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At least 307 records · Page 17

Attaining the promise of plant gene editing at scale

Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.

59 BASIC BIOLOGICAL SCIENCES↗

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive Data Screening for Multi-Angle Polarimetric Aerosol and Ocean Color Remote Sensing Accelerated by Automatic Differentiation

Remote sensing measurements from multi-angle polarimeters (MAPs) contain rich aerosol microphysical property information, and these sensors have been used to perform retrievals in optically complex atmosphere and ocean systems. Previous studies have concluded that, generally, five moderately separated viewing angles in each spectral band provide sufficient accuracy for aerosol property retrievals, with performance gradually saturating as angles are added above that threshold. The Hyper-Angular Rainbow Polarimeter (HARP) instruments provide high angular sampling with a total of 90-120 unique angles across four bands, a capability developed mainly for liquid cloud retrievals. In practice, not all view angles are optimal for aerosol retrievals due to impacts of clouds, sun glint, and other impediments. The many viewing angles of HARP can provide resilience to these effects, if the impacted views are screened from the dataset, as the remaining views may be sufficient for successful analysis. In this study, we discuss how the number of available viewing angles impacts aerosol and ocean color retrieval uncertainties, as applied to two versions of the HARP instrument. AirHARP is an airborne prototype that was deployed in the ACEPOL field campaign, while HARP2 is an instrument in development for the upcoming NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission. Based on synthetic data, we find that a total of 20-30 angles across all bands (i.e. five to eight viewing angles per band) are sufficient to achieve good retrieval performance. Following from this result, we develop an adaptive multi-angle polarimetric data screening (MAPDS) approach to evaluate data quality by comparing measurements with their best-fitted forward model. The FastMAPOL retrieval algorithm is used to retrieve scene geophysical values, by matching an efficient, deep learning-based, radiative transfer emulator to observations. The data screening method effectively identifies and removes viewing angles affected by thin cirrus clouds and other anomalies, improving retrieval performance. This was tested with AirHARP data, and we found agreement with the High Spectral Resolution Lidar-2 (HSRL-2) aerosol data. The data screening approach can be applied to modern satellite remote sensing missions, such as PACE, where a large amount of multi-angle, hyperspectral, polarimetric measurements will be collected.

multi-angle polarimeter↗

Dispersive and nondispersive 𝐾-matrix formalisms

The modeling of coupled-channel effects has become increasingly important due to the availability of highly precise data for a large variety of hadronic (re)scattering processes. The 𝐾-matrix is a powerful, yet comparatively simple, method to describe scattering amplitudes, including coupled-channel effects, with the aim of interpreting experimental data. Throughout the literature, a range of dispersive and nondispersive 𝐾-matrix methods are employed. Here, we compare the dispersive and nondispersive formulations in the context of the N/D method. It is shown that the methods are equivalent in the physical region under 𝐾-matrix reparametrization. Differences away from the physical region are examined. Applications to synthetic data are used to illustrate the effects of model choices concerning form factors and the application of dispersion relations, with the goal of clarifying best practices. We find no clear preference with regard to dispersive modeling. In contrast, we find that interpretational ambiguity of the bare model parameters—and even of the form of the bare model—is endemic, and recommend a thorough sampling of data and model spaces to assess conclusion robustness.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulated thermonuclear performance of auto-magnetizing helical liner MagLIF target implosions

Magnetized liner inertial fusion (MagLIF) implosions on the Z accelerator require magnetization of the fuel to reduce thermal conduction losses of energy from the laser-preheated deuterium fusion fuel to the surrounding liner material. While external field coils traditionally used to axially magnetize MagLIF targets are limited to 10–20 T (or perhaps ∼ 30 T with technological development), calculations suggest that higher axial magnetic fields would improve thermal insulation of the fuel and improve MagLIF target performance. We present results from three-dimensional radiation-magnetohydrodynamic simulations of MagLIF implosions employing auto-magnetizing helical liners composed of discrete metallic helical conduction paths separated by electrically insulating material. These simulated auto-magnetizing (AutoMag) liners produce axial magnetic fields >30 T inside the fusion fuel prior to implosion. Simulations indicate that higher thermonuclear yields and burn-averaged fuel ion temperatures are attained for implosions using AutoMag liners compared to standard MagLIF implosions. Comparable implosion morphology is evident in synthetic x-ray images of AutoMag–MagLIF and standard MagLIF implosions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Accelerating Combustion and Surface Chemistry Simulations

