O-GlcNAcylation is a critical post-translational modification of proteins observed in both plants and animals and plays a key role in growth and development. While considerable knowledge exists about over 3000 substrates in animals, our understanding of this modification in plants remains limited. Unlike animals, plants possess two putative homologs: SECRET AGENT (SEC) and SPINDLY (SPY), with SPY also exhibiting O-fucosylation activity. To investigate the role of SEC as a major O-GlcNAc transferase in plants, we utilized LWAC enrichment and SILIA labeling, quantifying at both MS1 and MS2 levels. Our findings reveal a significant reduction in O-GlcNAc levels in the sec mutant, indicating a critical role of SEC in mediating O-GlcNAcylation. Through a comprehensive approach, combining HCD and EThcD fragmentation with substantial fractionations, we expanded our GlcNAc profiling, identifying 436 O-GlcNAc targets, including 227 new targets. The targets span diverse cellular processes, suggesting broad regulatory functions of O-GlcNAcylation. The expanded targets also enabled exploration of crosstalk between O-GlcNAcylation and O-fucosylation. We also examined EThcD fragmentation for site assignment. This report advances our understanding of O-GlcNAcylation in plants, facilitating further research in this field.

Plant cell expansion is driven by turgor pressure and regulated by hormones. How plant cells avoid cell wall rupture during hormone-induced cell expansion remains a mystery. Here we show that brassinosteroid (BR), while stimulating cell elongation, promotes the plasma membrane (PM) accumulation of the receptor kinase FERONIA (FER), which monitors cell wall damage and in turn attenuates BR-induced cell elongation to prevent cell rupture. The GSK3-like kinase BIN2 phosphorylates FER, resulting in reduced FER accumulation and translocation from endoplasmic reticulum to PM. By inactivating BIN2, BR signaling promotes dephosphorylation and increases PM accumulation of FER, thereby enhancing the surveillance of cell wall integrity. Our study reveals a vital signaling circuit that coordinates hormone signaling with mechanical sensing to prevent cell bursting during hormone-induced cell expansion.

For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for both basal and systemic acquired resistance (SAR). SA activates these immune responses by reprogramming up to 20% of the transcriptome through the function of NPR1. However, components in the NPR1-signaling hub, which appears as nuclear condensates, and the NPR1-signaling cascade remained elusive due to difficulties in studying transcriptional cofactors whose chromatin associations are often indirect and transient. To overcome this challenge, we applied TurboID to divulge the NPR1-proxiome, which detected almost all known NPR1-interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, NPR1-proxiome shares a striking similarity to GBPL3-proxiome involved in SA synthesis, except associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise greenCUT&RUN analyses showed that, upon SA-induction, NPR1 initiates the transcriptional cascade primarily through association with TGA TFs to induce expression of secondary TFs, predominantly WRKYs. WRKY54 and WRKY70 then play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, a loss of NPR1 condensate formation decreases its chromatin-association and transcriptional activity, indicating the importance of condensates in organizing the NPR1-signaling hub and initiating the transcriptional cascade. This study demonstrates how combinatorial applications of TurboID, and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades.

We present the final data from the Sloan Digital Sky Survey (SDSS) Reverberation Mapping (RM) project, a precursor to the SDSS-V Black Hole Mapper RM program. This data set includes 11 yr photometric and 7 yr spectroscopic light curves for 849 broad-line quasars over a redshift range of 0.1 < z < 4.5 and a luminosity range of L-bol = 10(44-47.5) erg s(-1), along with spectral and variability measurements. We report 23, 81, 125, and 110 RM lags (relative to optical continuum variability) for broad H alpha, H beta, Mg II, and C IV using the SDSS-RM sample, spanning much of the luminosity and redshift ranges of the sample. Using 30 low-redshift RM active galactic nuclei with dynamical-modeling black hole masses, we derive a new estimate of the average virial factor of < log f > = 0.62 +/- 0.07 for the line dispersion measured from the rms spectrum. The intrinsic scatter of individual virial factors is 0.31 +/- 0.07 dex, indicating a factor of 2 systematic uncertainty in RM black hole masses. Our lag measurements reveal significant R-L relations for H beta and Mg II at high redshift, consistent with the latest measurements based on heterogeneous samples. While we are unable to robustly constrain the slope of the R-L relation for C IV given the limited dynamic range in luminosity, we found substantially larger scatter in C IV lags at fixed L-1350. Using the SDSS-RM lag sample, we derive improved single-epoch (SE) mass recipes for H beta, Mg II, and C IV, which are consistent with their respective RM masses as well as between the SE recipes from two different lines, over the luminosity range probed by our sample. The new H beta and Mg II recipes are approximately unbiased estimators at given RM masses, but there are systematic biases in the C IV recipe. The intrinsic scatter of SE masses around RM masses is similar to 0.45 dex for H beta and Mg II, increasing to similar to 0.58 dex for C IV.

