The water stress-associated hormone abscisic acid (ABA) acts through a well-defined signal transduction cascade to mediate downstream transcriptional events important for acclimation to stress. Although ABA signaling is known to function in specific tissues to regulate root growth, little is understood regarding the spatial pattern of ABA-mediated transcriptional regulation. Here, we describe the construction and evaluation of an ABSCISIC ACID RESPONSIVE ELEMENT (ABRE)-based synthetic promoter reporter that reveals the transcriptional response of tissues to different levels of exogenous ABA and stresses. Genome-scale yeast one-hybrid screens complemented these approaches and revealed how promoter sequence and architecture affect the recruitment of diverse transcription factors (TFs) to the ABRE. Our analysis also revealed ABA-independent activity of the ABRE-reporter under nonstress conditions, with expression being enriched at the quiescent center and stem cell niche. We show that the WUSCHEL RELATED HOMEOBOX5 and NAC DOMAIN PROTEIN13 TFs regulate QC/SCN expression of the ABRE reporter, which highlights the convergence of developmental and DNA-damage signaling pathways onto this cis-element in the absence of water stress. This work establishes a tool to study the spatial pattern of ABA-mediated transcriptional regulation and a repertoire of TF-ABRE interactions that contribute to the developmental and environmental control of gene expression in roots.

Photosynthesis in leaves generates fixed-carbon resources and essential metabolites that support sink tissues, such as roots. Two of these metabolites, sucrose and auxin, promote growth in root systems, but the explicit connection between photosynthetic activity and control of root architecture has not been explored. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the Arabidopsis thaliana CYCLOPHILIN 38 (CYP38) gene, which causes accumulation of pre-emergent stage lateral roots. CYP38 was previously reported to stabilize photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in shoots, and grafting experiments show that the gene acts non-cell-autonomously to promote lateral root emergence. Growth of wild-type plants under low-light conditions phenocopies the cyp38 lateral root emergence defect, as does the inhibition of PSII-dependent electron transport or Nicotinamide adenine dinucleotide phosphate (NADPH) production. Importantly, these perturbations to photosynthetic activity rapidly suppress lateral root emergence, which is separate from their effects on shoot size. Supplementary exogenous sucrose largely rescued primary root (PR) growth in cyp38, but not lateral root growth. Auxin (indole-3-acetic acid (IAA)) biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Consistently, we found that wild-type seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. IAA treatment rescued the cyp38 lateral root defect, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. These data directly confirm the importance of CYP38-dependent photosynthetic activity in supporting root growth, and define the specific contributions of two metabolites in refining root architecture under light-limited conditions.

Stratospheric aerosol injection is one of the most widely studied solar radiation modification methods to reduce some effects of anthropogenic warming. We perform idealized simulations to analyze climate response to different latitudinal and altitudinal distributions of additional stratospheric sulphate aerosols. We analyze climate response to both large volcanic-size aerosols that are representative of sulphate aerosols which form when SO2 is injected into the stratosphere by major volcanic eruptions or by proposed stratospheric sulphate aerosol geoengineering option, and small background-size aerosols which are present in the stratosphere during quiescent periods with no major volcanic eruptions. Our simulations show that under the climate state with doubled atmospheric CO2, for the same total mass, independent of size-distributions, aerosols concentrated at higher latitudes produce less negative effective radiative forcing but larger surface cooling as a result of larger forcing efficacy. For the same latitudinal distribution, small background-size aerosols added at lower altitudes cause larger surface cooling as a result of hygroscopic growth that increases scattering of sunlight. In contrast, large volcanic-size aerosols added at lower altitudes cause smaller surface cooling than at higher altitudes as a result of enhanced stratospheric heating and associated water vapor feedback that enhance absorption of solar and terrestrial radiation. For both background-size and volcanic-size aerosols, asymmetric distributions about the equator induce substantial cross-equatorial energy transport, causing the Intertropical Convergence Zone to move to the warmer hemisphere with less aerosol loading. Our study helps to understand the climate consequences of different spatial patterns and size distributions of stratospheric aerosol perturbation.

In this commentary, we provide additional context for Ocko and Hamburg (2022) related to the climate consequences of replacing fossil fuels with clean hydrogen alternatives. We first provide a tutorial for the derivations of underlying differential equations that describe the radiative forcing of hydrogen emissions, which differ slightly from equations relied on by previous studies. Ocko and Hamburg (2022) defined a metric based on time-integrated radiative forcing from continuous emissions. To complement their analysis, we further present results for temperature and radiative forcing over the next centuries for unit pulse and continuous emissions scenarios. Our results are qualitatively consistent with previous studies, including Ocko and Hamburg (2022). Our results clearly show that for the same quantity of emissions, hydrogen shows a consistently smaller climate impact than methane. As with other short-lived species, the radiative forcing from a continuous emission of hydrogen is proportional to emission rates, whereas the radiative forcing from a continuous emission of carbon dioxide is closely related to cumulative emissions. After a cessation of hydrogen emissions, the Earth cools rapidly, whereas after a cessation of carbon dioxide emissions, the Earth continues to warm somewhat and remains warm for many centuries. Regardless, our results support the conclusion of Ocko and Hamburg (2022) that, if methane were a feedstock for hydrogen production, any possible near-term consequences will depend primarily on methane leakage and secondarily on hydrogen leakage.

