Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering
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59 BASIC BIOLOGICAL SCIENCES↗
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Bioinformatic Prediction and High Throughput In Vivo Screening to Identify Cis-Regulatory Elements for the Development of Algal Synthetic Promoters
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59 BASIC BIOLOGICAL SCIENCES↗
Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly
Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.
Bacteria↗
Design and Characterization of a Transcriptional Repression Toolkit for Plants
Regulation of gene expression is essential for all life. Tools to manipulate the gene expression level have therefore proven to be very valuable in efforts to engineer biological systems. However, there are few well-characterized genetic parts that reduce gene expression in plants, commonly known as transcriptional repressors. We characterized the repression activity of a library consisting of repression motifs from approximately 25% of the members of the largest known family of repressors. Combining sequence information with our trans-regulatory function data, we next generated a library of synthetic transcriptional repression motifs with function predicted in advance. After characterizing our synthetic library, we demonstrated not only that many of our synthetic constructs were functional as repressors but also that our advance predictions of repression strength were better than random guesses. Finally, we assessed the functionality of known transcriptional repression motifs from a wide range of eukaryotes. Our study represents the largest plant repressor motif library experimentally characterized to date, providing unique opportunities for tuning transcription in plants.
59 BASIC BIOLOGICAL SCIENCES↗
Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators
Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.
Cell signaling↗
Water-Soluble Flexible Organic Frameworks That Include and Deliver Proteins
Four water-soluble hydrazone-based three-dimensional (3D) flexible organic frameworks FOF-1-4 have been synthesized from a semirigid tetracationic tetraaldehyde and four flexible dihydrazides. 1 H NMR spectroscopy indicated the quantitative formation of FOF-1-4 in D 2 O, while dynamic light scattering experiments revealed that, depending on the concentration, these porous frameworks display hydrodynamic diameters ranging from 50 to 120 nm. The porosity of the frameworks is confirmed by ethanol vapor adsorption experiments of the solid samples as well as the high loading capacity for a 2.3 nm porphyrin guest in water. The new water-soluble frameworks exhibit low cytotoxicity and form inherent pores with diameters of 5.3 or 6.7 nm, allowing rapid inclusion of proteins such as bovine serum albumin and green and orange fluorescent proteins, and efficient delivery of the proteins into normal and cancer cells. Flow cytometric analysis reveals percentages of the delivered cells up to 99.8%.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deep Bayesian local crystallography
Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.
36 MATERIALS SCIENCE↗
The association of structural chirality and liquid crystal anchoring in polymer stabilized cholesteric liquid crystals
Polymer stabilized cholesteric liquid crystals (PSCLCs) are electrically reconfigurable reflective elements. Prior studies have hypothesized and indirectly confirmed that the electro-optic response of these composites is associated with the electrically mediated distortion of the stabilizing polymer network. The proposed mechanism is based on the retention of structural chirality in the polymer stabilizing network, which upon deformation is spatially distorted, which accordingly affects the pitch of the surrounding low molar-mass liquid crystal host. Here, we utilize fluorescent confocal polarized microscopy to directly assess the electro-optic response of PSCLCs. By utilizing dual fluorescent probes, sequential imaging experiments confirm that the periodicity of the polymer stabilizing network matches that of the low molar-mass liquid crystal host. Further, we isolate distinct ion-polymer interactions that manifest in certain photopolymerization conditions.
