A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present, generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g., the rbs locus and pykF) and species (e.g., Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide a method and mathematical justification for exploration of biological networks in higher dimensions.

Margarete M.S. Heck, professor of cell biology and genetics, University of Edinburgh, died peacefully at home amid her loving family under a blue moon on August 30, 2023, after a long journey with ovarian cancer.

One of the largest explosive eruptions instrumentally recorded occurred at Hunga volcano on 15 January 2022. The magma plumbing system under this volcano is unexplored because of inherent difficulties caused by its submarine setting. We use marine gravity data derived from satellite altimetry combined with multibeam bathymetry to model the architecture and dynamics of the magmatic system before and after the January 2022 eruption. We provide geophysical evidence for substantial high-melt content magma accumulation in three reservoirs at shallow depths (2 to 10 kilometers) under the volcano. We estimate that less than ~30% of the existing magma was evacuated by the main eruptive phases, enough to trigger caldera collapse. The eruption and caldera collapse reorganized magma storage, resulting in an increased connectivity between the two spatially distinct reservoirs. Modeling global satellite altimetry-derived gravity data at undersea volcanoes offer a promising reconnaissance tool to probe the subsurface for eruptible magma.

We report on a chemo-dynamical analysis of SPLUS J142445.34-254247.1 (SPLUS J1424-2542), an extremely metal-poor halo star enhanced in elements formed by the rapid neutron-capture process (r-process). This star was first selected as a metal-poor candidate from its narrowband S-PLUS photometry and followed up spectroscopically in medium resolution with Gemini-South/GMOS, which confirmed its low-metallicity status. High-resolution spectroscopy was gathered with GHOST at Gemini-South, allowing for the determination of the chemical abundances for 36 elements, from carbon to thorium. At [Fe/H] = -3.39, SPLUS J1424-2542 is one of the lowest-metallicity stars with measured Th and has the highest log is an element of(Th/Eu) observed to date, making it part of the "actinide-boost" category of r-process-enhanced stars. The analysis presented here suggests that the gas cloud from which SPLUS J1424-2542 formed must have been enriched by at least two progenitor populations. The light-element (Z <= 30) abundance pattern is consistent with the yields from a supernova explosion of metal-free stars with 11.3-13.4 M circle dot, and the heavy-element (Z >= 38) abundance pattern can be reproduced by the yields from a neutron star merger (1.66 M circle dot and 1.27 M circle dot) event. A kinematical analysis also reveals that SPLUS J1424-2542 is a low-mass, old halo star with a likely in situ origin, not associated with any known early merger events in the Milky Way.

Protein O-glycosylation is a nutrient signaling mechanism that plays an essential role in maintaining cellular homeostasis across different species. In plants, SPINDLY (SPY) and SECRET AGENT (SEC) posttranslationally modify hundreds of intracellular proteins with O-fucose and O-linked N-acetylglucosamine, respectively. SPY and SEC play overlapping roles in cellular regulation, and loss of both SPY and SEC causes embryo lethality in Arabidopsis (Arabidopsis thaliana). Using structure-based virtual screening of chemical libraries followed by in vitro and in planta assays, we identified a SPY O-fucosyltransferase inhibitor (SOFTI). Computational analyses predicted that SOFTI binds to the GDP-fucose-binding pocket of SPY and competitively inhibits GDP-fucose binding. In vitro assays confirmed that SOFTI interacts with SPY and inhibits its O-fucosyltransferase activity. Docking analysis identified additional SOFTI analogs that showed stronger inhibitory activities. SOFTI treatment of Arabidopsis seedlings decreased protein O-fucosylation and elicited phenotypes similar to the spy mutants, including early seed germination, increased root hair density, and defective sugar-dependent growth. In contrast, SOFTI did not visibly affect the spy mutant. Similarly, SOFTI inhibited the sugar-dependent growth of tomato (Solanum lycopersicum) seedlings. These results demonstrate that SOFTI is a specific SPY O-fucosyltransferase inhibitor that can be used as a chemical tool for functional studies of O-fucosylation and potentially for agricultural management.

