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DOE OSTI2025

A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2

Abstract The Mediator complex coordinates regulatory input for transcription driven by RNA polymerase II in eukaryotes. reduced epidermal fluorescence4-3 (ref4-3) is a semidominant mutation that results in a single amino acid substitution in the Mediator tail subunit Med5b. Previous characterization of ref4-3 revealed altered expression of a variety of loci in Arabidopsis, including those contributing to phenylpropanoid biosynthesis. Examination of existing RNA-seq data indicated that loci enriched for the transcriptionally repressive chromatin modification H3K27me3 are overrepresented among genes that are misregulated in ref4-3. We used ChIP-seq and RNA-seq to examine the possibility that perturbation of H3K27me3 homeostasis in ref4-3 plants contributed to altered transcript levels. We observed that ref4-3 results in a modest global reduction of H3K27me3 at enriched loci and that this reduction is not dependent on gene expression; however, altered H3K27me3 was not strongly predictive of altered expression in ref4-3 plants. Instead, our analyses revealed a substantial enrichment of targets of the MYC2 transcriptional regulator among genes that exhibit decreased expression in ref4-3. Consistent with previous characterization of ref4-3, we observed that ref4-3-dependent decreased expression of MYC2 targets can be suppressed by loss of another Mediator tail subunit, MED25. This observation is consistent with previous biochemical characterization of MYC2. Our data highlight the diverse and distinct impacts that a single amino acid change in the tail subunit of Mediator can have on transcriptional circuits and raise the prospect that Mediator directly contributes to H3K27me3 homeostasis in plants.

Long, Jiaxin (ORCID:0000000335150706)↗

DOE OSTI2020

Imaging systematics and clustering of DESI main targets

ABSTRACT We evaluate the impact of imaging systematics on the clustering of luminous red galaxies (LRG), emission-line galaxies (ELG), and quasars (QSO) targeted for the upcoming Dark Energy Spectroscopic Instrument (DESI) survey. Using Data Release 7 of the DECam Legacy Survey, we study the effects of astrophysical foregrounds, stellar contamination, differences between north galactic cap and south galactic cap measurements, and variations in imaging depth, stellar density, galactic extinction, seeing, airmass, sky brightness, and exposure time before presenting survey masks and weights to mitigate these effects. With our sanitized samples in hand, we conduct a preliminary analysis of the clustering amplitude and evolution of the DESI main targets. From measurements of the angular correlation functions, we determine power law fits $r_0 = 7.78 \pm 0.26\, h^{-1}$Mpc, γ = 1.98 ± 0.02 for LRGs and $r_0 = 5.45 \pm 0.1\, h^{-1}$Mpc, γ = 1.54 ± 0.01 for ELGs. Additionally, from the angular power spectra, we measure the linear biases and model the scale-dependent biases in the weakly non-linear regime. Both sets of clustering measurements show good agreement with survey requirements for LRGs and ELGs, attesting that these samples will enable DESI to achieve precise cosmological constraints. We also present clustering as a function of magnitude, use cross-correlations with external spectroscopy to infer dN/dz and measure clustering as a function of luminosity, and probe higher order clustering statistics through counts-in-cells moments.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Scheduling strategies for the ESPRESSO follow-up of TESS targets

ABSTRACT Radial-velocity follow-up of stars harbouring transiting planets detected by TESS is expected to require very large amounts of expensive telescope time in the next few years. Therefore, scheduling strategies should be implemented to maximize the amount of information gathered about the target planetary systems. We consider myopic and non-myopic versions of a novel uniform-in-phase scheduler, as well as a random scheduler, and compare these scheduling strategies with respect to the bias, accuracy and precision achieved in recovering the mass and orbital parameters of transiting and non-transiting planets. This comparison is carried out based on realistic simulations of radial-velocity follow-up with ESPRESSO of a sample of 50 TESS target stars, with simulated planetary systems containing at least one transiting planet with a radius below 4R⊕. Radial-velocity data sets were generated under reasonable assumptions about their noise component, including that resulting from stellar activity, and analysed using a fully Bayesian methodology. We find the random scheduler leads to a more biased, less accurate, and less precise, estimation of the mass of the transiting exoplanets. No significant differences are found between the results of the myopic and non-myopic implementations of the uniform-in-phase scheduler. With only about 22 radial velocity measurements per data set, our novel uniform-in-phase scheduler enables an unbiased (at the level of 1 per cent) measurement of the masses of the transiting planets, while keeping the average relative accuracy and precision around 16 per cent and 23 per cent, respectively. The number of non-transiting planets detected is similar for all the scheduling strategies considered, as well as the bias, accuracy and precision with which their masses and orbital parameters are recovered.

