BackgroundGenetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.ResultsHere, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.ConclusionOur study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.

We report new total-intensity visible-light high-contrast imaging of the TW Hya disk taken with the Space Telescope Imaging Spectrograph (STIS) on the Hubble Space Telescope. This represents the first published images of the disk with STIS since 2016, when a moving shadow on the disk surface was reported. We continue to see the shadow moving in a counterclockwise fashion, but in these new images the shadow has evolved into two separate shadows, implying a change in behavior for the occulting structure. Based on radiative-transfer models of optically thick disk structures casting shadows, we infer that a plausible explanation for the change is that there are now two misaligned components of the inner disk. The first of these disks is located between 5 and 6 au with an inclination of 5.5 degrees and position angle (PA) of 170 degrees, and the second between 6 and 7 au with an inclination of 7 degrees and PA of 50 degrees. Finally, we speculate on the implications of the new shadow structure and determine that additional observations are needed to disentangle the nature of TW Hya's inner-disk architecture.

We use observations with the infrared-optimized Magellan Adaptive Optics (MagAO) system and Clio camera in 3.9 mu m light to place stringent mass constraints on possible undetected companions to Sirius A. We suppress the light from Sirius A by imaging it through a grating vector-apodizing phase plate coronagraph with a 180 degrees dark region (gvAPP-180). To remove residual starlight in postprocessing, we apply a time-domain principal-components-analysis-based algorithm we call PCA-Temporal, which uses eigen time series rather than eigenimages to subtract starlight. By casting the problem in terms of eigen time series, we reduce the computational cost of postprocessing the data, enabling the use of the fully sampled data set for improved contrast at small separations. We also discuss the impact of retaining fine temporal sampling of the data on final contrast limits. We achieve postprocessed contrast limits of 1.5 x 10(-6)-9.8 x 10(-6) outside of 0.'' 75, which correspond to planet masses of 2.6-8.0 M (J). These are combined with values from the recent literature of high-contrast imaging observations of Sirius to synthesize an overall completeness fraction as a function of mass and separation. After synthesizing these recent studies and our results, the final completeness analysis rules out 99% of >= 9 M (J) planets from 2.5 to 7 au.

Data science and informatics tools are developing at a blistering rate, but their users often lack the educational background or resources to efficiently apply the methods to their research. Training resources and vignettes that accompany these tools often deprecate because their maintenance is not prioritized by funding, giving teams little time to devote to such endeavors. Our group has developed Open-source Tools for Training Resources (OTTR) to offer greater efficiency and flexibility for creating and maintaining these training resources. OTTR empowers creators to customize their work and allows for a simple workflow to publish using multiple platforms. OTTR allows content creators to publish training material to multiple massive online learner communities using familiar rendering mechanics. OTTR allows the incorporation of pedagogical practices like formative and summative assessments in the form of multiple choice questions and fill in the blank problems that are automatically graded. No local installation of any software is required to begin creating content with OTTR. Thus far, 15 training courses have been created with OTTR repository template. By using the OTTR system, the maintenance workload for updating these courses across platforms has been drastically reduced. For more information about OTTR and how to get started, go to ottrproject.org.

The formation of lateral microdomains is emerging as a central organizing principle in bacterial membranes. These microdomains are targets of antibiotic development and have the potential to enhance natural product synthesis, but the rules governing their assembly are unclear. Previous studies have suggested that microdomain formation is promoted by lipid phase separation, particularly by cardiolipin (CL) and isoprenoid lipids, and there is strong evidence that CL biosynthesis is required for recruitment of membrane proteins to cell poles and division sites. New work demonstrates that additional bacterial lipids may mediate membrane protein localization and function, opening the field for mechanistic evaluation of lipid-driven membrane organization in vivo.

The biogeochemical cycling of nitrogen (N) plays a critical role in supporting marine ecosystems and controlling primary production. Nitrification, the oxidation of ammonia (NH3) by microorganisms, is an important process in the marine N cycle, supplying nitrate (NO3-, the primary source of N that fuels new phytoplankton growth, and the primary substrate for the microbial process of denitrification. Understanding nitrification in the Chukchi Sea, the shallow sea overlying the continental shelf north of Alaska and the Bering Strait, is particularly important as phytoplankton growth there has been shown to be limited by N. However, the controls on nitrification in the water column and potential effects of climate change remain unknown. This study seeks to characterize the controls on nitrification in the Chukchi Sea. We found light to be a strong control on nitrification rates. Nitrification was undetectable at light levels above 23 mu mol photons m(-2) s(-1). Subsequently, sea ice concentration was related to nitrification, with rates being higher at stations with high ice cover where light transmission to the water column was reduced. High ammonium (NH4+ concentrations also enhanced nitrification, suggesting that nitrifying organisms were substrate-limited, likely due to competition for NH4+ from phytoplankton. Unlike previous experimental studies, we found that nitrification rates were higher under low pH conditions. As the effects of ocean acidification and warming disproportionately impact the Arctic, nitrification rates will undoubtedly be affected. Our results will help guide future studies on potential implications of climate change on the biogeochemistry of N in the Chukchi Sea.

