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At least 811 records · Page 45

Cryogenic optical beam steering for superconducting device calibration

We have developed a calibration system based on a micro-electromechanical systems (MEMS) mirror that is capable of delivering an optical beam over a wavelength range of 180 -- 2000 nm (0.62 -- 6.89 eV) in a sub-Kelvin environment. This portable, integrated system can steer the beam over a $\sim$3 cm $\times$ 3 cm area on the surface of any sensor with a precision of $\sim$100 $μ$m, enabling characterization of device response as a function of position. This fills a critical need in the landscape of calibration tools for sub-Kelvin devices, including those used for dark matter detection and quantum computing. These communities have a shared goal of understanding the impact of ionizing radiation on device performance, which can be pursued with our system. This paper describes the design of the first-generation calibration system and the results from successfully testing its performance at room temperature and 20 mK.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Visualizing energy transfer between redox-active colloids

Redox-active colloids (RACs) represent a novel class of energy carriers that exchange electrical energy upon contact. Understanding contact-mediated electron transfer dynamics in RACs offers insights into physical contact events in colloidal suspensions and enables quantification of electrical energy transport in nonconjugated polymers. Redox-based electron transport was directly observed in monolayers of micron-sized RACs containing ethyl-viologen side groups via fluorescence microscopy through an unexpected nonlinear electrofluorochromism that is quantitatively coupled to the redox state of the colloid. Via imaging studies, using this electrofluorochromism, the apparent charge transfer diffusion coefficient D CT of the RAC was easily determined. The visualization of energy transport within suspensions of redox-active colloids was also demonstrated. Our work elucidates fundamental mechanisms of energy transport in colloidal systems, informs the development of next-generation redox flow batteries, and may inspire new designs of smart active soft matter including conductive polymers for applications ranging from electrochemical sensors and organic electronics to colloidal robotics.

Qu, Alan Subing [Univ. of Illinois at Urbana-Champ↗

Data for "Field-scale Evaluation of Ecosystem Service Benefits of Bioenergy Switchgrass"

Purpose-grown perennial herbaceous species are nonfood crops specifically cultivated for bioenergy production and have the potential to secure bioenergy feedstock resources while enhancing ecosystem services. This study assessed soil greenhouse gas emissions (CO2 and N2O), nitrate (NO3-N) leaching reduction potential, evapotranspiration (ET), and water-use efficiency (WUE) of bioenergy switchgrass ( Panicum virgatum L.) in comparison to corn ( Zea mays L.). The study was conducted on field-scale plots in Urbana, IL, during the 2020–2022 growing seasons. Switchgrass was established in 2020 and urea-fertilized at 56 kg N ha−1 year−1. Corn management followed best management practices for the US Midwest, including no-till and 202 kg N ha−1 year−1 fertilization, applied as urea–ammonium nitrate (32%). Our results showed lower direct N2O emissions in switchgrass compared to corn. Although soil CO2 emissions did not differ significantly during the establishment year, emissions in subsequent years were over 50% higher in switchgrass than in corn, likely due to increased belowground biomass, which was over five times higher in switchgrass. Nitrate-N leaching decreased as the switchgrass stand matured, reaching 80% lower than in corn by the third year. Differences in ET and WUE between corn and switchgrass were not significant; however, results indicate a trend toward reduced WUE in switchgrass under drought, driven by lower aboveground biomass production. Our study demonstrates that switchgrass can be implemented at a commercial scale without negatively impacting the hydrological cycle, while potentially reducing N losses through nitrate-N leaching and soil N2O emissions, and enhancing belowground C storage.

field data↗

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing↗

Data for Resourceful and Economical Designing of Fermentation Medium for Lab and Commercial Strains of Yeast from Alternative Feedstock: Transgenic Oilcane