Cabona, L.↗

DOE OSTI2023

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site

Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA damage responses independent of the canonical SOS pathway. However, the molecular mechanisms by which DriD and other WYL-regulators sense environmental signals and recognize DNA are not well understood. We showed DriD DNA-binding is triggered by its interaction with ssDNA, which is produced during DNA damage. Here we describe the structure of the full-length C. crescentus DriD bound to both target DNA and effector ssDNA. DriD consists of an N-terminal winged-HTH (wHTH) domain, linker region, three-helix bundle, WYL-domain and C-terminal WCX-dimer domain. Strikingly, DriD binds DNA using a novel, asymmetric DNA-binding mechanism that results from different conformations adopted by the linker. Although the linker does not touch DNA, our data show that contacts it makes with the wHTH are key for specific DNA binding. The structure indicates how ssDNA-effector binding to the WYL-domain impacts wHTH DNA binding. In conclusion, we present the first structure of a WYL-activator bound to both effector and target DNA. The structure unveils a unique, asymmetric DNA binding mode that is likely conserved among WYL-activators.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Direct Reactions and Spectroscopy with Hydrogen Targets at the RIBF

The implementation of MINOS, a liquid-hydrogen target and vertex-tracking system, at the Radioactive Isotope Beam Factory (RIBF) of the RIKEN Nishina Center has led to numerous nuclear physics discoveries. In experiments involving rare-isotope beams at intermediate energies, MINOS was integrated with the DALI2 + γ-ray spectrometer and other auxiliary devices. These were positioned in front of both the ZeroDegree Spectrometer and the SAMURAI magnetic spectrometers for the identification of ejectiles following quasi-free scattering direct reactions. Notable outcomes include the first spectroscopy of unstable doubly magic nucleus, investigations into multi-neutron decays, and the study of shell evolution along isotopic chains. These studies have significantly advanced our understanding of nuclear structure, as well as the mechanism of direct reactions with fast beams. Simultaneously, these direct reactions enabled raising new physics questions and paved the way for next-generation experimental setups to address them. Through the combination of particle- and γ-spectroscopy with a broad range of nuclear reactions, new frontiers will be established in our understanding of nuclear structure and reaction mechanisms. Here, we review the past ten years of studies on direct reactions and spectroscopy of exotic nuclei with liquid-hydrogen targets at the RIBF and define a vision for the future.

Bertulani, Carlos A [East Texas A & M Univ., Comme↗

DOE OSTI2022

Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1

In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyses the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine-2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for inborn errors of metabolism such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR and show that it is activated by alkylation of cysteine 414 by N-ethylmaleimide. We also provide evidence that AASS is rate-limiting upon high lysine exposure of mice. Finally, we present the crystal structure of the human LOR domain. Our combined work should enable future efforts to identify inhibitors of this novel drug target.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Characterization and automated optimization of laser-driven proton beams from converging liquid sheet jet targets

Compact, stable, and versatile laser-driven ion sources hold great promise for applications ranging from medicine to materials science and fundamental physics. While single-shot sources have demonstrated favorable beam properties, including the peak fluxes necessary for several applications, high-repetition-rate operation will be necessary to generate and sustain the high average flux needed for many of the most exciting applications of laser-driven ion sources. Further, to navigate through the high-dimensional space of laser and target parameters toward experimental optima, it is essential to develop ion acceleration platforms compatible with machine learning techniques and capable of autonomous real-time optimization. Here, we present a multi-Hz ion acceleration platform employing a liquid sheet jet target. We characterize the laser-plasma interaction and the laser-driven proton beam across a variety of key parameters governing the interaction using an extensive suite of online diagnostics. We also demonstrate real-time, closed-loop optimization of the ion beam maximum energy by tuning the laser wave front using a Bayesian optimization scheme. This approach increased the maximum proton energy by 11% compared to a manually optimized wave front by enhancing the energy concentration within the laser focal spot, demonstrating the potential for closed-loop optimization schemes to tune future ion accelerators for robust high-repetition-rate operation.