Radka, Brian P.↗
Horizon-scale variability of M87* from 2017–2021 EHT observations
Here, we report three epochs of polarized images of M87* at 230 GHz using data from the Event Horizon Telescope (EHT) taken in 2017, 2018, and 2021. The baseline coverage of the 2021 observations is significantly improved through the addition of two new EHT stations: the 12 m Kitt Peak Telescope and the Northern Extended Millimetre Array (NOEMA). All observations result in images dominated by a bright, asymmetric ring with a persistent diameter of 43.9 ± 0.6 µas, consistent with expectations for lensed synchrotron emission encircling the apparent shadow of a supermassive black hole. We find that the total intensity and linear polarization of M87* vary significantly across the three epochs. Specifically, the azimuthal brightness distribution of the total intensity images varies from year to year, as expected for a stochastic accretion flow. However, despite a gamma-ray flare erupting in M87 quasi-contemporaneously to the 2018 observations, the 2018 and 2021 images look remarkably similar. The resolved linear polarization fractions in 2018 and 2021 peak at ∼5%, compared to ∼15% in 2017. The spiral polarization pattern on the ring also varies from year to year, including a change in the electric vector position angle helicity in 2021 that could reflect changes in the magnetized accretion flow or an external Faraday screen. The improved 2021 coverage also provides the first EHT constraints on jet emission outside the ring, on scales of ≲ 1 mas. Overall, these observations provide strong proof of the reliability of the EHT images and probe the dynamic properties of the horizon-scale accretion flow surrounding M87*.
accretion, accretion disks↗
Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA–DNA hybrid imaging
R-loops are three-stranded nucleic acid structures with both physiological and pathological roles in cells. R-loop imaging generally relies on detection of the RNA–DNA hybrid component of these structures using the S9.6 antibody. We show that the use of this antibody for imaging can be problematic because it readily binds to double-stranded RNA (dsRNA) in vitro and in vivo, giving rise to nonspecific signal. In contrast, purified, catalytically inactive human RNase H1 tagged with GFP (GFP-dRNH1) is a more specific reagent for imaging RNA–DNA hybrids. GFP-dRNH1 binds strongly to RNA–DNA hybrids but not to dsRNA oligonucleotides in fixed human cells and is not susceptible to binding endogenous RNA. Furthermore, we demonstrate that purified GFP-dRNH1 can be applied to fixed cells to detect hybrids after their induction, thereby bypassing the need for cell line engineering. GFP-dRNH1 therefore promises to be a versatile tool for imaging and quantifying RNA–DNA hybrids under a wide range of conditions.
59 BASIC BIOLOGICAL SCIENCES↗
Galaxy clustering in the DESI Legacy Survey and its imprint on the CMB
ABSTRACT We use data from the DESI Legacy Survey imaging to probe the galaxy density field in tomographic slices covering the redshift range 0 < z < 0.8. After careful consideration of completeness corrections and galactic cuts, we obtain a sample of 4.9 × 107 galaxies covering 17 739 deg2. We derive photometric redshifts with precision σz/(1 + z) = 0.012−0.015, and compare with alternative estimates.1 Cross-correlation of the tomographic galaxy maps with Planck maps of cosmic microwave background (CMB) temperature and lensing convergence probe the growth of structure since z = 0.8. The signals are compared with a fiducial Planck ΛCDM model, and require an overall scaling in amplitude of Aκ = 0.901 ± 0.026 for the lensing cross-correlation and AISW = 0.984 ± 0.349 for the temperature cross-correlation, interpreted as the integrated Sachs–Wolfe effect. The ISW amplitude is consistent with the fiducial Λ cold dark matter (ΛCDM) prediction, but lies significantly below the prediction of the AvERA model of Rácz et al., which has been proposed as an alternative explanation for cosmic acceleration. Within ΛCDM, our low amplitude for the lensing cross-correlation requires a reduction either in fluctuation normalization or in matter density compared to the Planck results, so that $\Omega _\mathrm{ m}^{0.78}\sigma _8=0.297\pm 0.009$. In combination with the total amplitude of CMB lensing, this favours a shift mainly in density: Ωm = 0.274 ± 0.024. We discuss the consistency of this figure with alternative evidence. A conservative compromise between lensing and primary CMB constraints would require Ωm = 0.296 ± 0.006, where the 95 per cent confidence regions of both probes overlap.
Hang, Qianjun↗
Neutron Scattering in High Magnetic Fields: Community Recommendations to Seize the Moment for Scientific Breakthroughs
Oak Ridge National Laboratory (ORNL) operates the world’s two most powerful neutron sources: the High Flux Isotope Reactor (HFIR) and the Spallation Neutron Source (SNS). These form a national user facility that provides neutron scattering instruments to probe and image static and dynamic properties of materials down to the atomic scale. Because the neutron carries a magnetic moment and the energies and wavelengths of neutrons match energy and length scales associated with magnetic materials, these facilities provide unique sensitivity to magnetism.