Sugarcane plant engineered to accumulate lipids in its vegetative tissue is being developed as a new bioenergy crop. The new crop would be a source of juice, oil, and cellulosic sugars. However, limited tolerance of industrially recognized yeasts towards inhibitors generated during the processing of lignocellulosic biomass to produce fermentable sugars is a major challenge in developing scalable processes for second-generation drop-in fuel production. To this end, hydrolysates generated from engineered sugarcane—‘oilcane’ bagasse contain added phenolics and fatty acids that further restrict the growth of fermenting microorganisms and necessitate nutrient supplementation and/or detoxification of hydrolysate which makes the fermentation process expensive. Herein, we propose a resourceful and economical approach for growing lab and commercial strains of S. cerevisiae on unrefined cellulosic sugars aerobically and fermentatively. An equal ratio of hydrolysate and juice was found optimum for growth and fermentation by lab and commercial strains of Saccharomyces cerevisiae engineered for xylose fermentation. The industrial strain grew and fermented efficiently under low aeration conditions having an ethanol titer, yield, specific and volumetric productivities of 46.96 ± 0.19 g/l, 0.51 ± 0.00 g/g, 0.27 ± 0.02 g/g.h and 1.95 ± 0.01 g/l.h, respectively, while the lab strain grew better under higher aeration conditions having the ethanol titer, yield, specific and volumetric productivities of 24.93 ± 0.09, 0.27 ± 0.00 g/g, 0.17 ± 0.00 g/g.h and 1.04 ± 0.00 g/l.h, respectively. Acclimation of cultures in a blended medium significantly improved the performance of the yeast strains. The addition of transgenic oilcane juice, which is inedible and rich in amino acids, to the hydrolysate averted the need for expensive nutrient supplementation and detoxification steps of hydrolysate. The approach provides an economical solution to reduce the cost of fermentation at an industrial scale for second-generation drop-in fuel production.

Biomass Analytics↗

Data for Identifying the best high-biomass sorghum hybrids based on biomass yield potential and feedstock quality affected by nitrogen fertility management under various environments

Data were collected from agronomy fields in Urbana and Ewing, IL, during the 2022 and 2023 growing seasons. The dataset includes dry biomass yield, nitrogen, phosphorus, and potassium concentrations and removals, and chemical composition elements (cellulose, hemicellulose, lignin, and soluble fractions) for 13 high-biomass sorghum hybrids. data_sharing.xlsx contains 20 columns and 104 rows. Below is the explanation of all variables in the file: Year: 2022; 2023 Location: Urbana, IL; Ewing, IL N rate (kg-N/ha): 0; 112 Hybrid #: H1-H13 Pedigree: Pedigree for 13 hybrids Dry biomass yield (Mg/ha): Aboveground dry biomass yield N (g/kg): Nitrogen concentration in plant tissue P (g/kg): Phosphorus concentration in plant tissue K (g/kg): Potassium concentration in plant tissue N (kg/ha): Nitrogen removal by aboveground biomass P (kg/ha): Phosphorus removal by aboveground biomass K (kg/ha): Potassium removal by aboveground biomass Cellulose (g/kg): Cellulose concentration in plant tissue Hemicellulose (g/kg): Hemicellulose concentration in plant tissue Lignin (g/kg): Lignin concentration in plant tissue Soluble (g/kg): Soluble concentration in plant tissue Cellulose (Mg/ha): Cellulose content in aboveground biomass Hemicellulose (Mg/ha): Hemicellulose content in aboveground biomass Lignin (Mg/ha): Lignin content in aboveground biomass Soluble (Mg/ha): Soluble content in aboveground biomass

environmental adaptability↗

Data for "Enhancing Lipid Production in Plant Cells through Automated High-Throughput Genome Engineering and Phenotyping"

Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.