Design of modern combustion systems relies on computer models to predict how changes in design will affect performance. These models have largely displaced previous methods that rely on the designer’s intuition or costly and time-consuming physical testing. By using improved models, design cycles can be shortened, and cleaner and more efficient combustion devices can be created. This project aims to improve computer simulations of transportation fuels with the goal of making these simulations faster and more accurate for predicting combustion in vehicles.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Evaluation of Synthetic Diamond Detectors for Fast Neutron and X-ray Detection [Slides]

Element6 has come out of a two year production pause (pre-COVID) with material that lacks their previous QC – some is excellent, but screening is needed. Applied Diamond can now make usable polycrystalline material, for applications not requiring absolute flux calibration. A large area possible (1cm 2 ). Great Lakes Crystal Technology has made great progress in two years, but still needs development to become a trusted supplier of single crystal material. LANL staff (Dongsung Kim) has developed proficient lithography and bonding expertise at CINT to make devices from vendor supplied material. LANL staff has continued and expanded capabilities for device testing at NSLS-II.

42 ENGINEERING↗

3D hybrid fluid-particle jet simulations and the importance of synchrotron radiative losses

Context. Relativistic jets in active galactic nuclei are known for their exceptional energy output, and imaging the synthetic synchrotron emission of numerical jet simulations is essential for a comparison with observed jet polarization emission. Aims. Through the use of 3D hybrid fluid-particle jet simulations (with the PLUTO code), we overcome some of the commonly made assumptions in relativistic magnetohydrodynamic (RMHD) simulations by using non-thermal particle attributes to account for the resulting synchrotron radiation. Polarized radiative transfer and ray-tracing (via the RADMC-3D code) highlight the differences in total intensity maps when (i) the jet is simulated purely with the RMHD approach, (ii) a jet tracer is considered in the RMHD approach, and (iii) a hybrid fluid-particle approach is used. The resulting emission maps were compared to the example of the radio galaxy Centaurus A. Methods. We applied the Lagrangian particle module implemented in the latest version of the PLUTO code. This new module contains a state-of-the-art algorithm for modeling diffusive shock acceleration and for accounting for radiative losses in RMHD jet simulations. The module implements the physical postulates missing in RMHD jet simulations by accounting for a cooled ambient medium and strengthening the central jet emission. Results. We find a distinction between the innermost structure of the jet and the back-flowing material by mimicking the radio emission of the Seyfert II radio galaxy Centaurus A when considering an edge-brightened jet with an underlying purely toroidal magnetic field. We demonstrate the necessity of synchrotron cooling as well as the improvements gained when directly accounting for non-thermal synchrotron radiation via non-thermal particles.

79 ASTRONOMY AND ASTROPHYSICS↗

Harnessing Machine Learning and Data Fusion for Accurate Undocumented Well Identification in Satellite Images

This study utilizes satellite data to detect undocumented oil and gas wells, which pose significant environmental concerns, including greenhouse gas emissions. Three key findings emerge from the study. Firstly, the problem of imbalanced data is addressed by recommending oversampling techniques like Rotation–GaussianBlur–Solarization data augmentation (RGS), the Synthetic Minority Over-Sampling Technique (SMOTE), or ADASYN (an extension of SMOTE) over undersampling techniques. The performance of borderline SMOTE is less effective than that of the rest of the oversampling techniques, as its performance relies heavily on the quality and distribution of data near the decision boundary. Secondly, incorporating pre-trained models trained on large-scale datasets enhances the models’ generalization ability, with models trained on one county’s dataset demonstrating high overall accuracy, recall, and F1 scores that can be extended to other areas. This transferability of models allows for wider application. Lastly, including persistent homology (PH) as an additional input improves performance for in-distribution testing but may affect the model’s generalization for out-of-distribution testing. A careful consideration of PH’s impact on overall performance and generalizability is recommended. Overall, this study provides a robust approach to identifying undocumented oil and gas wells, contributing to the acceleration of a net-zero economy and supporting environmental sustainability efforts.