Glenn, G. D. [SLAC National Accelerator Laboratory↗

DOE OSTI2021

Validation of neutron-induced reactions on natural carbon using an active target at neutron energies up to 22 MeV at LANSCE

A single crystal chemical vapor deposited (sCVD) diamond detector is used as an active target to measure neutron-induced reactions on natural carbon using the neutrons produced by spallation, with a broad energy spectrum at LANSCE. Additionally, the neutron-induced reactions are detected in the diamond as low as E n = 400 keV and up to approximately 100 MeV. Relative cross sections for C 12 ( n , α 0 ) , C 12 ( n , p 0 ) , C 12 ( n , d 0 + p 1 ) , and C 13 ( n , α 0 ) are reported up to E n = 22 MeV and comparisons on detected pulse-height spectra and detector response of scattering reactions are made with GEANT4 simulations using the ENDF/B-VIII.0 evaluated nuclear data library up to 20 MeV. The results are compared with past experimental data, including other works that incorporate diamond detectors as an active carbon target. In addition, R-matrix calculations for the C 13 + n system are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Spectroscopic study of a possible $Λnn$ resonance and a pair of $ΣNN$ states using the $(e,e'K^+)$ reaction with a tritium target

Here, a mass spectroscopy experiment with a pair of nearly identical high resolution spectrometers and a tritium target was performed in Hall A at Jefferson Lab. Utilizing the (e,e'K + ) reaction, enhancements, which may correspond to a possible $\Lambda$nn resonance and a pair of ΣNN states, were observed with an energy resolution of about 1.21 MeV (σ), although greater statistics are needed to make definitive identifications. An experimentally measured Λnn state may provide a unique constraint in determining the Λn interaction, for which no scattering data exist. In addition, although bound A = 3 and 4 Σ hypernuclei have been predicted, only an A = 4 Σ hypernucleus ($^4_Σ$He) was found, utilizing the (K - ,π - ) reaction on a 4 He target. The possible bound ΣNN state is likely a Σ 0 nn state, although this has to be confirmed by future experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Structure studies of 13 Be from the 12 Be ⁢(𝑑,𝑝) reaction in inverse kinematics on a solid deuteron target

The low-lying structure of 13 Be has remained an enigma for decades. Despite numerous experimental and theoretical studies, large inconsistencies remain. Being both unbound and one neutron away from 14 Be, the heaviest bound beryllium nucleus, 13 Be is difficult to study through simple reactions with weak radioactive-ion beams or more complex reactions with stable-ion beams. Here, we present the results of a study using the 12 Be (𝑑,𝑝)⁢ 13 Be reaction in inverse kinematics using a 9.5 MeV per nucleon 12 Be beam from the ISAC-II facility. The solid deuteron target of IRIS was used to achieve an increased areal thickness compared to conventional deuterated polyethylene targets. The 𝑄-value spectrum below −4.4 MeV was analyzed using a Bayesian method with geant4 simulations. A three-point angular distribution with the same 𝑄-value gate was fit with a mixture of 𝑠- and 𝑝-wave, 𝑠- and 𝑑-wave, or pure 𝑝-wave transfer. The 𝑄-value spectrum was also compared with geant simulations obtained using the energies and widths of states reported in four previous works. As a result, it was found that our results are incompatible with works that revealed a wide 5/2 + resonance but shows better agreement with ones that reported a narrower width.