AI/ML↗

Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Carbon↗

Data for FUN-PROSE: A Deep Learning Approach to Predict Condition-Specific Gene Expression in Fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Genomics↗

Data for "Constitutive Down-Regulation of Liguleless Alleles in Sorghum Drives Increased Productivity and Water Use Efficiency"

Plant architecture influences the microenvironment throughout the canopy layer. Plants with a more erect leaf architecture allow for an increase in planting densities and allow more light to reach lower canopy leaves. This is predicted to increase crop carbon assimilation. Frictional resistance to wind reduces air movement in the lower canopy, resulting in higher humidity. By increasing the proportion of canopy photosynthesis in the more humid lower canopy, gains in the efficiency of water use might be expected, although this may be slightly offset by the more open erectophile form canopy. An anatomical feature in members of the Poaceae family that impacts leaf angle is the articulated junction of the sheath and blade, which also bares the ligule and auricles. Mutants, which lack ligules and auricles, show no articulation at this junction, resulting in leaves that are near vertical. In maize, these phenotypes termed liguleless result from null mutations of genes: ZmLG1 (Zm00001eb67740) and ZmLG2 (Zm00001eb147220). In sorghum, SbiRTx430.06G264300 (SbLG1) and SbiRTx430.03G392300 (SbLG2) are annotated as the respective maize homologues. A hair-pin element designed to down-regulate both SbLG1 and SbLG2 was introduced into the grain sorghum genotype RTx430. Derived transgenic events harbouring the hair-pin failed to develop ligules and displayed reduced leaf angles to the vertical, but less vertical than in null mutations. Under field settings, plots sown with these sorghum events having an erect architecture phenotype displayed an increase in photosynthesis in lower canopy levels, which led to increases in above-ground biomass and seed yield, without an increase in water use.

Genome Engineering↗

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

Constraints on Inflationary Gravitational Waves with Two Years of SPT-3G Data

We present a measurement of the $B$-mode polarization power spectrum of the cosmic microwave background anisotropies at 32 $\le$$\ell$$<$ 502 for three bands centered at 95, 150, and 220 GHz using data from the SPT-3G receiver on the South Pole Telescope. This work uses SPT-3G observations from the 2019 and 2020 winter observing seasons of a $\sim$1500 deg$^2$ patch of sky that directly overlaps with fields observed with the BICEP/Keck family of telescopes, and covers part of the proposed Simons Observatory and CMB-S4 deep fields. Employing new techniques for mitigating polarized atmospheric noise, the SPT-3G data demonstrates a white noise level of 9.3 (6.7) $\mu$K-arcmin at $\ell \sim 500$ for the 95 GHz (150 GHz) data, with a $1/\ell$ noise knee at $\ell$=128 (182). We fit the observed six auto- and cross-frequency $B$-mode power spectra to a model including lensed $\Lambda$CDM $B$-modes and a combination of Galactic and extragalactic foregrounds. This work characterizes foregrounds in the vicinity of the BICEP/Keck survey area, finding foreground power consistent with that reported by the BICEP/Keck collaboration within the same region, and a factor of $\sim$ 3 higher power over the full SPT-3G survey area. Using SPT-3G data over the BICEP/Keck survey area, we place a 95% upper limit on the tensor-to-scalar ratio of $r < 0.25$ and find the statistical uncertainty on $r$ to be $\sigma(r) = 0.067$.

Zebrowski, J. A. [Chicago U., KICP; Chicago U., As↗

SPT-3G D1: Maps of the millimeter-wave sky from 2019 and 2020 observations of the SPT-3G Main field

Maps of the sky in millimeter wavelengths contain rich information on cosmology through anisotropies of the cosmic microwave background (CMB). Creating multifrequency sky maps of anisotropies in the $I$, $Q$, and $U$ Stokes parameters is one of the first steps of CMB cosmology analyses. In this work, we describe the production and validation of a set of sky maps from the South Pole Telescope's third-generation camera, SPT-3G. The maps are from data taken in frequency bands centered at 95, 150, and 220 GHz and taken during the first two years, 2019 and 2020, of the SPT-3G Main survey, which covers $4\%$ of the sky. We applied high-pass filters to time series of individual detectors and binned the filtered time series samples into map pixels. After that, we calibrated and cleaned the maps to reduce known systematic errors. In addition, we searched for other systematic errors through null tests and mitigated a significant systematic error detected therein. The white noise levels of the full-depth maps of the $I$ Stokes parameter are $5.4$, $4.4$, and $16.2$$\mathrm{μK}$-$\mathrm{arcmin}$ in the 95, 150, and 220 GHz bands, respectively, and $8.4$, $6.6$, and $25.8$$\mathrm{μK}$-$\mathrm{arcmin}$ for $Q/U$. These maps are the deepest to date used for measurements of mid-to-high-$\ell$ primary temperature and $E$-mode polarization CMB anisotropies, and reconstructions of the CMB gravitational lensing potential. We make these maps and supporting data products publicly accessible.