SMOTE↗

Recent Advances in Radar Polarimetry and Polarimetric SAR Interferometry

The development of Radar Polarimetry and Radar Interferometry is advancing rapidly, and these novel radar technologies are revamping Synthetic Aperture Radar Imaging decisively. In this exposition the successive advancements are sketched; beginning with the fundamental formulations and high-lighting the salient points of these diverse remote sensing techniques. Whereas with radar polarimetry the textural fine-structure, target-orientation and shape, symmetries and material constituents can be recovered with considerable improvements above that of standard amplitude-only Polarization Radar ; with radar interferometry the spatial (in depth) structure can be explored. In Polarimetric-Interferometric Synthetic Aperture Radar (POL-IN-SAR) Imaging it is possible to recover such co-registered textural plus spatial properties simultaneously. This includes the extraction of Digital Elevation Maps (DEM) from either fully Polarimetric (scattering matrix) or Interferometric (dual antenna) SAR image data takes with the additional benefit of obtaining co-registered three-dimensional POL-IN-DEM information. Extra-Wide-Band POL-IN-SAR Imaging - when applied to Repeat-Pass Image Overlay Interferometry - provides differential background validation and measurement, stress assessment, and environmental stress-change monitoring capabilities with hitherto unattained accuracy, which are essential tools for improved global biomass estimation. More recently, by applying multiple parallel repeat-pass EWB-POL-D(RP)-IN-SAR imaging along stacked (altitudinal) or displaced (horizontal) flight-lines will result in Tomographic (Multi- Interferometric) Polarimetric SAR Stereo-Imaging , including foliage and ground penetrating capabilities. It is shown that the accelerated advancement of these modern EWB-POL-D(RP)-IN-SAR imaging techniques is of direct relevance and of paramount priority to wide-area dynamic homeland security surveillance and local-to-global environmental ground-truth measurement and validation, stress assessment, and stress-change monitoring of the terrestrial and planetary covers. In addition, various closely related topics of (i) acquiring additional and protecting existing spectral windows of the Natural Electromagnetic Spectrum (NES) pertinent to Remote Sensing; (ii) mitigating against common "Radio Frequency Interference (RFI)" and intentional Directive Jamming of Airborne & Space borne POL-IN-SAR Imaging Platforms are appraised.

Boerner, Wolfgang-Martin↗

Utilization of the Critic Subnetwork of a Generative Adversarial Network as Detector of Morphological Material Change in Image Data

The resolution of computed tomography (CT) has become high enough to monitor morphological changes due to aging in materials in long-term applications. For this work, we explored the utility of the critic of a generative adversarial network (GAN) to automatically detect such changes. The GAN was trained with images of pristine Pharmatose, which is used as a surrogate energetic material. It is important to note that images of the material with altered morphology were only used during the test phase. The GAN-generated images reproduced the microstructure of Pharmatose well, although some unrealistic particle fusion was seen. Calculated morphological metrics (volume fraction, interfacial line length, and local thickness) for the synthetic images also showed good agreement with the training data, albeit with signs of mode collapse in the interfacial line length. While the critic exposed changes in particle size, it showed limited ability to distinguish images by particle shape. The detection of shape differences was also a more challenging task for the selected morphological metrics that related to energetic material performance. We further tested the critic with images of aged Pharmatose. Subtle changes due to aging are difficult for the human analyst to detect; but both critic and morphological metrics analysis showed image differentiation.

36 MATERIALS SCIENCE↗

Dynamic Deformation of ETNA Volcano Observed by GPS and SAR Interferometry

Synthetic aperture radar (SAR) interferometry and GPS have shown that during the quiescent period from 1993-1995 Mt. Etna volcano, Italy, inflated. Since the initiation of eruptive activity since late 1995 the deformation has been more contentious. We will explore the detailed deformation during the period from 1995-1996 spanning the late stages of inflation and the beginning of eruptive activity. We use SAR interferometry and GPS data to measure the volcano deformation. We invert the observed deformation for both simple point source. le crack elastic sources or if warranted for a spheroidal pressure So In particular, we will examine the evolution of the inflation and the transition to a lesser deflation observed at the end of 1995. We use ERS-1/2 SAR data from both ascending and descending passes to allow for dense temporal 'sampling of the deformation and to allow us to critically assess atmospheric noise. Preliminary results from interferometry suggest that the inflation rate accelerated prior to resumption of activity in 1995, while GPS data suggest a more steady inflation with some fluctuation following the start of activity. This study will compare and contrast the interferometric SAR and GPS results and will address the strengths and weaknesses of each technique towards volcano deformation studies.

