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DOE OSTI2024

A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology

Equitable and accessible education in life sciences, bioengineering, and synthetic biology is crucial for training the next generation of scientists, fostering transparency in public decision-making, and ensuring biotechnology can benefit a wide-ranging population. As a groundbreaking technology for genome engineering, CRISPR has transformed research and therapeutics. However, hands-on exposure to this technology in educational settings remains limited due to the extensive resources required for CRISPR experiments. Here, we develop CRISPRkit, an affordable kit designed for gene editing and regulation in high school education. CRISPRkit eliminates the need for specialized equipment, prioritizes biosafety, and utilizes cost-effective reagents. By integrating CRISPRi gene regulation, colorful chromoproteins, cell-free transcription-translation systems, smartphone-based quantification, and an in-house automated algorithm (CRISPectra), our kit offers an inexpensive (~$2) and user-friendly approach to performing and analyzing CRISPR experiments, without the need for a traditional laboratory setup. Experiments conducted by high school students in classroom settings highlight the kit’s utility for reliable CRISPRkit experiments. Furthermore, CRISPRkit provides a modular and expandable platform for genome engineering, and we demonstrate its applications for controlling fluorescent proteins and metabolic pathways such as melanin production. We envision CRISPRkit will facilitate biotechnology education for communities of diverse socioeconomic and geographic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Hierarchical Inference with Bayesian Neural Networks: An Application to Strong Gravitational Lensing

In the past few years, approximate Bayesian Neural Networks (BNNs) have demonstrated the ability to produce statistically consistent posteriors on a wide range of inference problems at unprecedented speed and scale. However, any disconnect between training sets and the distribution of real-world objects can introduce bias when BNNs are applied to data. This is a common challenge in astrophysics and cosmology, where the unknown distribution of objects in our universe is often the science goal. In this work, we incorporate BNNs with flexible posterior parameterizations into a hierarchical inference framework that allows for the reconstruction of population hyperparameters and removes the bias introduced by the training distribution. We focus on the challenge of producing posterior PDFs for strong gravitational lens mass model parameters given Hubble Space Telescope–quality single-filter, lens-subtracted, synthetic imaging data. We show that the posterior PDFs are sufficiently accurate (statistically consistent with the truth) across a wide variety of power-law elliptical lens mass distributions. We then apply our approach to test data sets whose lens parameters are drawn from distributions that are drastically different from the training set. We show that our hierarchical inference framework mitigates the bias introduced by an unrepresentative training set's interim prior. Simultaneously, we can precisely reconstruct the population hyperparameters governing our test distributions. Our full pipeline, from training to hierarchical inference on thousands of lenses, can be run in a day. The framework presented here will allow us to efficiently exploit the full constraining power of future ground- and space-based surveys (https://github.com/swagnercarena/ovejero).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Impact of Solution Chemistry on Growth and Structural Features of Mo-Substituted Spinel Iron Oxides

The effect of crystallizing solution chemistry on the chemistry of subsequently as-grown materials was investigated for Mo-substituted iron oxides prepared by thermally activated co-precipitation. In the presence of Mo ions, we find that varying the oxidation state of the iron precursor from Fe(II) to Fe(III) causes a progressive loss of atomic long-range order with the stabilization of 2-4 nm particles for the sample prepared with Fe(III). The oxidation state of the Fe precursor also affects the distribution of Fe and Mo cations within the spinel structure. Increasing the Fe precursor oxidation state gives decreased Fe-ion occupation and increased Mo-ion occupation of tetrahedral sites, as revealed by the extended X-ray absorption fine structure. The stabilization of Mo within tetrahedral sites appears to be unexpected, considering the octahedral preferred coordination number of Mo(VI). The analysis of the atomic structure of the sample prepared with Fe(III) indicates a local ordering of vacancies and that the occupation of tetrahedral sites by Mo induces a contraction of the interatomic distances within the polyhedra as compared to Fe atoms. Moreover, the occupancy of Mo into the thermodynamic site preference of a Mo dopant in Fe 2 O 3 assessed by density functional theory calculations points to a stronger preference for Mo substitution at octahedral sites. Hence, we suggest that the synthetized compound is thermodynamically metastable, that is, kinetically trapped. Such a state is suggested to be a consequence of the tetrahedral site occupation by Mo ions. The population of these sites, known to be reactive sites enabling particle growth, is concomitant with the stabilization of very small particles. Furthermore, we confirmed our hypothesis by using a blank experiment without Mo ions, further supporting the impact of tetrahedral Mo ions on the growth of iron oxide nanoparticles. Our findings provide new insights into the relationships between the Fechemistry of the crystallizing solution and the structural features of the as-grown Mo-substituted Fe-oxide materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1992