Quan, W. [Argonne (main); Chicago U., EFI; Chicago↗

CMB Lensing Reconstruction Using Two Years of Temperature Data from the SPT-3G Summer Survey

We present the first reconstruction of the cosmic microwave background (CMB) lensing potential from the SPT-3G Summer survey using two years of temperature data. The Summer survey has a total area of approximately 2640 deg$^2$, split into three fields covering 1210, 570, and 860 deg$^2$, respectively. A joint analysis of the three Summer fields yields a lensing amplitude of $A^{\rm comb} = 1.015 \pm 0.053$ relative to a fiducial Planck 2018 $Λ$CDM cosmology for the multipole range $50 < L < 2000$. These early results from the SPT-3G Summer survey highlight the potential for increasing the signal-to-noise ratio when combining the Summer fields with the SPT-3G Main and Wide fields for a total SPT-3G survey area of $\sim$ 10,000 deg$^2$.

Levy, K. [Melbourne U.]↗

First Direct-Detection Results on Sub-GeV Dark Matter Using the SENSEI Detector at SNOLAB

Here, we present the first results from a dark matter search using six Skipper-CCDs in the SENSEI detector operating at SNOLAB. We employ a bias-mitigation technique of hiding approximately 46% of our total data and aggressively mask images to remove backgrounds. Given a total exposure after masking of 100.72 gram-days from well-performing sensors, we observe 55 two-electron events, 4 three-electron events, and no events containing 4–10 electrons. The two-electron events are consistent with pileup from one-electron events. Among the 4 three-electron events, 2 appear in pixels that are likely impacted by detector defects, although not strongly enough to trigger our “hot-pixel” mask. We use these data to set world-leading constraints on sub-GeV dark matter interacting with electrons and nuclei.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SPT-3G D1: A Measurement of Secondary Cosmic Microwave Background Anisotropy Power

We report new measurements of millimeter-wave temperature power spectra in the angular multipole range $1700 \le \ell \le 11,000$ (wavelengths $13^\prime \gtrsim λ\gtrsim 2^\prime$). We use two years of data in three observing bands centered near 95, 150, and 220 GHz from the SPT-3G receiver on the South Pole Telescope that cover a 1646 deg$^2$ region of the Southern sky. Using the measured power spectra, we present constraints on the thermal and kinematic Sunyaev-Zel'dovich (SZ) effects, radio galaxies, and cosmic infrared background (CIB). We find that inferred SZ powers are dependent on the detailed modeling of the thermal SZ-CIB correlation, and to a lesser extent on the assumed angular dependence of the SZ spectra. We report constraints for simulation-based model templates as well as fits where the angular dependencies of the SZ and CIB power spectra are allowed to vary. In the latter case at $\ell=3000$, we find thermal SZ power at 143 GHz of $D_{3000}^{\rm tSZ} = 4.91\pm0.37\, μ{\rm K}^2$ and kinematic SZ power of $D_{3000}^{\rm kSZ} =1.75\pm0.86\, μ{\rm K}^2$. We use the measured kinematic SZ power to estimate the duration of reionization, noting that the reionization inferences are sensitive to the model choices and assumed level of homogeneous kinematic SZ power from the late-time universe. We find a 95% limit on the duration from an ionization fraction of 25% to 75% of $Δ^{50} z_{\rm re} <\,3.8$ based on a semi-analytic model, or a limit on the duration from an ionization fraction of 5% to 95% of $Δ^{90} z_{\rm re} <\,6.1$ based on the AMBER simulations.

Chaubal, P. [Melbourne U.]↗