The K-type star TOI-2525 has an estimated mass of M = 0.849(-0.033)(+0.024) M-circle dot and radius of R = 0.785(-0.007)(+0.007) R-circle dot observed by the TESS mission in 22 sectors (within sectors 1 and 39). The TESS light curves yield significant transit events of two companions, which show strong transit timing variations (TTVs) with a semiamplitude of similar to 6 hr. We performed TTV dynamical and photodynamical light-curve analysis of the TESS data combined with radial velocity measurements from FEROS and PFS, and we confirmed the planetary nature of these companions. The TOI-2525 system consists of a transiting pair of planets comparable to Neptune and Jupiter with estimated dynamical masses of m(b) = 0.088(-0.004)(+0.005) and m(c) = 0.709(-0.033)(+0.034) M-Jup, radii of r(b) = 0.88(-0.02)(+0.02) and r(c) = 0.98(-0.02)(+0.02) R-Jup, and orbital periods of P-b = 23.288(-0.002)(+0.001) and P-c = 49.260(-0.001)(+0.001) days for the inner and outer planet, respectively. The period ratio is close to the 2:1 period commensurability, but the dynamical simulations of the system suggest that it is outside the mean-motion resonance (MMR) dynamical configuration. Object TOI-2525 b is among the lowest-density Neptune-mass planets known to date, with an estimated median density of rho(b) = 0.174(-0.015)(+0.016) g cm(-3). The TOI-2525 system is very similar to the other K dwarf systems discovered by TESS, TOI-2202 and TOI-216, which are composed of almost identical K dwarf primaries and two warm giant planets near the 2:1 MMR.

We present the largest and most homogeneous collection of near-infrared (NIR) spectra of Type Ia supernovae (SNe Ia): 339 spectra of 98 individual SNe obtained as part of the Carnegie Supernova Project-II. These spectra, obtained with the FIRE spectrograph on the 6.5 m Magellan Baade telescope, have a spectral range of 0.8-2.5 mu m. Using this sample, we explore the NIR spectral diversity of SNe Ia and construct a template of spectral time series as a function of the light-curve-shape parameter, color stretch s ( BV ). Principal component analysis is applied to characterize the diversity of the spectral features and reduce data dimensionality to a smaller subspace. Gaussian process regression is then used to model the subspace dependence on phase and light-curve shape and the associated uncertainty. Our template is able to predict spectral variations that are correlated with s ( BV ), such as the hallmark NIR features: Mg ii at early times and the H-band break after peak. Using this template reduces the systematic uncertainties in K-corrections by similar to 90% compared to those from the Hsiao template. These uncertainties, defined as the mean K-correction differences computed with the color-matched template and observed spectra, are on the level of 4 x 10(-4) mag on average. This template can serve as the baseline spectral energy distribution for light-curve fitters and can identify peculiar spectral features that might point to compelling physics. The results presented here will substantially improve future SN Ia cosmological experiments, for both nearby and distant samples.

SN 2018aoz is a Type Ia SN with a B-band plateau and excess emission in infant-phase light curves ?1 day after the first light, evidencing an over-density of surface iron-peak elements as shown in our previous study. Here, we advance the constraints on the nature and origin of SN 2018aoz based on its evolution until the nebular phase. Near-peak spectroscopic features show that the SN is intermediate between two subtypes of normal Type Ia: core normal and broad line. The excess emission may be attributable to the radioactive decay of surface iron-peak elements as well as the interaction of ejecta with either the binary companion or a small torus of circumstellar material. Nebular-phase limits on Ha and He i favor a white dwarf companion, consistent with the small companion size constrained by the low early SN luminosity, while the absence of [O i] and He i disfavors a violent merger of the progenitor. Of the two main explosion mechanisms proposed to explain the distribution of surface iron-peak elements in SN 2018aoz, the asymmetric Chandrasekhar-mass explosion is less consistent with the progenitor constraints and the observed blueshifts of nebular-phase [Fe ii] and [Ni ii]. The helium-shell double-detonation explosion is compatible with the observed lack of C spectral features, but current 1D models are incompatible with the infant-phase excess emission, Bmax-Vmax

Using data from the Complete Nearby (redshift z (host) < 0.02) sample of Type Ia Supernovae (CNIa0.02), we find a linear relation between two parameters derived from the B - V color curves of Type Ia supernovae: the color stretch s ( BV ) and the rising color slope s(0)*(B-V) BV . The s ( BV ) parameter is known to be tightly correlated with the peak luminosity, especially for fast decliners (dim Type Ia supernovae), and the luminosity correlation with s ( BV ) is markedly better than with the classic light-curve width parameters such as ?m (15)(B). Thus, our new linear relation can be used to infer peak luminosity from s(0)* s ( BV ) (or ?m (15)(B)), the measurement of s(0)*(B-V)