6 ≤ A ≤ 19↗

DOE OSTI2021

Measurement of the production cross section of 31 GeV/ c protons on carbon via beam attenuation in a 90-cm-long target

The production cross section of 30.92 GeV/c protons on carbon is measured by the NA61/SHINE spectrometer at the CERN Super Proton Synchrotron by means of beam attenuation in a copy (replica) of the 90-cm-long target of the T2K neutrino oscillation experiment. The employed method for direct production cross-section estimation minimizes model corrections for elastic and quasielastic interactions. The obtained production cross section is $σ_{\text{prod}}$ = 227.6 ± 0.8(stat)$_{\text{-3.2}}^{\text{+1.9}}$(sys) – 0.8(mod) mb. It is in agreement with previous NA61/SHINE results obtained with a thin carbon target, while providing improved precision with a total fractional uncertainty of less than 2%. This direct measurement will reduce the uncertainty of the T2K neutrino flux prediction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Tools for probing new physics with newly discovered gamma-ray targets

Here, we present a computational tool, TweedleDEE, for empirically modeling diffuse gamma-ray background emission in a 1° region of the sky, using publicly available gamma-ray data off-axis from the region of interest. This background model allows a user to perform a purely data-driven search for anomalous localized sources of gamma-ray emission, including new physics. A major application of this tool would be in searching for dark matter annihilation in newly discovered astrophysical targets. For this purpose, we derive a scaling relation for determining velocity-dependent 𝐽-factors using only the stellar parameters, which can be broadly applied to obtain dark matter constraints from new targets. As an application of these tools, we use TweedleDEE and MADHATv2 to perform the first search for dark matter annihilation in the newly discovered Leo VI dwarf spheroidal galaxy, and present model constraints for a variety of choices of the annihilation channel and velocity dependence of the cross section.

dark matter↗

DOE OSTI2024

Three-dimensional particle-in-cell simulations of laser-driven multiradiation sources based on double-layer targets

Double-layer targets (DLTs), made of a low-density foam on top of a solid substrate, can efficiently convert the energy of a high-intensity laser to provide sources of photons and protons. We investigate a 30-fs pulse with a peak intensity of I ~ 8.7×10 20 W/cm 2 and a peak power of ~120 TW interacting with a DLT using three-dimensional (3D) particle-in-cell simulations. We focus on providing quantitative results in full 3D geometry on the foam thickness dependence; on the competition between two photon-generating processes in DLTs, i.e., nonlinear inverse Compton scattering (NICS) and bremsstrahlung (BS); and on the acceleration of protons via enhanced target-normal sheath acceleration. Here, we discuss conversion efficiency, average energy, and angular distributions of such multiradiation sources. We find that NICS can prevail over BS if the DLT's substrate is thin enough (~µ⁢m) and that the optimal foam thickness that maximizes the conversion efficiency in NICS and BS photons and the proton cutoff energy, among those considered, is the same (15µ⁢m). These results show that DLTs constitute an excellent tool for developing relatively compact and optimized laser-driven multicomponent radiation sources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Results on low-mass weakly interacting massive particles from an 11 kg d target exposure of DAMIC at SNOLAB

We present constraints on the existence of weakly interacting massive particles (WIMPs) from a 11 kg-day target exposure of the DAMIC experiment at the SNOLAB underground laboratory. The observed energy spectrum and spatial distribution of ionization events with electron-equivalent energies $>$200 eV$_{\rm ee}$ in the DAMIC CCDs are consistent with backgrounds from natural radioactivity. An excess of ionization events is observed above the analysis threshold of 50 eV$_{\rm ee}$. While the origin of this low-energy excess requires further investigation, our data exclude spin-independent WIMP-nucleon scattering cross sections $\sigma_{\chi-n}$ as low as $3\times 10^{-41}$ cm$^2$ for WIMPs with masses $m_{\chi}$ from 7 to 10 GeV$c^{-2}$ . These results are the strongest constraints from a silicon target on the existence of WIMPs with $m_{\chi}$$<$9 GeV$c^{-2}$ and are directly relevant to any dark matter interpretation of the excess of nuclear-recoil events observed by the CDMS silicon experiment in 2013.