36 MATERIALS SCIENCE↗
Accuracy and Resolution Evaluation of the E-Beam Profile Scanner at the Fermilab Main Injector
The objective of this work is to assess the accuracy of measurements made by the Electron Beam Profile Scanner (EBPS), which captures the trajectory of an electron beam with and without a proton beam present. The proton beam induces deflection in the electron beam, which is influenced by proton charges. For high-resolution images, the probe beam needs to be of high intensity, small diameter, and small divergence, evaluated using a phosphor screen and an optical transition radiation (OTR) screen. The capabilities of the Kimball Physics electron gun (eGun) will be considered for accuracy. Additionally, the Zemax software will be utilized to characterize the optical elements.
Mwaniki, M. W. [IIT, Chicago] (ORCID:0000000169057↗
Observations of supermicron-sized aerosols originating from biomass burning in southern Central Africa
During the 3 years of the ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES) campaign, the NASA Orion P-3 was equipped with a 2D stereo (2D-S) probe that imaged particles with maximum dimension (D) ranging from 10 < D < 1280 µm. The 2D-S recorded supermicron-sized aerosol particles (SAPs) outside of clouds within biomass burning plumes during flights over the southeastern Atlantic off Africa's coast. Numerous SAPs with 10 < D < 1520 µm were observed in 2017 and 2018 at altitudes between 1230 and 4000 m, 1000 km from the coastline, mostly between 7–11° S. No SAPs were observed in 2016 as flights were conducted further south and further from the coastline. Number concentrations of refractory black carbon (rBC) measured by a single particle soot photometer ranged from 200 to 1200 cm –3 when SAPs were observed. Transmission electron microscopy images of submicron particulates, collected on Holey carbon grid filters, revealed particles with potassium salts, black carbon (BC), and organics. Energy-dispersive X-ray spectroscopy spectra also detected potassium, a tracer for biomass burning. These measurements provided evidence that the submicron particles originated from biomass burning. NOAA Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) 3 d back trajectories show a source in northern Angola for times when large SAPs were observed. Fire Information for Resource Management System (FIRMS) Moderate Resolution Imaging Spectroradiometer (MODIS) 6 active fire maps showed extensive biomass burning at these locations. Given the back trajectories, the high number concentrations of rBC, and the presence of elemental tracers indicative of biomass burning, it is hypothesized that the SAPs imaged by the 2D-S are examples of BC aerosol, ash, or unburned plant material.
54 ENVIRONMENTAL SCIENCES↗
Revealing latent pole and zone line information in atom probe detector maps using crystallographically correlated metrics
Poles and zone lines observed within atom probe field evaporation images are useful for a range of atom probe crystallography studies, including calibration of the reconstruction and crystallographic characterisation of microstructural features such as grain boundaries. However, this information is not always readily apparent. Techniques for plotting crystallographically correlated metrics contained within atom probe data to enhance pole and zone line contrast across the detector space are developed. This includes consideration of the electric field, molecular ions, lattice structure retained within the reconstruction, specific elemental species, the number of pulses between detection events, and the lateral distance between sequential detection events. These approaches are then applied to experimental atom probe tomography datasets on technically pure Al, nanocrystalline Al, highly doped Si, and additively manufactured Inconel 738, Haynes 282, and Ti–6Al–4V. The results facilitate the extension of atom probe crystallography studies to a broader range of crystalline datasets where crystallographic information is not readily apparent from existing methods, as well as a deeper understanding of field evaporation behaviour during an atom probe experiment.