Science questions for the Magellan continuing mission

Magellan has completed two mapping cycles around the planet Venus, returning high resolution synthetic aperture images and altimetry data of over 95 percent of the planet's surface. Venus is dominated by low lying volcanic plains with an impact crater population indicating an average surface age of about 500 million years. Highland regions either tend to be characterized by volcanic shield complexes and rifting or by complex ridged terrain. Successful as the primary mission of Magellan has been, significant scientific questions remain to be addressed with imaging and gravity data that will be collected over the next several years.

Saunders, R. S.↗

NASA NTRS2002

An economic analysis of space solar power and its cost competitiveness as a supplemental source of energy for space and ground markets

Economic Growth has been historically associated with nations that first made use of each new energy source. There is no doubt that Solar Power Satellites is high as a potential energy system for the future. A conceptual cost model of the economics value of space solar power (SSP) as a source of complementary power for in-space and ground applications will be discussed. Several financial analysis will be offered based on present and new technological innovations that may compete with or be complementary to present energy market suppliers depending on various institutional arrangements for government and the private sector in a Global Economy. Any of the systems based on fossil fuels such as coal, oil, natural gas, and synthetic fuels share the problem of being finite resources and are subject to ever-increasing cost as they grow ever more scarce with drastic increase in world population. Increasing world population and requirements from emerging underdeveloped countries will also increase overall demand. This paper would compare the future value of SSP with that of other terrestrial renewable energy in distinct geographic markets within the US, in developing countries, Europe, Asia, and Eastern Europe.

electric power inter-regional electricity trading↗

DOE OSTI2025

Validation of the DESI 2024 Lyα forest BAO analysis using synthetic datasets

The first year of data from the Dark Energy Spectroscopic Instrument (DESI) contains the largest set of Lyman-α (Lyα) forest spectra ever observed. This data, collected in the DESI Data Release 1 (DR1) sample, has been used to measure the Baryon Acoustic Oscillation (BAO) feature at redshift z = 2.33. In this work, we use a set of 150 synthetic realizations of DESI DR1 to validate the DESI 2024 Lyα forest BAO measurement presented in [1]. The synthetic data sets are based on Gaussian random fields using the log-normal approximation. We produce realistic synthetic DESI spectra that include all major contaminants affecting the Lyα forest. The synthetic data sets span a redshift range 1.8 < z < 3.8, and are analyzed using the same framework and pipeline used for the DESI 2024 Lyα forest BAO measurement. To measure BAO, we use both the Lyα auto-correlation and its cross-correlation with quasar positions. We use the mean of correlation functions from the set of DESI DR1 realizations to show that our model is able to recover unbiased measurements of the BAO position. We also fit each mock individually and study the population of BAO fits in order to validate BAO uncertainties and test our method for estimating the covariance matrix of the Lyα forest correlation functions. Finally, we discuss the implications of our results and identify the needs for the next generation of Lyα forest synthetic data sets, with the top priority being to simulate the effect of BAO broadening due to non-linear evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A Search for Faint Resolved Galaxies Beyond the Milky Way in DES Year 6: A New Faint, Diffuse Dwarf Satellite of NGC 55

We report results from a systematic wide-area search for faint dwarf galaxies at heliocentric distances from 0.3 to 2 Mpc using the full 6 yr of data from the Dark Energy Survey (DES). Unlike previous searches over the DES data, this search specifically targeted a field population of faint galaxies located beyond the Milky Way virial radius. We derive our detection efficiency for faint, resolved dwarf galaxies in the Local Volume with a set of synthetic galaxies and expect our search to be complete to M$_{V}$ ∼ (−7, −10) mag for galaxies at D = (0.3, 2.0) Mpc. We find no new field dwarfs in the DES footprint, but we report the discovery of one high-significance candidate dwarf galaxy at a distance of , a potential satellite of the Local Volume galaxy NGC 55, separated by 47′ (physical separation as small as 30 kpc). We estimate this dwarf galaxy to have an absolute V-band magnitude of and an azimuthally averaged physical half-light radius of , making this one of the lowest surface brightness galaxies ever found with . This is the largest, most diffuse galaxy known at this luminosity, suggesting possible tidal interactions with its host.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Energetic considerations for engineering novel biochemistries in photosynthetic organisms