Lundgren, P.↗

Investigating Abiotic and Biotic Mechanisms of Pyrite Reduction

Pyrite (FeS 2 ) has a very low solubility and therefore has historically been considered a sink for iron (Fe) and sulfur (S) and unavailable to biology in the absence of oxygen and oxidative weathering. Anaerobic methanogens were recently shown to reduce FeS 2 and assimilate Fe and S reduction products to meet nutrient demands. However, the mechanism of FeS 2 mineral reduction and the forms of Fe and S assimilated by methanogens remained unclear. Thermodynamic calculations described herein indicate that H 2 at aqueous concentrations as low as 10 –10 M favors the reduction of FeS 2 , with sulfide (HS – ) and pyrrhotite (Fe 1–x S) as products; abiotic laboratory experiments confirmed the reduction of FeS 2 with dissolved H 2 concentrations greater than 1.98 × 10 –4 M H 2 . Growth studies of Methanosarcina barkeri provided with FeS 2 as the sole source of Fe and S resulted in H 2 production but at concentrations too low to drive abiotic FeS 2 reduction, based on abiotic laboratory experimental data. A strain of M. barkeri with deletions in all [NiFe]-hydrogenases maintained the ability to reduce FeS 2 during growth, providing further evidence that extracellular electron transport (EET) to FeS 2 does not involve H 2 or [NiFe]-hydrogenases. Physical contact between cells and FeS 2 was required for mineral reduction but was not required to obtain Fe and S from dissolution products. The addition of a synthetic electron shuttle, anthraquinone-2,6-disulfonate, allowed for biological reduction of FeS 2 when physical contact between cells and FeS 2 was prohibited, indicating that exogenous electron shuttles can mediate FeS 2 reduction. Here, transcriptomics experiments revealed upregulation of several cytoplasmic oxidoreductases during growth of M. barkeri on FeS 2 , which may indicate involvement in provisioning low potential electrons for EET to FeS 2 . Collectively, the data presented herein indicate that reduction of insoluble FeS 2 by M. barkeri occurred via electron transfer from the cell surface to the mineral surface resulting in the generation of soluble HS – and mineral-associated Fe 1–x S. Solubilized Fe(II), but not HS – , from mineral-associated Fe 1–x S reacts with aqueous HS – yielding aqueous iron sulfur clusters (FeS aq ) that likely serve as the Fe and S source for methanogen growth and activity. FeS aq nucleation and subsequent precipitation on the surface of cells may result in accelerated EET to FeS 2 , resulting in positive feedback between cell activity and FeS 2 reduction.

59 BASIC BIOLOGICAL SCIENCES↗

PowerCell aboard the EuCROPIS satellite - Results from the first synthetic biology experiment in space

Synthetic biology is the design and construction of new biological parts and systems not found in nature, a technology that we believe will be a game-changing technology for space exploration. The PowerCell concept is an ecology based on photosynthetic microbes taking advantage of in situ materials and energy to generate, on-demand, useful products (food, fuel, cloths, drugs, etc.) that satisfy specific needs of long-term human presence away from Earth. This first PowerCell experiment is testing this concept as well as several key mechanisms of engineering biology in a 48-well plate microfluidics system. NASA's PowerCell experiment was loaded in the fluidics system at NASA Ames in May 2016, and subsequently integrated on the DLR's compact satellite Eu:CROPIS (Euglena Combined Regenerative Organic food Production In Space), as a secondary payload. Launched into Earth’s orbit from the Vandenberg Air Force Base, California, USA, in December 3, 2019, the Eu:CROPIS platform has provided an artificial gravity through rotational acceleration, simulating gravity ranges compatible to those found on Mars and on the Moon, as well as microgravity in the absence of acceleration. Each set of biological experiments performed at Earth's orbit was compared to ground controls. Over 400 days' worth of mission data showed that all hardware and software worked as planned, and microbial growth was observed in all four gravity regimes, including growth on cyanobacterial cell extract in three out of four gravity regimes. The genetic transformation experiment was successful in microgravity and provided valuable long-term reagent stability data, including antibiotic efficacy. The demonstrated ability of hardy bacterial spores to recover from a long-term stasis period will be fundamental for deep human space missions. Lessons learned from hardware design to experimental operations are leading to improved designs and capabilities for future missions.

Ivan Glaucio Paulino Lima↗

Achieving GPT-4o level performance in astronomy with a specialized 8B-parameter large language model

AstroSage-Llama-3.1-8B is a domain-specialized natural-language AI assistant tailored for research in astronomy, astrophysics, cosmology, and astronomical instrumentation. Trained on the complete collection of astronomy-related arXiv papers from 2007 to 2024 along with millions of synthetically-generated question-answer pairs and other astronomical literature, AstroSage-Llama-3.1-8B demonstrates remarkable proficiency on a wide range of questions. AstroSage-Llama-3.1-8B scores 80.9% on the AstroMLab-1 benchmark, greatly outperforming all models—proprietary and open-weight—in the 8-billion parameter class, and performing on par with GPT-4o. This achievement demonstrates the potential of domain specialization in AI, suggesting that focused training can yield capabilities exceeding those of much larger, general-purpose models. AstroSage-Llama-3.1-8B is freely available, enabling widespread access to advanced AI capabilities for astronomical education and research.