47 OTHER INSTRUMENTATION↗
Etching sharp tips from thin metallic wires for tuning-fork-based scanning probe microscopy
Sharp tips are critical for obtaining high resolution images in scanning probe microscopy (SPM), particularly in samples with large variations in topography. For tuning-fork-based SPM, such tips are commonly obtained by electrochemical etching of metallic wires (e.g., tungsten). Electrochemical etching of metallic wires is the preferred means of preparing tips for scanning tunneling microscopy (STM), and techniques for obtaining sharp tips have been investigated extensively. However, the requirements for STM and tuning-fork-based SPM are different. In particular, the wires used in STM are typically 250-500 μ m in diameter, while the wires used for tuning-fork-based SPM are usually an order of magnitude narrower in order to minimize loading of the tuning fork: 25-50 μ m and sometimes down to a few micrometers in diameter. Consequently, many of the recipes developed for etching thicker metallic wires for STM tips do not give optimal results for smaller diameter wires. The authors describe here a modification of the etching circuit of Ibe et al . that significantly improves the reproducibility and reliability of the etching process for thin wires, and discuss the parameters that affect the aspect ratio of produced tips.
42 ENGINEERING↗
Far-field speckle correlations as a function of object position for microscopically distinguishing objects hidden in a randomly scattering medium
Super-resolution optical sensing is of critical importance in science and technology and has required prior information about an imaging system or obtrusive near-field probing. Additionally, coherent imaging and sensing in heavily scattering media such as biological tissue has been challenging, and practical approaches have either been restricted to measuring the field transmission of a single point source, or to where the medium is thin. We present the concept of far-subwavelength spatial sensing with relative object motion in speckle as a means to coherently sense through heavy scatter. Experimental results demonstrate the ability to distinguish nominally identical objects with nanometer-scale translation while hidden in randomly scattering media, without the need for precise or known location and with imprecise replacement. The theory and supportive illustrations presented provide the basis for super-resolution sensing and the possibility of virtually unlimited spatial resolution, including through thick, heavily scattering media with relative motion of an object in a structured field. This work provides enabling opportunities for material inspection, security, and biological sensing.
Hastings, Ryan L. (ORCID:0009000095977807)↗
The Interstellar Mapping And Acceleration Probe High Energy (IMAP-Hi) Neutral Atom Imager
The IMAP-Hi Energetic Neutral Atom (ENA) Imager on NASA’s Interstellar Mapping and Acceleration Probe (IMAP) mission (McComas et al. 2018a, 2025) is designed to measure ENAs from the global interaction between the heliosphere and the local interstellar medium (LISM). These ENAs are initially plasma ions of solar wind origin that are neutralized by charge exchange with the cold neutral atoms of LISM that freely flow through the heliosphere-LISM interaction region. IMAP-Hi consists of two identical single-pixel sensors, each covering the ENA spectral range from 0.44 keV to 15.6 keV over nine contiguous energy passbands and having an approximately conical field-of-view (FOV) of 4.1o full width at half maximum (FWHM). The Hi-45 sensor points 45o relative to the spacecraft spin axis from the antisunward direction; each spacecraft spin, it measures ENA intensity over a circular swath with half-cone angle 45o centered on the ecliptic plane. The Hi-90 sensor points 90o relative to the spin axis; each spacecraft spin, it measures ENA intensity over a great circle in the sky, sampling both the north and south ecliptic poles. As the IMAP spin vector is re-pointed daily toward the Sun, the ecliptic longitude of the swaths moves daily by ∼1o such that a full sky map is acquired by Hi-90 every six months and a complete low latitude (−45o to +45o) map is acquired by Hi-45 annually. The IMAP-Hi sensor design has direct heritage from the IBEX-Hi imager on the Interstellar Boundary Explorer (IBEX) mission, with substantial improvements in energy range, energy resolution, angular resolution, signal-to-noise ratio, and, for ecliptic latitudes within ±45o, temporal resolution and exposure time. The global ENA maps acquired by IMAP-Hi partially overlap in energy and viewing with the ENA maps acquired by the IMAP-Lo and IMAP-Ultra ENA imagers, which we combine to answer fundamental questions about the structure and dynamics of the interaction of the heliosphere and the LISM.
79 ASTRONOMY AND ASTROPHYSICS↗