WIMP search, Dark Matter, DAMIC, SNOLAB↗

DOE OSTI2023

First Measurement of Λ Electroproduction off Nuclei in the Current and Target Fragmentation Regions

Here, we report results of Λ hyperon production in semi-inclusive deep-inelastic scattering off deuterium, carbon, iron, and lead targets obtained with the CLAS detector and the Continuous Electron Beam Accelerator Facility 5.014 GeV electron beam. These results represent the first measurements of the Λ multiplicity ratio and transverse momentum broadening as a function of the energy fraction (z) in the current and target fragmentation regions. The multiplicity ratio exhibits a strong suppression at high z and an enhancement at low z. The measured transverse momentum broadening is an order of magnitude greater than that seen for light mesons. This indicates that the propagating entity interacts very strongly with the nuclear medium, which suggests that propagation of diquark configurations in the nuclear medium takes place at least part of the time, even at high z. The trends of these results are qualitatively described by the Giessen Boltzmann-Uehling-Uhlenbeck transport model, particularly for the multiplicity ratios. These observations will potentially open a new era of studies of the structure of the nucleon as well as of strange baryons.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Anisotropic Flow in Fixed-Target 208 Pb + 20 Ne Collisions as a Probe of Quark-Gluon Plasma

The System for Measuring Overlap with Gas (SMOG2) at the LHCb detector enables the study of fixed-target ion-ion collisions at relativistic energies ($\sqrt{𝑠_{NN}}$ ∼ 100 GeV in the center of mass). Here, with input from ab initio calculations of the structure of 16 O and 20 Ne , we compute 3+1⁢D hydrodynamic predictions for the anisotropic flow of Pb+Ne and Pb+O collisions to be tested with upcoming LHCb data. This will allow the detailed study of quark-gluon plasma formation as well as experimental tests of the predicted nuclear shapes. Elliptic flow (𝑣 2 ) in Pb + Ne collisions is greatly enhanced compared to the Pb + O baseline due to the shape of 20 Ne , which is deformed in a bowling-pin geometry. Owing to the large 208 Pb radius, this effect is seen in a broad centrality range, a unique feature of this collision configuration. Larger elliptic flow further enhances the quadrangular flow (𝑣 4 ) of Pb + Ne collisions via nonlinear coupling, and impacts the sign of the kurtosis of the elliptic flow vector distribution (𝑐 2 ⁡{4}). Exploiting the shape of 20 Ne proves thus an ideal method to investigate the formation of quark-gluon plasma in fixed-target experiments at LHCb, and demonstrates the power of System for Measuring Overlap with Gas as a tool to image nuclear ground states.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals

The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.

Lahey-Rudolph, J. Mia (ORCID:0000000152797267)↗

DOE OSTI2022

Load Margin Constrained Moving Target Defense against False Data Injection Attacks

Cyber physical security of power systems with high penetration of renewable generation has attracted attention from researchers. One critical issue is that cyber-physical attacks, disguised as uncertain renewable generation, can target conventional power system state estimation (SE). Moving target defense (MTD) is a promising defense strategy to detect stealthy false data injection (FDI) attacks against SE. However, all existing studies myopically perturb the reactance of transmission lines equipped with distributed flexible AC transmission system (D-FACTS) devices without adequately considering the system voltage stability. Exacerbated by the renewable generation uncertainty, existing MTD may cause voltage instability when the power grid is under stress. To address this issue, we propose a novel MTD framework that explicitly considers system voltage stability by using continuation power flow. We utilize the sensitivity matrix of power injection to line impedance, on which an optimization problem for maximizing load margin is formulated. This framework is validated on the IEEE 14-bus system and the IEEE 118-bus system, in which net load redistribution attacks are launched by sophisticated attackers. Steady-state simulations and dynamic simulations on PSS/E show the effectiveness of the proposed framework in circumventing the voltage instability while maintaining the detection effectiveness of MTD. The impact of the proposed method on attack detection effectiveness is also revealed.

Zhang, Hang↗