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At least 577 records · Page 32

From quantitative trait loci towards mechanisms: Linkage Integration Hypothesis Testing (LIgHT) sheds light on the mechanisms of genetically modulated stress tolerance

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTLs) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea ( Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of PSI and PSII, photoprotective non-photochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLMs). The patterns of QTL linkages indicated that chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLMs. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation appears to be modulated by thylakoid fatty acid composition, previously associated with the same genetic loci and now supported by broader mechanistic evidence. We propose that the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.

MultispeQ↗

A family of α/β hydrolases removes phytol from chlorophyll metabolites for tocopherol biosynthesis in Arabidopsis

Tocopherol synthesis requires phytyl diphosphate derived from phytol esterified to chlorophyll metabolites. The >600-member Arabidopsis thaliana α/β hydrolase (ABH) gene family contains 4 members that can release phytol from chlorophyll metabolites in vitro; however, only pheophytinase (PPH) affects tocopherol synthesis when mutated, reducing seed tocopherols by 5%. We report the biochemical analysis of 2 previously uncharacterized ABHs, chlorophyll dephytylase 2 (CLD2) and CLD3, and their respective mutants singly and in combinations with pph and cld1 alleles. While all CLDs localized to the thylakoid and could hydrolyze phytol from chlorophylls and Pheophytin a in vitro, CLD3 had the highest in vitro activity and the largest effect on tocopherol synthesis in vivo. The 3 CLDs acted cooperatively to provide phytol for 31% of tocopherols synthesized in light-grown leaf tissue. Dark-induced leaf senescence assays showed PPH is required for 18% of the tocopherols synthesized. Though the cld123 triple mutant had no impact on dark-induced tocopherol content, cld123 in the pph background reduced tocopherol levels by an additional 18%. In seeds, pph and cld123 each reduced tocopherol content by 5% and by 15% in the cld123pph quadruple mutant. VTE7 ( ViTamin E7 ) is an envelope-localized ABH that specifically affects chlorophyll biosynthetic intermediates in vivo and is required for 55% of seed tocopherol synthesis. The introduction of cld123pph into the vte7 background further reduced seed tocopherol levels to 23% of that of the wild type. Our findings demonstrate that phytol provision for tocopherol biosynthesis and homeostasis is a complex process involving the coordinated spatiotemporal expression of multiple ABH family members.

arabidopsis↗

Modeling with uncertainty quantification reveals the essentials of a non-canonical algal carbon-concentrating mechanism

The thermoacidophilic red alga Cyanidioschyzon merolae survives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated that C. merolae 's cellular affinity for CO 2 is stronger than the affinity of its rubisco for CO 2 . This finding provided additional evidence that C. merolae operates a CCM while lacking the structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM, distinct from those we have seen previously described in detail. The results of our modeling supported the feasibility of this proposed minimal and non-canonical CCM in C. merolae . To facilitate the robust modeling of this process, we measured and incorporated physiological and enzymatic parameters into the model. Additionally, we trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met the experimentally derived criteria for functional carbon concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO 2 membrane permeability. Our exploration thus suggested that a non-canonical CCM could exist in C. merolae and illuminated the essential features generally necessary for CCMs to function.

Steensma, Anne K. [Michigan State Univ., East Lans↗

Low Carbon Inducible2/Fatty Acid Desaturase4 locus in C. reinhardtii directs plastid peroxidase location and trans fatty acid production

Light capture and photosynthetic energy conversion depend on photosynthetic complexes that are embedded within lipid membranes. Components of these complexes are vulnerable to damage by reactive oxygen species, byproducts of photosynthesis that accumulate under environmental stress. Here we explore the basis for a lipid-based sensing mechanism allowing plants or algae to assess and respond to damage to the photosynthetic membranes. In Chlamydomonas reinhardtii, Low Carbon Inducible2 (LCI2) and Fatty Acid Desaturase4 (FAD4) are two proteins derived from the same locus by a differential splicing event, sharing an N-terminus encoded by the first two exons. FAD4 produces a 16-carbon, trans double bond-containing fatty acid found exclusively in phosphatidylglycerol of chloroplast membranes, while LCI2 recruits peroxidase activity to the membrane. The unique organization and transcriptional regulation of the LCI2/FAD4 locus represents a regulatory interface that allows cells to initiate the biosynthesis of a fatty acid unique to the photosynthetic membranes while also linking it to the production of an enzyme involved in the mitigation of reactive oxygen species.