Humans have been harnessing biology to make valuable compounds for generations. From beer and biofuels to pharmaceuticals, biology provides an efficient alternative to industrial processes. With the continuing advancement of molecular tools to genetically modify organisms, biotechnology is poised to solve urgent global problems related to environment, increasing population, and public health. However, the light dependent reactions of photosynthesis are constrained to produce a fixed stoichiometry of ATP and reducing equivalents that may not match the newly introduced synthetic metabolism, leading to inefficiency or damage. While photosynthetic organisms have evolved several ways to modify the ATP/NADPH output from their thylakoid electron transport chain, it is unknown if the native energy balancing mechanisms grant enough flexibility to match the demands of the synthetic metabolism. In this review we discuss the role of photosynthesis in the biotech industry, and the energetic considerations of using photosynthesis to power synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

Atomic data and level populations of highly ionized Ti for tokamak plasmas

The paper presents calculations of electron impact collision strengths and spontaneous radiative decay rates for titanium ions of the LiI through FI isoelectronic sequences for transitions between levels of the 2S(2)2p(k), 2s2p(k+1), and 2p(k+2) configurations. From these atomic data, excitation-rate coefficients are calculated along with level populations for these three configurations. The calculations of level populations include the effects of proton excitation, and are carried out at electron temperatures and densities typical of tokamak plasmas. Wavelengths of forbidden and intersystem lines are given, and a synthetic spectrum is presented for a typical temperature and density.

Bhatia, A. K.↗

NASA NTRS2019

Unraveling the Internal Magnetic Field Structure of the Earth-Directed Interplanetary Coronal Mass Ejections During 1995-2015

The magnetic field configurations associated with interplanetary coronal mass ejections (ICMEs) are the in situ manifestations of the entrained magnetic structure associated with coronal mass ejections (CMEs). We present a comprehensive study of the internal magnetic field configurations of ICMEs observed at 1 AU by the Wind mission during 1995-2015. The goal is to unravel the internal magnetic structure associated with the ICMEs and establish the signatures that validate a flux-rope structure. We examine the expected magnetic field signatures by simulating spacecraft trajectories within a simple flux rope, i.e., with circular–cylindrical (CC) helical magnetic field geometry. By comparing the synthetic configurations with the 353 ICME in situ observations, we find that only 152 events ( Fr ) display the clear signatures of an expected axial-symmetric flux rope. Two more populations exhibit possible signatures of flux rope; 58 cases ( F− ) display a small rotation ( <90° ) of the magnetic field direction, interpreted as a large separation of the spacecraft from the center, and, 62 cases ( F+ ) exhibit larger rotations, possibly arising from more complex configuration. The categories, Cx (14%) and E events (9%), reveal signatures of complexity possibly related with evolutionary processes. We then reconstruct the flux ropes assuming CC geometry. We examine the orientation and geometrical properties during the solar activity levels at the end of Solar Cycle 22 (SC22), SC23 and part of SC24. The orientation exhibits solar cycle trends and follow the heliospheric current sheet orientation. We confirm previous studies that found a Hale cycle dependence of the poloidal field reversal. By comparing our results with the occurrence of CMEs with large angular width ( AW>60∘ ) we find a broad correlation suggesting that such events are highly inclined CMEs. The solar cycle distribution of bipolar vs. unipolar Bz configuration confirms that the CMEs may remove solar cycle magnetic field and helicity.

