this method are acceptable for preliminary policy evaluation to determine if greater financial investment to obtain more accurate results is justified. The Denver metropolitan area is used to demonstrate Cordon Screen capabilities, with mid-range assumption results suggesting the policy is most effective at generating net income and increasing vehicle speeds on major interstates. For Denver, the policy is comparably less effective at reducing air pollution and increasing speeds on minor roadways. Validation against early implementation results from the London cordon are acceptable. Still, users should discount revenue generation projections. Choice of cordon area may be the most difficult obstacle when using the Cordon Screen. With refinement, Cordon Screen could serve as a low-cost, open-source planning evaluation tool for growing and congested U.S. cities.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Low-Cost Screening of Algae for Extreme Tolerance to pH, Temperature, Salinity, and Light

AbstractBioprospecting algae strains with tolerance to extreme conditions such as pH, temperature, salinity, and light is crucial for advancing biotechnology and environmental applications. However, traditional screening methods often involve significant costs and labor, restricting their accessibility and practical use. In this study, we developed and validated low-cost, high-throughput screening techniques, predominantly employing agar plates and liquid culture assays, to effectively differentiate tolerance levels among various algae strains. The methodologies were optimized using the model microalgaChlamydomonas reinhardtiiand its closely related speciesChlamydomonas incertaand the recently discovered extremophilicChlamydomonas pacifica. We systematically evaluated the algae for tolerance to extremes by establishing precise gradients of pH (acidic to alkaline conditions), salinity (0 to 5 M NaCl), temperature (34–42°C), and light intensity (40 to 2977 μE·m⁻²·s⁻¹). Our results demonstrated that these cost-effective, agar plate-based methods effectively distinguished algae strains exhibiting superior tolerance to extreme environmental conditions. These screening techniques not only provided clear differentiation among the closely related strains but also delivered reproducible outcomes suitable for scaling up to larger bioprospecting efforts. Furthermore, the affordability and simplicity of these methods facilitate their implementation in resource-limited laboratories, thereby broadening participation in algae bioprospecting endeavors. This study highlights the potential of low-cost, accessible screening techniques to significantly enhance the discovery and characterization of algal strains with extreme traits. Ultimately, these methods support the development of robust algae-based resources, driving innovation in diverse industrial processes and environmental solutions.Graphical Abstract

Saucedo, Barbara (ORCID:0009000008860839)↗

DOE OSTI2020

Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis

Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) User’s Manual: Python_V5.0

This user’s manual guides the use of the National Energy Technology Laboratory’s (NETL) CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) tool, which was developed to aid users screening geologic formations for prospective CO 2 storage resources. This manual is specific to the CO 2 -SCREEN 5.0 version which is based in Python. The 5.0 version of CO 2 -SCREEN adds in newly updated storage efficiency factors for saline formations for open storage reservoirs and new capability to calculate CO 2 storage in closed and semi-closed storage reservoirs.

58 GEOSCIENCES↗

DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening (CRADA Final Report)

The engineering of microbes for biomanufacturing (e.g. of fuels, chemicals, materials) applications has advanced to a stage where researchers screen genetic libraries with millions of variations each for those with enhanced productivity. This screening, however, can be slow and expensive, as screening individual variants in a high-throughput yet cost-effective manner is challenging. In this project, we aimed to reduce by 3-fold costs associated with the sequencing aspects of the screening process (to determine which genetic variant is responsible for an observed change in productivity), while being able to process over 1,000 samples per batch.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Develop High-Throughput Workflows for Whole-Genome Sequencing and Insertion Site Screening

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

DOE OSTI2022

A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Towards the first plasma-electron screening experiment

The enhancement of fusion reaction rates in a thermonuclear plasma by electron screening of the Coulomb barrier is an important plasma-nuclear effect that is present in stellar models but has not been experimentally observed. Experiments using inertial confinement fusion (ICF) implosions may provide a unique opportunity to observe this important plasma-nuclear effect. Herein, we show that experiments at the National Ignition Facility (NIF) have reached the relevant physical regime, with respect to the density and temperature conditions, but the estimated impacts of plasma screening on nuclear reaction rates are currently too small and need to be increased to lower the expected measurement uncertainty. Detailed radiation hydrodynamics simulations show that practical target changes, like adding readily available high-Z gases, and significantly slowing the inflight implosion velocity, while maintaining inflight kinetic energy, might be able to push these conditions to those where plasma screening effects may be measurable. We also perform synthetic data exercises to help understand where the anticipated experimental uncertainties will become important. But challenges remain, such as the detectability of the reaction products, non-thermal plasma effects, species separation, and impacts of spatial and temporal gradients. This work lays the foundation for future efforts to develop an important platform capable of the first plasma electron screening observation.

inertial confinement fusion↗

DOE OSTI2020

A Rapid and High Throughput MIC Determination Method to Screen Uranium Resistant Microorganisms

The assessment of minimum inhibitory concentration (MIC) is a conventional technique used for the screening of microbial resistance against antibiotics, biocides, and contaminants such as heavy metals. However, as part of our ongoing work, we have observed biases associated with using traditional liquid MIC method to screen microbial heavy metal resistance, including both bacterial and fungal strains. Specifically, the addition of uranium into synthetic media causes immediate precipitation prior to the initiation of microbial growth, thus hampering the optical density measurements, and the obtained MIC values are thus flawed and inaccurate. To address this discrepancy, we report the optimization and development of a serial-dilution-based MIC method conducted on solid growth media supplemented with uranium, which is more accurate, relative to the testing of MICs performed in liquid cultures. Notably, we report on the efficacy of this method to screen not only bacteria that are resistant to uranium but also demonstrate the successful application to yeast and fungal isolates, for their ability to resist uranium, is more accurate and sensitive relative to the liquid method. We believe that this newly developed method to screen heavy metal resistance, such as uranium, is far superior to the existing liquid MIC method and propose replacing the liquid assay with the solid plate MIC reported herein.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Using the Monte Carlo Method to Evaluate the Reliability of Screening Multifamily Housing for Radon