Nicodemus, Timothy J [Michigan State University, E↗

Exploring isospin symmetry breaking in exotic nuclei: High-precision mass measurement of 23 Si and shell-model calculations of 𝑇 = 5/2 nuclei

Here, we present a high-precision mass measurement of the proton-rich nucleus 23 Si, performed with the LEBIT Penning trap at the Facility for Rare Isotope Beams (FRIB) utilizing the time-of-flight ion cyclotron resonance (TOF-ICR) technique. We determined a mass excess of 23362.9(5.8) keV, which agrees with a recent storage-ring measurement from the experimental Cooler-Storage Ring (CSRe) in Lanzhou but has a factor of 20 improved precision 23 Si is hence the nucleus with the most precisely known mass among all nuclei with an isospin projection of 𝑇 𝑧 = −5/2. We performed shell-model calculations with the USDC and USDCm Hamiltonians to study binding energy differences and Thomas-Ehrmann shifts in mirror systems with an isospin up to 𝑇 = 5/2. Our experimental result and other recently reported masses of neutron-deficient sd-shell nuclei agree well with the theoretical predictions, demonstrating that isospin symmetry breaking in sd-shell nuclei—even at high isospin values—is well described by modern shell-model calculations.

20 ≤ A ≤ 38↗

DESI DR2 results. I. Baryon acoustic oscillations from the Lyman alpha forest

We present the baryon acoustic oscillation (BAO) measurements with the Lyman-𝛼 (Ly⁢𝛼) forest from the second data release (DR2) of the Dark Energy Spectroscopic Instrument (DESI) survey. Our BAO measurements include both the autocorrelation of the Ly⁢𝛼 forest absorption observed in the spectra of high-redshift quasars and the cross-correlation of the absorption with the quasar positions. The total sample size is approximately a factor of 2 larger than the DR1 dataset, with forest measurements in over 820,000 quasar spectra and the positions of over 1.2 million quasars. We describe several significant improvements to our analysis in this paper, and two supporting papers describe improvements to the synthetic datasets that we use for validation and how we identify damped Ly⁢𝛼 absorbers. Our main result is that we have measured the BAO scale with a statistical precision of 1.1% along and 1.3% transverse to the line of sight, for a combined precision of 0.65% on the isotropic BAO scale at 𝑧 eff =2.33. This excellent precision, combined with recent theoretical studies of the BAO shift due to nonlinear growth, motivated us to include a systematic error term in Ly⁢𝛼 BAO analysis for the first time. We measure the ratios 𝐷 𝐻 ⁡(𝑧 eff )/𝑟 𝑑 = 8.632 ± 0.098 ± 0.026 and 𝐷 𝑀 ⁡(𝑧 eff )/𝑟 𝑑 = 38.99 ± 0.52 ± 0.12, where 𝐷 𝐻 = 𝑐/𝐻⁡(𝑧) is the Hubble distance, 𝐷 𝑀 is the transverse comoving distance, 𝑟 𝑑 is the sound horizon at the drag epoch, and we quote both the statistical and the theoretical systematic uncertainty. The companion paper presents the BAO measurements at lower redshifts from the same dataset and the cosmological interpretation.

baryon acoustic oscillations↗

Measurements and models of enhanced recombination following inner-shell vacancies in liquid xenon

Electron-capture decays of 125 Xe and 127 Xe , and double-electron-capture decays of 124 Xe , are backgrounds in searches for weakly interacting massive particles (WIMPs) conducted by dual-phase xenon time projection chambers such as LUX-ZEPLIN (LZ). These decays produce signals with more light and less charge than equivalent-energy 𝛽 decays and correspondingly overlap more with WIMP signals. We measure three electron-capture charge yields in LZ: the 1.1 keV M-shell, 5.2 keV L-shell, and 33.2 keV K-shell at drift fields of 193 and 96.5 V/cm. The LL double-electron-capture decay of 124 Xe exhibits even more pronounced shifts in charge and light. We provide a first model of double-electron-capture charge yields using the link between ionization density and electron-ion recombination, and identify a need for more accurate calculations. Finally, we discuss the implications of the reduced charge yield of these decays and other interactions creating inner-shell vacancies for future dark matter searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dark Matter Search Results from 4.2 Tonne−Years of Exposure of the LUX-ZEPLIN (LZ) Experiment