Nieves-Chinchilla, Teresa↗

DOE OSTI2024

Advancing process-based flood frequency analysis for assessing flood hazard and population flood exposure

Recent studies have showcased the use of process-based hydrological models with Stochastic Storm Transposition (SST) techniques to conduct Flood Frequency Analysis (FFA). This framework, referred hereby FFA-SST, has proved to be a robust strategy to estimate peak flows of specific annual exceedance probability (e.g., 100-year peak flow) that can reflect natural and anthropogenic disturbances, including changes in land use and meteorological patterns. With the objective of advancing the FFA-SST framework, this study presents for the first time the use of an Integrated Surface-Subsurface Hydrological Model (ISSHM) to conduct FFA-SST by extending the analysis from peak flow responses to flood extent, enabling a unique view and analysis of flood hazard and population flood exposure at the basin scale. As a proof-of-concept, we used the ISSHM, Advanced Terrestrial Simulator (Amanzi-ATS) model, and the SST model, RainyDay, to conduct FFA-SST by simulating the flood response to 5,000 annual synthetic storm events in a 2,227 $km^2$ Southeast Texas watershed. We demonstrate that ATS, without site-specific calibration, provides a robust process-based representation of peak flows, flood extent, streamflow, evapotranspiration, soil moisture content, and water storage changes. Our results and analyses, covering frequency curves up to a 500-year return period for peak flows, basin inundation fractions, and the number of people exposed to flooding, offer a unique perspective to analyze flood impacts across spatial scales. Overall, this study provides critical insights for flood risk management by extending the FFA-SST framework to include both flood hazard and population flood exposure analyses at the basin scale. Such an approach will empower stakeholders and disaster emergency agencies with a more comprehensive understanding of flood impacts across the entire basin domain, facilitating informed decision-making for flood risk assessment and management.

58 GEOSCIENCES↗

DOE OSTI2024

Time-Resolved X-ray Emission Spectroscopy and Synthetic High-Spin Model Complexes Resolve Ambiguities in Excited-State Assignments of Transition-Metal Chromophores: A Case Study of Fe-Amido Complexes

To fully harness the potential of abundant metal coordination complex photosensitizers, a detailed understanding of the molecular properties that dictate and control the electronic excited-state population dynamics initiated by light absorption is critical. In the absence of detectable luminescence, optical transient absorption (TA) spectroscopy is the most widely employed method for interpreting electron redistribution in such excited states, particularly for those with a charge-transfer character. The assignment of excited-state TA spectral features often relies on spectroelectrochemical measurements, where the transient absorption spectrum generated by a metal-to-ligand charge-transfer (MLCT) electronic excited state, for instance, can be approximated using steady-state spectra generated by electrochemical ligand reduction and metal oxidation and accounting for the loss of absorptions by the electronic ground state. However, the reliability of this approach can be clouded when multiple electronic configurations have similar optical signatures. Using a case study of Fe(II) complexes supported by benzannulated diarylamido ligands, we highlight an example of such an ambiguity and show how time-resolved X-ray emission spectroscopy (XES) measurements can reliably assign excited states from the perspective of the metal, particularly in conjunction with accurate synthetic models of ligand-field electronic excited states, leading to a reinterpretation of the long-lived excited state as a ligand-field metal-centered quintet state. Furthermore, a detailed analysis of the XES data on the long-lived excited state is presented, along with a discussion of the ultrafast dynamics following the photoexcitation of low-spin Fe(II)-N amido complexes using a high-spin ground-state analogue as a spectral model for the 5 T 2 excited state.

14 SOLAR ENERGY↗

DOE OSTI2024

Identification of synthetic consortia from a set of plant-beneficial bacteria

The use of microbial inoculants in agriculture as biofertilisers and/or biopesticides is an appealing alternative to replace or reduce the practice of agrochemicals. Plant microbiota studies are revealing the different bacterial groups which are populating plant microbiomes re-energising the plant probiotic bacteria (PPB) translational research sector. Some single-microbial strain bioinoculants have proven valid in agriculture (e.g., based on Trichoderma, mycorrhiza or rhizobia); however, it is now recommended to consider multistrain consortia since plant-beneficial effects are often a result of community-level interactions in plant microbiomes. A limiting step is the selection of a fitting combination of microbial strains in order to accomplish the best beneficial effect upon plant inoculation. In this study, we have used a subset of 23 previously identified and characterised rice-beneficial bacterial colonisers to design and test a series of associated experiments aimed to identify potential PPB consortia which are able to co-colonise and induce plant growth promotion. Bacterial strains were co-inoculated in vitro and in planta using several different methods and their co-colonisation and co-persistence monitored. Results include the identification of two 5-strain and one 2-strain consortia which displayed plant growth-promoting features. Future practical applications of microbiome research must include experiments aimed at identifying consortia of bacteria which can be most effective as crop amendments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Abstract Background Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. Results To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum ( Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea , Filomicrobium , and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. Conclusions The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

