Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.

The Mars 2020 Perseverance rover has examined and sampled sulfate-rich clastic rocks from the Hogwallow Flats member at Hawksbill Gap and the Yori Pass member at Cape Nukshak. Both strata are located on the Jezero crater western fan front, are lithologically and stratigraphically similar, and have been assigned to the Shenandoah formation. In situ analyses demonstrate that these are fine-grained sandstones composed of phyllosilicates, hematite, Ca-sulfates, Fe-Mg-sulfates, ferric sulfates, and possibly chloride salts. Sulfate minerals are found both as depositional grains and diagenetic features, including intergranular cement and vein- and vug-cements. Here, we describe the possibility of various sulfate phases to preserve potential biosignatures and the record of paleoenvironmental conditions in fluid and solid inclusions, based on findings from analog sulfate-rich rocks on Earth. The samples collected from these outcrops, Hazeltop and Bearwallow from Hogwallow Flats, and Kukaklek from Yori Pass, should be examined for such potential biosignatures and environmental indicators upon return to Earth.

We present the first comprehensive study of a giant, approximate to 70 kpc-scale nebula around a radio-quiet quasar at z < 1. The analysis is based on deep integral field spectroscopy with Multi-Unit Spectroscopic Explorer of the field of HE 0238-1904, a luminous quasar at z = 0.6282. The nebula emits strongly in [O II], H ss, and [O III], and the quasar resides in an unusually overdense environment for a radio-quiet system. The environment likely consists of two groups which may be merging, and in total have an estimated dynamical mass of M-dyn approximate to 4 x10(13) to 10(14) M-circle dot. The nebula exhibits largely quiescent kinematics and irregular morphology. The nebula may arise primarily through interaction-related stripping of circumgalactic and interstellar medium (CGM/ISM) of group members, with some potential contributions from quasar outflows. The simultaneous presence of the giant nebula and a radio-quiet quasar in a rich environment suggests a correlation between such circum-quasar nebulae and environmental effects. This possibility can be tested with larger samples. The upper limits on the electron number density implied by the [O II] doublet ratio range from log( n e,[O II]/cm(-3)) < 1.2 to 2.8. However, assuming a constant quasar luminosity and negligible projection effects, the densities implied from the measured line ratios between different ions (e.g. [O II], [O III], and [Ne V]) and photoionization simulations are often 10-400 times larger. This large discrepancy can be explained by quasar variability on a time-scale of approximate to 10(4)-10(5) yr.

Application of the best available science to improve quantification of greenhouse gas (GHG) emissions at regional and national scales is key to climate action. Here, we present a two-decade (2000-2019) GHG (CO2, CH4, and N2O) budget for Mexico derived from multiple products. Data from the National GHG Inventory, global observations, and the scientific literature were compared to identify knowledge gaps on GHG flux dynamics and discrepancies among estimates. Total mean annual GHG emissions were estimated at 695-910 TgCO2-eq year-1 over these two decades, with 70% of the emissions attributable to CO2, 23% to CH4, and 5% to N2O (2% to other gases). When divided by sectors, we found agreement across emission estimates from various sources for fossil fuels, cattle, agriculture, and waste for all GHGs. However, considerable discrepancies were identified in the fluxes from terrestrial ecosystems. The disagreement was particularly large for the land CO2 sink, where net biome production estimations from the national inventory were double those from any other observational product. Extensive knowledge gaps exist, mainly related to aquatic systems (e.g., outgassing in rivers) and the lateral fluxes (e.g., wood trade). In addition, limited information is available on CH4 emissions from wetlands and soil CH4 consumption. We expect these results to guide future research to reduce estimation uncertainties and fill the information gaps across Mexico.

Understanding new mechanisms for phase transformation in carbon is of considerable interest. This study investigates on the compression conditions required to create recoverable diamond during room-temperature high-pressure compression of glassy carbon. Under non-hydrostatic compression conditions when shear is present, glassy carbon transforms into an oriented graphitic structure at similar to 45 GPa, and then forms mixed diamond and lonsdaleite nanocrystals when the pressure is higher than similar to 80 GPa. In contrast, during hydrostatic compression no significant changes in the microstructure was observed, highlighting glassy carbon's resilience under compression. Molecular dynamics modelling supports the proposed model that shear drives the phase transition mechanism and causes a temperature spike that drives crystallisation. Our work demonstrates that shear is key to high-pressure diamond formation in the absence of heating.

Amoeboid olivine aggregates (AOAs) are the most abundant type of refractory inclusions found in most carbonaceous chondrite groups. AOAs are thought to be genetically related to calcium-aluminum-rich inclusions (CAIs) and potential chondrule precursor components, although the precise physical and temporal details of AOA formation and their relationship to other chondritic components remain unclear. In this study, we measured the chromium and titanium isotopic compositions of eight AOAs from four different CV chondrites with the goal of evaluating potential genetic links between AOAs, CAIs, and chondrules. These are the first Cr and Ti isotopic data reported beyond a single AOA previously measured for Cr and a different single AOA previously measured for Ti. The results presented here show that the epsilon 54Cr and epsilon 50Ti isotopic compositions of AOAs are indistinguishable from those of CAIs, suggesting that AOAs and CAIs formed from a common region of the disk. We also demonstrate, based on the comparison of the Cr and Ti isotopic composition of AOAs to previously measured chondrules, that mixing between AOAs and an NC compositional endmember alone cannot fully explain the range of measured chondrule compositions. Although AOAs may have been important chondrule precursor components along with AOA olivine, CAIs, fragments of earlier generation chondrules, and fine-grained matrix material, this observation requires another currently unknown component to be involved in chondrule formation.

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 an analysis of spectroscopic data of the cool, highly magnetic, and polluted white dwarf 2MASS J0916-4215. The atmosphere of the white dwarf is dominated by hydrogen, but numerous spectral lines of magnesium, calcium, titanium, chromium, iron, and strontium, along with Lii, Nai, Ali, and Ki lines, are found in the incomplete Paschen-Back regime, most visibly, in the case of Caii lines. Extensive new calculations of the Paschen-Back effect in several spectral lines are presented and results of the calculations are tabulated for the Caii H&K doublet. The abundance pattern shows a large lithium and strontium excess, which may be viewed as a signature of planetary debris akin to Earth's continental crust accreted on to the star, although the scarcity of silicon indicates possible dilution in bulk Earth material. Accurate abundance measurements proved sensitive to the value of the broadening parameter due to collisions with neutral hydrogen ((Hi)), particularly in saturated lines such as the resonance lines of Cai and Caii. We found that (Hi) if formulated with values from the literature could be overestimated by a factor of 10 in most resonance lines.