We report results of a search for nuclear recoils induced by weakly interacting massive particle (WIMP) dark matter using the LUX-ZEPLIN (LZ) two-phase xenon time projection chamber. This analysis uses a total exposure of 4.2 ±0.1 tonne-years from 280 live days of LZ operation, of which 3.3 ± 0.1 tonne-years and 220 live days are new. A technique to actively tag background electronic recoils from 214 Pb 𝛽 decays is featured for the first time. Enhanced electron-ion recombination is observed in two-neutrino double electron capture decays of 124 Xe, representing a noteworthy new background. After removal of artificial signal-like events injected into the dataset to mitigate analyzer bias, we find no evidence for an excess over expected backgrounds. World-leading constraints are placed on spin-independent (SI) and spin-dependent WIMP-nucleon cross sections for masses ≥9 GeV/𝑐 2 . The strongest SI exclusion set is 2.2×10 −48 cm 2 at the 90% confidence level and the best SI median sensitivity achieved is 5.1 ×10 −48 cm 2 , both for a mass of 40 GeV/𝑐 2 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Demonstration of x-ray fluorescence spectroscopy as a sensitive temperature diagnostic for high-energy-density physics experiments

We present the use of x-ray fluorescence spectroscopy (XFS) to a sensitive temperature diagnostic in shocked foams at temperatures of 30–75 eV. Cobalt-doped foams were shock compressed using a planar drive at the OMEGA laser facility and photo-pumped with a Zn He⁢𝛼 x-ray source. Analysis of the resulting cobalt 𝐾⁢𝛽 x-ray fluorescence spectra using collisional radiative codes allows the temperature to be determined in the shocked foams. Furthermore, this method provides a sensitive and robust technique to determine temperatures in high-energy-density physics experiments in the tens of electronvolts temperature range. In these experiments, we find that radiation hydrodynamic simulations predict a lower temperature in the shocked foams compared to analysis of the XFS data using collisional radiative models. Although additional experiments with an independent temperature diagnostic to absolutely calibrate XFS spectra for these conditions will be required to resolve this discrepancy, these results demonstrate the excellent temperature sensitivity of XFS spectra for high-energy-density physics experiments.

Atomic spectra↗

Resonance Ionization Spectroscopy Experiment at Facility for Rare Isotope Beams

This manuscript reports on the commissioning of the Resonance Ionization Spectroscopy Experiment (RISE) at the BEam COoler and LAser spectroscopy (BECOLA) facility at Facility for Rare Isotope Beams (FRIB). The instrument implements the collinear resonance ionization spectroscopy technique for sensitive measurements of isotope shifts and hyperfine structure of short-lived isotopes produced at FRIB. The existing BECOLA beamline was extended to integrate an electrostatic ion-beam bender and an ion detector at ultrahigh vacuum. An injection-seeded titanium-sapphire laser and a multiharmonic pulsed neodymium-doped yttrium aluminum garnet laser were installed to perform resonant excitation and selective ionization. Commissioning tests were performed to demonstrate the capabilities of the instrument by measuring the hyperfine structure of stable 27 Al produced in an offline ion source. The RISE instrument is ready and operational for future studies of short-lived isotopes at FRIB.

Atomic spectra↗

New Constraints on Cosmic Ray-Boosted Dark Matter from the LUX-ZEPLIN Experiment

While dual-phase xenon time projection chambers have driven the sensitivity toward weakly interacting massive particles at the GeV/c 2 to TeV/c 2 mass scale, the scope for sub-GeV/c 2 dark matter particles is hindered by a limited nuclear recoil energy detection threshold. One approach to probe for lighter candidates is to consider cases where they have been boosted by collisions with cosmic rays in the Milky Way, such that the additional kinetic energy lifts their induced signatures above the nominal threshold. In this Letter, we report first results of a search for cosmic ray-boosted dark matter (CRDM) with a combined 4.2 metric ton/yr exposure from the LUX-ZEPLIN experiment. We observe no excess above the expected backgrounds and establish world-leading constraints on the spin-independent CRDM-nucleon cross section as small as 3.9×10 −33 cm 2 at 90% confidence level for sub-GeV/c 2 masses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DESI 2024: Constraints on physics-focused aspects of dark energy using DESI DR1 BAO data