The metallicity and luminosity of RV Tauri variables from medium-resolution spectra

Results are reported from spectroscopic observations of members of the RV Tauri class of pulsating variable stars at moderate resolution, and from photometric observations of these stars with the B and V filters of the Johnson UBV system and the first four filters of the Wing eight-color narrowband near-IR system. Of the 22 variables observed, TiO absorption was detected in eight, and 10 variables displayed hydrogen-line emission at some phase. Spectral classifications were assigned relative to the MK process. Color excesses were determined for those variables for which spectroscopic and photometric data were obtained within a few days of each other. The spectra obtained at a resolution of 2.5 A were fitted with synthetic spectra to determine the stellar atmospheric parameters. The range in metallicity among the variables was found to be quite extensive, -0.3 to -0.7, and may reflect a mixture of stellar populations or masses.

Wahlgren, Glenn M.↗

NASA NTRS2017

Effects of Inventory Bias on Landslide Susceptibility Calculations

Many landslide inventories are known to be biased, especially inventories for large regions such as Oregon's SLIDO or NASA's Global Landslide Catalog. These biases must affect the results of empirically derived susceptibility models to some degree. We evaluated the strength of the susceptibility model distortion from postulated biases by truncating an unbiased inventory. We generated a synthetic inventory from an existing landslide susceptibility map of Oregon, then removed landslides from this inventory to simulate the effects of reporting biases likely to affect inventories in this region, namely population and infrastructure effects. Logistic regression models were fitted to the modified inventories. Then the process of biasing a susceptibility model was repeated with SLIDO data. We evaluated each susceptibility model with qualitative and quantitative methods. Results suggest that the effects of landslide inventory bias on empirical models should not be ignored, even if those models are, in some cases, useful. We suggest fitting models in well-documented areas and extrapolating across the study region as a possible approach to modeling landslide susceptibility with heavily biased inventories.

Oregon↗

NASA NTRS2017

Effects of Inventory Bias on Landslide Susceptibility Calculations

Many landslide inventories are known to be biased, especially inventories for large regions such as Oregons SLIDO or NASAs Global Landslide Catalog. These biases must affect the results of empirically derived susceptibility models to some degree. We evaluated the strength of the susceptibility model distortion from postulated biases by truncating an unbiased inventory. We generated a synthetic inventory from an existing landslide susceptibility map of Oregon, then removed landslides from this inventory to simulate the effects of reporting biases likely to affect inventories in this region, namely population and infrastructure effects. Logistic regression models were fitted to the modified inventories. Then the process of biasing a susceptibility model was repeated with SLIDO data. We evaluated each susceptibility model with qualitative and quantitative methods. Results suggest that the effects of landslide inventory bias on empirical models should not be ignored, even if those models are, in some cases, useful. We suggest fitting models in well-documented areas and extrapolating across the study region as a possible approach to modelling landslide susceptibility with heavily biased inventories.

landslide↗

NASA NTRSDate not supplied

Autonomous Measurement of Electrochemical Redox Couples for In-Situ Characterization of Enceladus Plume Samples

A 3D-printed microfluidic electrochemical cell with integrated electrodes was developed to demonstrate autonomous in-situ electrochemical characterization of terrestrial seawater samples. The system is designed to extend the capabilities of the 2008 Phoenix Lander’s Wet Chemistry Laboratory (WCL) that analyzed the soluble chemistry of the Martian soil, by miniaturizing its fluidic architecture for analysis of µL-volume samples as expected from an Enceladus fly-by mission. The microfluidic device has a total fluid volume of 48 µL and includes dual channels each populated with 7 electrodes. Measurement of pH was measured using an iridium oxide electrode. Cyclic voltammetry with Au, Pt, and glassy carbon working electrodes was used to measure redox couples in synthetic seawater that contained inorganic and bio-organic molecules. Glassy carbon was found to have minimal risk of interference from constituents of synthetic seawater when measuring molecular organic redox species; however, care must be used to prevent interference due to potential oxidation or dissolution in the case of Au working electrodes. A completely autonomous end-to-end run including sample delivery was performed, to demonstrate the feasibility of microfluidic-based cyclic voltammetry measurements for in-situ characterization of redox couples in Ocean World samples.

Planetary Instruments↗