The radio galaxy 3C 66B has been hypothesized to host a supermassive black hole binary (SMBHB) at its center based on electromagnetic observations. Its apparent 1.05 yr period and low redshift (similar to 0.02) make it an interesting testbed to search for low-frequency gravitational waves (GWs) using pulsar timing array ( PTA) experiments. This source has been subjected to multiple searches for continuous GWs from a circular SMBHB, resulting in progressively more stringent constraints on its GW amplitude and chirp mass. In this paper, we develop a pipeline for performing Bayesian targeted searches for eccentric SMBHBs in PTA data sets, and test its efficacy by applying it to simulated data sets with varying injected signal strengths. We also search for a realistic eccentric SMBHB source in 3C 66B using the NANOGrav 12.5 yr data set employing PTA signal models containing Earth term-only as well as Earth+pulsar term contributions using this pipeline. Due to limitations in our PTA signal model, we get meaningful results only when the initial eccentricity e(0) < 0.5 and the symmetric mass ratio eta > 0.1. We find no evidence for an eccentric SMBHB signal in our data, and therefore place 95% upper limits on the PTA signal amplitude of 88.1 +/- 3.7 ns for the Earth term-only and 81.74 +/- 0.86 ns for the Earth+pulsar term searches for e(0) < 0.5 and eta > 0.1. Similar 95% upper limits on the chirp mass are (1.98 +/- 0.05) x 10(9) and (1.81 +/- 0.01) x 10(9) M-circle dot. These upper limits, while less stringent than those calculated from a circular binary search in the NANOGrav 12.5 yr data set, are consistent with the SMBHB model of 3C 66B developed from electromagnetic observations.

Capturing images of the nuclear dynamics within live cells is an essential technique for comprehending the intricate biological processes inherent to plant cell nuclei. While various methods exist for imaging nuclei, including combining fluorescent proteins and dyes with microscopy, there is a dearth of commercially available dyes for live-cell imaging. In Arabidopsis thaliana, we discovered that nuclei emit autofluorescence in the near-infrared (NIR) range of the spectrum and devised a non-invasive technique for the visualization of live cell nuclei using this inherent NIR autofluorescence. Our studies demonstrated the capability of the NIR imaging technique to visualize the dynamic behavior of nuclei within primary roots, root hairs, and pollen tubes, which are tissues that harbor a limited number of other organelles displaying autofluorescence. We further demonstrated the applicability of NIR autofluorescence imaging in various other tissues by incorporating fluorescence lifetime imaging techniques. Nuclear autofluorescence was also detected across a wide range of plant species, enabling analyses without the need for transformation. The nuclear autofluorescence in the NIR wavelength range was not observed in animal or yeast cells. Genetic analysis revealed that this autofluorescence was caused by the phytochrome protein. Our studies demonstrated that nuclear autofluorescence imaging can be effectively employed not only in model plants but also for studying nuclei in non-model plant species.