Baryon acoustic oscillation data from the first year of the Dark Energy Spectroscopic Instrument (DESI) provide near percent-level precision of cosmic distances in seven bins over the redshift range z=0.1–4.2. Here, this paper is the follow-up to the original DESI BAO cosmology paper [A. G. Adame et al. (DESI Collaboration), arXiv:2404.03002], which considered the conventional w 0 w a cold dark matter (CDM) model. We use the novel DESI data, together with other cosmic probes, to constrain the background expansion history using some well-motivated physical classes of dark energy. In particular, we explore three physics-focused behaviors of dark energy from the equation of state and energy density perspectives: the thawing class (matching many simple quintessence potentials), emergent class (where dark energy comes into being recently, as in phase transition models), and mirage class [where phenomenologically the distance to cosmic microwave background (CMB) last scattering is close to that from a cosmological constant Λ despite dark energy dynamics]. All three classes fit the data at least as well as Λ ⁢CDM, and indeed can improve on it by Δ⁢χ 2 ≈ –5 to –17 for the combination of DESI BAO with CMB and supernova data while having one more parameter. The mirage class does essentially as well as w 0 ⁢w a CDM and exhibits moderate to strong Bayesian evidence preference with respect to Λ⁢ CDM. These classes of dynamical behaviors highlight worthwhile avenues for further exploration into the nature of dark energy.

79 ASTRONOMY AND ASTROPHYSICS↗

First Measurement of Missing Energy due to Nuclear Effects in Monoenergetic Neutrino Charged-Current Interactions

We present the first measurement of the missing energy due to nuclear effects in monoenergetic, muon neutrino charged-current interactions on carbon, originating from 𝐾 + → 𝜇 + ⁢𝜈 𝜇 decay at rest (𝐸 𝜈 𝜇 = 235.5 MeV), performed with the J-PARC Sterile Neutrino Search at the J-PARC Spallation Neutron Source liquid scintillator based experiment. Toward characterizing the neutrino interaction, ostensibly 𝜈 𝜇 ⁢𝑛 → 𝜇 − ⁢𝑝 or 𝜈 𝜇 ⁢ 12 C → 𝜇 − ⁢ 12 N, we define the missing energy as the energy transferred to the nucleus (𝜔) minus the kinetic energy of the outgoing proton(s), 𝐸 𝑚 ≡ 𝜔−∑ 𝑇 𝑝 , and relate this to visible energy in the detector, 𝐸 𝑚 = 𝐸 𝜈 𝜇 ⁡(235.5 MeV) − 𝑚 𝜇⁡ (105.7 MeV) + [𝑚 𝑛 − 𝑚 𝑝⁡ (1.3 MeV)] − 𝐸 vis . The missing energy, which is naively expected to be zero in the absence of nuclear effects (e.g., nucleon separation energy, Fermi momenta, and final-state interactions), is uniquely sensitive to many aspects of the interaction, and has previously been inaccessible with neutrinos. The shape-only, differential cross section measurement reported, based on a (77 ± 3)% pure double-coincidence kaon decay-at-rest signal (621 total events), provides detailed insight into neutrino-nucleus interactions, allowing even the nuclear orbital shell of the struck nucleon to be inferred. The measurement provides an important benchmark for models and event generators at hundreds of MeV neutrino energies, characterized by the difficult-to-model transition region between neutrino-nucleus and neutrino-nucleon scattering, and relevant for applications in nuclear physics, neutrino oscillation measurements, and Type-II supernova studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Extended dark energy analysis using DESI DR2 BAO measurements

