center dot Spatiotemporal patterns of phenology may be affected by mosaics of environmental and genetic variation. Environmental drivers may have temporally lagged impacts, but patterns and mechanisms remain poorly known. center dot We combine multiple genomic, remotely sensed, and physically modeled datasets to determine the spatiotemporal patterns and drivers of canopy phenology in quaking aspen, a widespread clonal dioecious tree species with diploid and triploid cytotypes. center dot We show that over 391 km(2) of southwestern Colorado: greenup date, greendown date, and growing season length vary by weeks and differ across sexes, cytotypes, and genotypes; phenology has high phenotypic plasticity and heritabilities of 31- 61% (interquartile range); and snowmelt date, soil moisture, and air temperature predict phenology, at temporal lags of up to 3 yr. center dot Our study shows that lagged environmental effects are needed to explain phenological variation and that the effect of cytotype on phenology is obscured by its correlation with topography. Phenological patterns are consistent with responses to multiyear accumulation of carbon deficit or hydraulic damage.

Directly imaging temperate rocky planets orbiting nearby, Sun-like stars with a 6 m class IR/O/UV space telescope, recently dubbed the Habitable Worlds Observatory, is a high-priority goal of the Astro2020 Decadal Survey. To prepare for future direct imaging (DI) surveys, the list of potential targets should be thoroughly vetted to maximize efficiency and scientific yield. We present an analysis of archival radial velocity data for southern stars from the NASA/NSF Extreme Precision Radial Velocity (EPRV) Working Group's list of high-priority target stars for future DI missions (drawn from the HabEx, LUVOIR, and Starshade Rendezvous studies). For each star, we constrain the region of companion mass and period parameter space we are already sensitive to based on the observational baseline, sampling, and precision of the archival radial velocity (RV) data. Additionally, for some of the targets, we report new estimates of magnetic activity cycle periods, rotation periods, improved orbital parameters for previously known exoplanets, and new candidate planet signals that require further vetting or observations to confirm. Our results show that for many of these stars we are not yet sensitive to even Saturn-mass planets in the habitable zone, let alone smaller planets, highlighting the need for future EPRV vetting efforts before the launch of a DI mission. We present evidence that the candidate temperate super-Earth exoplanet HD 85512b is most likely due to the star's rotation, and report an RV acceleration for delta Pav that supports the existence of a distant giant planet previously inferred from astrometry.

The habitability of exoplanets can be strongly influenced by the presence of an exomoon, and in some cases the exomoon itself could be a possible place for life to develop. For moons outside of the habitable zone, significant tidal heating may raise their surface temperatures enough for them to be considered habitable. Tidal heating of a moon depends on numerous factors such as eccentricity, semimajor axis, size of parent planet, and the presence of additional moons. In this work, we explore the degree of tidal heating possible for multimoon systems in resonance using a combination of semianalytic and numerical models. This demonstrates that even for a moon with zero initial eccentricity, when it moves into resonance with an outer moon, it can generate significant eccentricity and associated tidal heating. Depending on the mass ratio of the two moons, this resonance can either be short-lived (<= 200 Myr) or continue to be driven by the tidal migration of the moons. This tidal heating can also assist in making the exomoons easier to discover, and we explore two scenarios: secondary eclipses and outgassing of volcanic species. We then consider hypothetical moons orbiting known planetary systems to identify which will be best suited for finding exomoons with these methods. We conclude with a discussion of current and future instrumentation and missions.

Plant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signalling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and their activation of defense also requires the lipase domain proteins EDS1, SAG101 and PAD4. We investigated how the helper NLR NRG1 supports TNL-initiated immunity with EDS1 and SAG101. We find that NRG1 associates with EDS1 and SAG101 at the plasma membrane and in the nucleus, but only self-associates at the plasma membrane. Activation of TNLs is sufficient to trigger NRG1-EDS1-SAG101 interaction, but cell surface receptor-initiated defense is also required to form an oligomeric Resistosome. The data point to formation of NRG1-EDS1-SAG101 heterotrimers in the nucleus upon intracellular receptor activation alone and indicate formation of NRG1-EDS1-SAG101 Resistosomes at the plasma membrane upon co-activation of intracellular and cell surface-receptor pathways.

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.

Marine oxygen-deficient zones represent a natural source of nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent. To investigate controls on N2O production, the responses of ammonia oxidation (AO) to nitrite (NO2-) and N2O with respect to oxygen (O-2), ammonium (NH4+) and NO2- concentrations were evaluated using N-15 - NH4+ tracer incubations in the Eastern Tropical North Pacific. Within the oxycline, additions of NH4+ and O-2 stimulated N2O production according to Michaelis-Menten kinetics, indicating that both substrates were limiting, and that N2O production, even if the exact mechanisms remain uncertain, is mediated by predictable kinetics. Low half-saturation constants for NH4+ (12-28 nM) and O-2 (460 +/- 130 nM) during N2O production indicate that AO communities are well adapted to low concentrations of both substrates. Hybrid N2O formation (i.e., from one (NH4+)-N-15 , and one unlabeled nitrogen (N) source, e.g., NO2-, NO) accounted for similar to 90% of the N2O production from NH4+ and was robust across the different O-2 , NO2+, and NH4+ conditions. Lack of response to variable substrate concentrations implies that the unlabeled N source was not limiting for N2O production. Although both O-2 and NH4+ were key modulators of N2O production rates, N2O yield (N2O produced per NO2- produced) seemed to be controlled solely by O-2 . The N2O yield increased when O-2 concentrations dropped below the half-saturation concentration for AO to NO2+ (<1.4 mu M), the range where NO2- production decreased faster than N2O production. Our study shows that O-2 control on N2O yield from AO is robust across stations and depths.

SummaryThe chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the prediction of A/B compartment prediction from Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in dataset with low sequencing depth.Availabilitygithub.com/scoutzxb/CscoreToolContactxzheng@carnegiescience.edu

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in aiding these studies. We approached assembling the Sciara genome using multiple sequencing technologies: PacBio, Oxford Nanopore MinION, and Illumina. To find an optimal assembly using these datasets, we generated 44 Illumina assemblies using 7 short-read assemblers and 50 long-read assemblies of PacBio and MinION sequence data using 6 long-read assemblers. We ranked assemblies using a battery of reference-free metrics, and scaffolded a subset of the highest-ranking assemblies using BioNano Genomics optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. Moreover, we anchored nearly half of the Sciara genome sequence into chromosomes. Finally, we used the signal level of both the PacBio and Oxford Nanopore data to explore the presence or absence of DNA modifications in the Sciara genome since DNA modifications may play a role in imprinting in Sciara, as they do in mammals. These data serve as the foundation for future research by the growing community studying the unique features of this emerging model system.

Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long non-coding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, and Tetrahymena models, but not in parasitic protozoa, including clinically relevant human parasites. Here, using the protozoan parasite, Trypanosoma brucei (T. brucei) as a model, we have identified the interactome of T. brucei TERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors of TbTERT, highlighting unique features of T. brucei telomerase biology. These unique interactions with TbTERT, suggest mechanistic differences in telomere maintenance between T. brucei and other eukaryotes.