We collect a sample of 42 Type Ia supernovae (SNe Ia) with Swift UV photometry and well-measured early time light-curve rises and find that 2002es-like and 2003fg-like SNe Ia have different prepeak UV color evolutions compared to normal SNe Ia and other spectroscopic subtypes. Specifically, 2002es-like and 2003fg-like SNe Ia are cleanly separated from other SNe Ia subtypes by UVM2 - UVW1 greater than or similar to 1.0 mag at t = - 10 days relative to B-band maximum. Furthermore, the SNe Ia that exhibit nonmonotonic bumps in their rising light curves, to date, consist solely of 2002es-like and 2003fg-like SNe Ia. We also find that SNe Ia with two-component power-law rises are more luminous than SNe Ia with single-component power-law rises at prepeak epochs. Given the similar UV colors, along with other observational similarities, we discuss a possible progenitor scenario that places 2002es-like and 2003fg-like SNe Ia along a continuum and may explain the unique UV colors, early time bumps, and other observational similarities between these objects. Ultimately, further observations of both subtypes, especially in the near-infrared, are critical for constraining models of these peculiar thermonuclear explosions.

X-ray free electron laser (XFEL) sources coupled to high-power laser systems offer an avenue to study the structural dynamics of materials at extreme pressures and temperatures. The recent commissioning of the DiPOLE 100-X laser on the high energy density (HED) instrument at the European XFEL represents the state-of-the-art in combining x-ray diffraction with laser compression, allowing for compressed materials to be probed in unprecedented detail. Here, we report quantitative structural measurements of molten Sn compressed to 85(5) GPa and similar to 3500 K. The capabilities of the HED instrument enable liquid density measurements with an uncertainty of similar to 1 % at conditions which are extremely challenging to reach via static compression methods. We discuss best practices for conducting liquid diffraction dynamic compression experiments and the necessary intensity corrections which allow for accurate quantitative analysis. We also provide a polyimide ablation pressure vs input laser energy for the DiPOLE 100-X drive laser which will serve future users of the HED instrument.

Data exploration, usually the first step in data analysis, is a useful method to tackle challenges caused by big geoscience data. It conducts quick analysis of data, investigates the patterns, and generates/refines research questions to guide advanced statistics and machine learning algorithms. The background of this work is the open mineral data provided by several sources, and the focus is different types of associations in mineral properties and occurrences. Researchers in mineralogy have been applying different techniques for exploring such associations. Although the explored associations can lead to new scientific insights that contribute to crystallography, mineralogy, and geochemistry, the exploration process is often daunting due to the wide range and complexity of factors involved. In this study, our purpose is implementing a visualization tool based on the adjacency matrix for a variety of datasets and testing its utility for quick exploration of association patterns in mineral data. Algorithms, software packages, and use cases have been developed to process a variety of mineral data. The results demonstrate the efficiency of adjacency matrix in real-world usage. All the developed works of this study are open source and open access. (c) 2024 China University of Geosciences (Beijing) and Peking University. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

The aluminous calcium-ferrite type phase (CF) and new aluminous phase (NAL) are thought to hold the excess alumina produced by the decomposition of garnet in MORB compositions in the lower mantle. The respective stabilities of CF and NAL in the nepheline-spinel binary (NaAlSiO4-MgAl2O4 ) are well established. However with the addition of further components the phase relations at lower mantle conditions remain unclear. Here we investigate a range of compositions around the nepheline apex of the nepheline-kalsilite-spinel compositional join (NaAlSiO4-KAlSiO4-MgAl2O4) at 28-78 GPa and 2000 K. Our experiments indicate that even small amounts of a kalsilite (KAlSiO4) component dramatically impact phase relations. We find NAL to be stable up to at least 71 GPa in potassium-bearing compositions. This demonstrates the stabilizing effect of potassium on NAL, because NAL is not observed at pressures above 48 GPa on the nepheline-spinel binary. We also observe a broadening of the CF stability field to incorporate larger amounts of potassium with increasing pressure. For pressures below 50 GPa only minor amounts (<0.011(1)K/K+Na+Mg) of potassium are soluble in CF, whereas at 68 GPa, we find a solubility in CF of at least 0.088(3)K/K+Na+Mg . This indicates that CF and NAL are suitable hosts of the alkali content of MORB compositions at lower mantle conditions. For sedimentary compositions at lower mantle pressures, we expect K-Hollandite to be stable in addition to CF and NAL for pressures of 28-48 GPa, based on our simplified compositions.