Cobalamin (vitamin B12), is a cofactor for crucial metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonise the algal phycosphere, forming stable communities that gain preferential access to exudates and in return provide compounds, such as B12. Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12-dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12-independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesise that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12-dependent algae.

Genome assembly tools are used to reconstruct genomic sequences from raw sequencing data, which are then used for identifying the organisms present in a metagenomic sample. More recently, machine learning approaches have been applied to a variety of bioinformatics problems, and in this paper, we explore their use for organism identification. We start out by evaluating several commonly used metagenomic assembly tools, including PhyloFlash, MEGAHIT, MetaSPAdes, Kraken2, Mothur, UniCycler, and PathRacer, and compare them against state-of-the art deep learning-based machine learning classification approaches represented by DNABERT and DeLUCS, in the context of two synthetic mock community datasets. Our analysis focuses on determining whether ensembling metagenome assembly tools with machine learning tools has the potential to improve identification performance relative to using the tools individually. We find that this is indeed the case, and analyze the level of effectiveness of potential tool ensembling for organisms with different characteristics (based on factors such as repetitiveness, genome size, and GC content).

Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

The intermediate Palomar Transient Factory reports our discovery of a young supernova, iPTF13bvn, in the nearby galaxy, NGC 5806 (22.5 Mpc). Our spectral sequence in the optical and infrared suggests a Type Ib classification. We identify a blue progenitor candidate in deep pre-explosion imaging within a 2 sigma error circle of 80 mas (8.7 pc). The candidate has an M-B luminosity of -5.52 +/- 0.39 mag and a B-I color of 0.25 +/- 0.25 mag. If confirmed by future observations, this would be the first direct detection for a progenitor of a Type Ib. Fitting a power law to the early light curve, we find an extrapolated explosion date around 0.6 days before our first detection. We see no evidence of shock cooling. The pre-explosion detection limits constrain the radius of the progenitor to be smaller than a few solar radii. iPTF13bvn is also detected in centimeter and millimeter wavelengths. Fitting a synchrotron self-absorption model to our radio data, we find a mass-loading parameter of 1.3x10(12) g cm(-1). Assuming a wind velocity of 10(3) km s(-1), we derive a progenitor mass-loss rate of 3 x 10(-5) M-circle dot yr(-1). Our observations, taken as a whole, are consistent with a Wolf-Rayet progenitor of the supernova iPTF13bvn.

Recent theoretical studies indicate that applying high pressure (up to tens of gigapascals) to simple compounds with triple bonds can convert the triple bonds to conjugated double bonds, which results in these compounds becoming electrically conductive or even superconductive. This might indicate a new route for the synthesis of inorganic/organic conductors of various compositions and properties and could greatly expand the field of conductive polymers. Here, we present a study of the phase behavior and electrical properties of K3Fe(CN)(6) up to similar to 15 GPa using Raman spectroscopy, synchrotron X-ray diffraction, and impedance spectroscopy at room temperature. In this pressure range, two new crystalline phases were identified, and their unit cells and space groups were determined. The cyanide ions react to form conjugated C=N bonds in two steps, and the electronic conductivity is enhanced by 3 orders of magnitude, from 10(-7) to 10(-4) S.cm(-1). Because this material is also an ionic conductor, these studies might "shed light" on the development of new cathode materials for alkali metal batteries. Enhancing the electrical conductivity by applying high pressure to compounds containing triple bonds could provide a potential route for synthesizing multifunctional conductive materials.

The motif of distinct H2O molecules in H-bonded networks is believed to persist up to the densest molecular phase of ice. At even higher pressures, where the molecule dissociates, it is generally assumed that the proton remains localized within these same networks. We report neutron-diffraction measurements on D2O that reveal the location of the D atoms directly up to 52 GPa, a pressure regime not previously accessible to this technique. The data show the onset of a structural change at similar to 13 GPa and cannot be described by the conventional network structure of ice VII above similar to 26 GPa. Our measurements are consistent with substantial deuteron density in the octahedral, interstitial voids of the oxygen lattice. The observation of this "interstitial" ice VII form provides a framework for understanding the evolution of hydrogen bonding in ice that contrasts with the conventional picture. It may also be a precursor for the superionic phase reported at even higher pressure with important consequences for our understanding of dense matter and planetary interiors.