AI assistant↗

Recent advancements in the genetic engineering of microalgae

The development of more sustainable food, feed, and bio-products is critical to mitigating the environmental stresses facing our world today. Algae, which includes seaweeds, eukaryotic microalgae, and cyanobacteria, are a promising platform to achieving this, as they have low energy and space requirements, are safe for human and animal consumption, and can be manipulated to produce a diversity of valuable bioproducts. This review focuses on microalgae, both eukaryotic and cyanobacteria. In the past, addressing the major challenges of bringing microalgal production systems to an economically viable scale only had a relatively small genetic toolset to work with, in comparison to other microbial systems such as bacteria and yeast. Expanding the molecular tools available for genetic engineering of microalgae will lead to higher product yields, and accelerate the development of new microalgal bioproducts for commercial applications, thereby supporting the shift towards more environmentally friendly products. In this review, we highlight significant advances from recent years on the design of microalgal expression vectors, discovery of genetic regulatory elements (promoters and transcription factors), optimization of transformation methods, and development of new strain improvement techniques, all aimed at advancing microalgae to become a more efficient biomanufacturing platform. We then discuss how these tools have been applied to improving recombinant protein production, and to enhance metabolic pathway engineering.

09 BIOMASS FUELS↗

Detecting Seasonal Ice Dynamics in Satellite Images

Fully understanding how glaciers respond to environmental change will require new methods to help us identify the onset of ice acceleration events and observe how dynamic signals propagate within glaciers. In particular, observations of ice dynamics on seasonal timescales may offer insights into how a glacier interacts with various forcing mechanisms throughout the year. The task of generating continuous ice velocity time series that resolve seasonal variability is made more difficult by a spotty satellite record that contains no optical observations throughout the dark, polar winters. Furthermore, velocities obtained by feature tracking are marked by high noise when image pairs are separated by short time intervals and contain no direct insights into variability that occurs between images separated by long time intervals. In this paper, we describe a method of analyzing optical or SAR-derived feature-tracked velocities to characterize the magnitude and timing of seasonal ice dynamic variability. Our method is agnostic to data gaps and is able to recover climatological average winter velocities regardless of the availability of direct observations during winter. Using characteristic image acquisition times and error distributions from Antarctic image pairs in the ITS_LIVE dataset, we generate synthetic ice velocity time series, then apply our method to recover imposed magnitudes of seasonal variability within ±1.4 m yr−1. We then validate the techniques by comparing our results to GPS data collected on Russell Glacier in Greenland. The methods presented here may be applied to better understand how ice dynamic signals propagate on seasonal timescales, and what mechanisms control the flow of the world’s ice.

Chad A. Greene↗

Integrated simulations of premagnetized and self-magnetizing dynamic screw pinch-driven MagLIF

Magnetically driven implosions such as in magnetized liner inertial fusion (MagLIF) on the Z accelerator suffer from magneto-Rayleigh–Taylor instabilities (MRTI) that dynamically redistribute liner mass during implosion, limiting fusion fuel compression and confinement, which ultimately degrades performance. Driving the implosion with an initially helical drive field that dynamically shifts the direction of the magnetic field surrounding the liner (i.e., a dynamic screw pinch, DSP) is a method proposed to mitigate MRTI in-flight and improve target performance. In DSPs, the axial drive magnetic field component implodes the liner and diffuses through the shocked, melted liner material into the fuel throughout the implosion. Liners can be designed to enable enough axial magnetic flux to diffuse through the liner material to effectively magnetize the fuel region without the need of an initial axial magnetic field (i.e., from external field coils). We present results from three-dimensional radiation-magnetohydrodynamic simulations of MagLIF implosions employing drive magnetic fields composed of axial and azimuthal components (a helical drive field). These simulated DSP-driven MagLIF targets demonstrate improved fuel conditions and thermonuclear yield compared to a traditional MagLIF target implosion. Synthetic x-ray radiography of the imploding liner material and x-ray emission images of the fuel region at the time of peak neutron yield rate indicate superior implosion morphology for DSP-MagLIF implosions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