Corals form an endosymbiotic relationship with the dinoflagellate algae Symbiodiniaceae, but ocean warming can trigger algal loss, coral bleaching and death, and the degradation of ecosystems. Mitigation of coral death requires a mechanistic understanding of coral-algal endosymbiosis. Here we report an RNA interference (RNAi) method and its application to study genes involved in early steps of endosymbiosis in the soft coral Xenia sp. We show that a host endosymbiotic cell marker called LePin (lectin and kazal protease inhibitor domains) is a secreted Xenia lectin that binds to algae to initiate phagocytosis of the algae and coral immune response modulation. The evolutionary conservation of domains in LePin among marine anthozoans performing endosymbiosis suggests a general role in coral-algal recognition. Our work sheds light on the phagocytic machinery and posits a mechanism for symbiosome formation, helping in efforts to understand and preserve coral-algal relationships in the face of climate change.

The intestines of animals are colonized by commensal microbes, which impact host development, health, and behavior. Precise quantification of colonization is essential for studying the complex interactions between host and microbe both to validate the microbial composition and study its effects. Drosophila melanogaster, which has a low native microbial diversity and is economical to rear with defined microbial composition, has emerged as a model organism for studying the gut microbiome. Analyzing the microbiome of an individual organism requires identification of which microbial species are present and quantification of their absolute abundance. This article presents a method for the analysis of a large number of individual fly microbiomes. The flies are prepared in 96-well plates, enabling the handling of a large number of samples at once. Microbial abundance is quantified by plating up to 96 whole fly homogenates on a single agar plate in an array of spots and then counting the colony forming units (CFUs) that grow in each spot. This plating system is paired with an automated CFU quantification platform, which incorporates photography of the plates, differentiation of fluorescent colonies, and automated counting of the colonies using an ImageJ plugin. Advantages are that (i) this method is sensitive enough to detect differences between treatments, (ii) the spot plating method is as accurate as traditional plating methods, and (iii) the automated counting process is accurate and faster than manual counting. The workflow presented here enables high-throughput quantification of CFUs in a large number of replicates and can be applied to other microbiology study systems including in vitro and other small animal models.

We model the early stages of planet formation in the solar system, including continual planetesimal formation, and planetesimal and pebble accretion onto planetary embryos in an evolving disk driven by a disk wind. The aim is to constrain aspects of planet formation that have large uncertainties by matching key characteristics of the solar system. The model produces a good fit to these characteristics for a narrow range of parameter space. Planetary growth beyond the ice line is dominated by pebble accretion. Planetesimal accretion is more important inside the ice line. Pebble accretion inside the ice line is slowed by higher temperatures, partial removal of inflowing pebbles by planetesimal formation and pebble accretion further out in the disk, and increased radial velocities due to gas advection. The terrestrial planets are prevented from accreting much water ice because embryos beyond the ice line reach the pebble-isolation mass before the ice line enters the terrestrial-planet region. When only pebble accretion is considered, embryos typically remain near their initial mass or grow to the pebble-isolation mass. Adding planetesimal accretion allows Mars-sized objects to form inside the ice line, and allows giant-planet cores to form over a wider region beyond the ice line. In the region occupied by Mercury, pebble Stokes numbers are small. This delays the formation of embryos and stunts their growth, so that only low-mass planets can form here.

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.