Pathway enrichment analysis is indispensable for interpreting omics datasets and generating hypotheses. However, the foundations of enrichment analysis remain elusive to many biologists. Here, we discuss best practices in interpreting different types of omics data using pathway enrichment analysis and highlight the importance of considering intrinsic features of various types of omics data. We further explain major components that influence the outcomes of a pathway enrichment analysis, including defining background sets and choosing reference annotation databases. To improve reproducibility, we describe how to standard-ize reporting methodological details in publications. This article aims to serve as a primer for biologists to leverage the wealth of omics resources and motivate bioinformatics tool developers to enhance the power of pathway enrichment analysis.

Earth's water, intrinsic oxidation state and metal core density are fundamental chemical features of our planet. Studies of exoplanets provide a useful context for elucidating the source of these chemical traits. Planet formation and evolution models demonstrate that rocky exoplanets commonly formed with hydrogen-rich envelopes that were lost over time1. These findings suggest that Earth may also have formed from bodies with hydrogen-rich primary atmospheres. Here we use a self-consistent thermodynamic model to show that Earth's water, core density and overall oxidation state can all be sourced to equilibrium between hydrogen-rich primary atmospheres and underlying magma oceans in its progenitor planetary embryos. Water is produced from dry starting materials resembling enstatite chondrites as oxygen from magma oceans reacts with hydrogen. Hydrogen derived from the atmosphere enters the magma ocean and eventually the metal core at equilibrium, causing metal density deficits matching that of Earth. Oxidation of the silicate rocks from solar-like to Earth-like oxygen fugacities also ensues as silicon, along with hydrogen and oxygen, alloys with iron in the cores. Reaction with hydrogen atmospheres and metal-silicate equilibrium thus provides a simple explanation for fundamental features of Earth's geochemistry that is consistent with rocky planet formation across the Galaxy.

Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.

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.