When screening for radon in a multifamily housing complex using a fixed sample density (e.g., testing 1 in 10 (10%) or 1 in 4 units (25%)), the statistical confidence is dependent upon the assumed elevated radon frequency. For example, testing 25% of units in a complex estimated to have eight units with elevated radon levels will provide 90% confidence. However, if it is assumed that, in the same complex, there are only three units with elevated radon levels, the confidence drops to around 58% for the same sample density. Furthermore, in the previous example, if elevated radon levels are not found during the screening, all that can be stated is that the screening provides 90% confidence that there are no more than seven units in the complex with elevated radon levels. To more fully illustrate this uncertainty, ten separate multifamily housing radon data sets with 1 to 10 units with radon levels ≥4 pCi/L (Table 1) were selected for analysis using the Monte Carlo statistical method. Unlike other mathematically based statistical approaches, the Monte Carlo statistical method relies on repeated analysis of randomly selected data. from a 100% sampled complex at various sample densities. Success for each simulation is defined as finding at least one unit with elevated radon levels. In this statistical method, confidence in the overarching conclusion can be greatly enhanced by repeating the simulated screening hundreds or even thousands of times. For this study, each of the ten data sets was simulated 1,000 times. For each simulation, the data set was randomized three times before the fixed percentage of data was selected.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

THERMAL ANALYSIS OF THE RHIC ARC DIPOLE MAGNET COLD MASS WITH THE EIC BEAM SCREEN

The EIC will make use of the existing RHIC storage rings with their superconducting (SC) magnet arcs. A stain-less-steel beam screen with co-laminated copper and a thin amorphous carbon (aC) film on the inner surface will be installed in the beam pipe of the SC magnets. The copper will reduce the beam-induced resistive-wall (RW) heating from operation with the higher intensity EIC beams, that if not addressed would make the magnets quench. Limiting the RW heating is also important to achieve an adequately low vacuum level. The aC coating will reduce secondary electron yield which could also cause heating and limit in-tensity. Among all the RHIC SC magnets, the arc dipoles present the biggest challenge to the design and installation of beam screens. The arc dipoles, which make up for 78% (2.5 km) length of all SC magnets in RHIC, expect the larg-est RW heating due to their smallest aperture. These mag-nets are also the longest (9.45 m each), thus experiencing the largest temperature rise over their length, and have a large sagitta (48.5 mm) that increases the difficulty to in-stall the beam screen in place. This paper presents a de-tailed thermal analysis of the magnet-screen system.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

“Multiagent” Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations

Enzyme evolution has enabled numerous advances in biotechnology and synthetic biology, yet still requires many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which is caused by epistatic mutations that only offer improvements when combined with other mutations. We report an approach that incorporates diverse substrate analogues in the screening process, where multiple substrates act like multiple agents navigating the fitness landscape, identifying epistatic mutant residues without a need for testing the entire combinatorial search space. We initially validate this approach by engineering a malonyl-CoA synthetase and identify numerous epistatic mutations improving activity for several diverse substrates. The majority of these mutations would have been missed upon screening for a single substrate alone. We expect that this approach can accelerate a wide array of enzyme engineering programs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high–throughput microbial screening platform

Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl-CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CAT Sa ) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only probe the alcohol substrate specificity of both native and engineered AATs but also identify the beneficial mutations in engineered AATs for enhanced ester synthesis. Here, we anticipate the high-throughput microbial screening platform provides a useful tool to identify novel wildtype and engineered AATs that have important roles in nature and industrial biocatalysis for designer bioester production.

2-phenhylethyl acetate↗

DOE OSTI2025

Low-Cost, Screen-Printed Silver Metal Complex Inks for Silicon Heterojunction Solar Cells

Screen printing using metal particle pastes, the current photovoltaic industry metallization standard, provides fast and reliable metal grids for silicon solar cells. Recently, metal complex or reactive metal inks are attracting research interest due to their significantly low cost and higher performance compared to traditional nanoparticle silver pastes. In this work, we demonstrate, for the first time, screen-printed high-efficiency silicon heterojunction solar cells metallized by silver metal complex inks on industrial G1-size (158.75 x 158.75 mm2) wafers. We demonstrate screen-printed Ag metal complex ink grid patterns with continuous fingers ~100-120 ..mu..m wide. The printed Ag grid is very thin (~1 ..mu..m), which is an order of magnitude thinner than the current ~20-30 ..mu..m fingers printed with low-temperature nanoparticle-based pastes. Double printing allows silicon heterojunction devices with efficiencies >20%. This is the highest efficiency so far, to our knowledge, of industrial solar cell precursors using this metallization technology. Simulation results suggested that increasing the thickness of the metal film does not significantly improve efficiency due to the dense, highly conductive films. So, a single print of ~1 ..mu..m finger would be enough to produce cells that perform similarly to a ~20 ..mu..m thick nanoparticle paste printed cells. Additionally, solar cells printed on G1 wafers with silver metal complex ink required more than 10 times less silver (~0.03 g) compared to those using silver/copper nanoparticle paste (~0.4 g of Ag). These results indicate that metal complex inks are a very promising replacement for silver nanoparticle pastes for industrial-scale metallization in an age of resource scarcity and high costs of noble metals.

14 SOLAR ENERGY↗