We conduct an extended analysis of dark energy constraints, in support of the findings of the Dark Energy Spectroscopic Instrument (DESI) second data release cosmology key paper, including DESI data, Planck cosmic microwave background observations, and three different supernova compilations. Using a broad range of parametric and nonparametric methods, we explore the dark energy phenomenology and find consistent trends across all approaches, in good agreement with the 𝑤 0⁢ 𝑤 𝑎⁢ CDM (cold dark matter) key paper results. Even with the additional flexibility introduced by nonparametric approaches, such as binning and Gaussian processes, we find that extending Λ⁢ CDM to include a two-parameter 𝑤⁡(𝑧) is sufficient to capture the trends present in the data. Finally, we examine three dark energy classes with distinct dynamics, including quintessence scenarios satisfying 𝑤 ≥ −1, to explore what underlying physics can explain such deviations. The current data indicate a clear preference for models that feature a phantom crossing; although alternatives lacking this feature are disfavored, they cannot yet be ruled out. Our analysis confirms that the evidence for dynamical dark energy, particularly at low redshift (𝑧 ≲ 0.3), is robust and stable under different modeling choices.

79 ASTRONOMY AND ASTROPHYSICS↗

Optical cycling on thorium monoxide for an improved test of fundamental symmetries

Optical cycling refers to repeated excitation and spontaneous emission on an electronic transition in an atom or molecule. Optical cycling in molecules can enable a wide range of quantum control and readout techniques, but unfortunately it has only been demonstrated on a small class of alkalilike or alkaline-earth-like molecules. Thorium monoxide (ThO), a molecule used in one of the most precise permanent electron electric dipole moment (eEDM) searches (ACME†) [Andreev et al., Nature (London) 562, 355 (2018)], does not fall into this category. In this work, we demonstrate the first optical cycling on this nonconventional class over a range of experimental parameter space, including laser intensity, polarization switching rate, and interaction time. We show that both the 𝐽 = 1 and 𝐽 = 2 rotational levels of ThO molecule are capable of cycling an average of 11(2) photons with a single laser, at scattering rates of 1.9⁢(6) × 10 6 and 2.3⁢(7) × 10 6 s −1 , respectively, before population is lost to other vibronic levels. We outline a scheme to apply this demonstrated optical cycling in an ACME-style eEDM measurement, improving the detection efficiency by over fourfold compared to noncycling fluorescence detection. This would lead to over a twofold enhancement in the statistical sensitivity of the eEDM search. This optical-cycling scheme can be further extended to scatter ∼100 photons, which would enable a wider range of quantum control and sensing using ThO molecules.

Atomic & molecular processes in external fields↗

First Constraint on Atmospheric Millicharged Particles with the LUX-ZEPLIN Experiment

We report on a search for millicharged particles (mCPs) produced in cosmic ray atmospheric interactions using data collected during the first science run of the LUX-ZEPLIN experiment. The mCPs produced by two processes—meson decay and proton bremsstrahlung—are considered in this study. This search utilized a novel signature unique to liquid xenon (LXe) time projection chambers, allowing sensitivity to mCPs with masses ranging from 10 to 1000 MeV/c 2 and fractional charges between 0.001 and 0.02 of the electron charge (𝑒). With an exposure of 60 live days and a 5.5 metric ton fiducial mass, we observed no significant excess over background. This represents the first experimental search for atmospheric mCPs and the first search for mCPs using an underground LXe experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States

ABSTRACT Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified ( ƒ nitrified ), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta‐glucosidase (BG) and N ‐acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒ nitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒ nitrified . The ƒ nitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒ nitrified , including for high soil C sites predicted to have low ƒ nitrified , which decreased the role of soil C as a predictor of ƒ nitrified . Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID‐19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒ nitrified . Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.

Nieland, Matthew A. [Stockbridge School of Agricul↗

New results in the CTEQ-TEA global analysis of parton distributions in the nucleon

This report summarizes the latest developments in the CTEQ-TEA global analysis of parton distribution functions (PDFs) in the nucleon. The focus is on recent NNLO fits to high-precision LHC data at 8 and 13 TeV, including Drell–Yan, jet, and top-quark pair production, pursued on the way toward the release of the new generation of CTEQ-TEA general-purpose PDFs. The report also discusses advancements in statistical and numerical methods for PDF determination and uncertainty quantification, highlighting the importance of robust and replicable uncertainties for high-stakes observables. Additionally, it covers phenomenological studies related to PDF determination, such as the interplay of experimental constraints, exploration of correlations between high-x nucleon sea and low-energy parity-violating measurements, fitted charm in the nucleon, the photon PDF in the neutron, and simultaneous SMEFT-PDF analyses.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