Copper shows limited isotopic variation in equilibrated mantle-derived silicate rocks, but large isotopic fractionation during kinetic processes. For example, lunar and terrestrial samples that have experienced evaporation were found to have an isotopic fractionation of up to 12.5%o in their Cu-65/Cu-63 ratios, while komatiites, lherzolites, mid-ocean ridge and ocean island basalts show negligible Cu isotope fractionation as a result of equilibrium partial melting and crystal fractionation. The contrast between the observed magnitudes of equilibrium and kinetic isotope fractionation for Cu calls for a better understanding of kinetic Cu isotope fractionation. One of the mechanisms for creating large kinetic isotopic fractionation even at magmatic temperatures is diffusion. In this study, we performed Cu isotopic measurements on Cu diffusion couple experiments to constrain the beta factor for Cu isotopic fractionation by diffusion. We demonstrate a Monte Carlo approach for the regression and error estimation of the measured isotope profiles, which yielded beta values of 0.16 +/- 0.03 and 0.18 +/- 0.03 for the two experimental charges measured. Our results are subsequently applied to a quantitative model for the evaporation of a molten sphere to discuss the role of diffusion in affecting the bulk Cu isotopic fractionation between liquid and vapor during evaporation. We apply the model to Cu evaporation experiments and tektite data to show that convection primarily governs mass transport for evaporation during tektite formation. In addition, we show that Cu isotopes can be used as a tool to test the role of kinetics during various magmatic processes such as magmatic sulfide ore deposit formation, porphyry-type ore deposit formation, and fluid-rock interactions.

We report a Fourier transform infrared analysis of functional groups in insoluble organic matter (IOM) extracted from a series of 100-500 mu m Ryugu grains collected during the two touchdowns of February 22 and July 11, 2019. IOM extracted from most of the samples is very similar to IOM in primitive CI, CM, and CR chondrites, and shows that the extent of thermal metamorphism in Ryugu regolith was, at best, very limited. One sample displays chemical signatures consistent with a very mild heating, likely due to asteroidal collision impacts. We also report a lower carbonyl abundance in Ryugu IOM samples compared to primitive chondrites, which could reflect the accretion of a less oxygenated precursor by Ryugu. The possible effects of hydrothermal alteration and terrestrial weathering are also discussed. Last, no firm conclusions could be drawn on the origin of the soluble outlier phases, observed along with IOM in this study and in the preliminary analysis of Ryugu samples. However, it is clear that the HF/HCl residues presented in this publication are a mix between IOM and the nitrogen-rich outlier phase.

Peripheral neurons terminate at the surface of tendons partly to relay nociceptive pain signals; however, the role of peripheral nerves in tendon injury and repair remains unclear. Here, we show that after Achilles tendon injury in mice, there is new nerve growth near tendon cells that express nerve growth factor (NGF). Conditional deletion of the Ngf gene in either myeloid or mesenchymal mouse cells limited both innervation and tendon repair. Similarly, inhibition of the NGF receptor tropomyosin receptor kinase A (TrkA) abrogated tendon healing in mouse tendon injury. Sural nerve transection blocked the postinjury increase in tendon sensory innervation and the expansion of tendon sheath progenitor cells (TSPCs) expressing tubulin polymerization promoting protein family member 3. Single cell and spatial transcriptomics revealed that disruption of sensory innervation resulted in dysregulated inflammatory signaling and transforming growth factor-beta (TGFbeta) signaling in injured mouse tendon. Culture of mouse TSPCs with conditioned medium from dorsal root ganglia neuron further supported a role for neuronal mediators and TGFbeta signaling in TSPC proliferation. Transcriptomic and histologic analyses of injured human tendon biopsy samples supported a role for innervation and TGFbeta signaling in human tendon regeneration. Last, treating mice after tendon injury systemically with a small-molecule partial agonist of TrkA increased neurovascular response, TGFbeta signaling, TSPC expansion, and tendon tissue repair. Although further studies should investigate the potential effects of denervation on mechanical loading of tendon, our results suggest that peripheral innervation is critical for the regenerative response after acute tendon injury.

Alka(e)nes are produced by many living organisms and exhibit diverse physiological roles, reflecting a high functional versatility. Alka(e)nes serve as water proof wax in plants, communicating pheromones for insects, and microbial signaling molecules in some bacteria. Although alka(e)nes have been found in cyanobacteria and algal chloroplasts, a possible role in photosynthesis and chloroplast function remains elusive. In this study, we investigated the consequences of the absence of alka(e)nes on membrane lipid remodeling and photosynthesis using the cyanobacteria Synechocystis PCC6803 as a model organism. By following the dynamics of membrane lipids and the photosynthetic performance in strains defected and altered in alka(e)ne biosynthesis, we show that a profound remodeling of the membrane lipidome and carotenoid content occur in the absence of alka(e)nes, including a decrease in the membrane carotenoid content, a decrease in some digalactosyldiacylglycerol (DGDG) species and a parallel increase in monogalactosyldiacylglycerol (MGDG) species. Under high light, this effect is accompanied in alka(e)ne deficient strains by a higher susceptibility of photosynthesis and growth, the effect being reversed by expressing an algal photoenzyme producing alka(e)nes from fatty acids. We conclude that alka(e)nes play a crucial role in maintaining lipid homeostasis of photosynthetic membranes, thereby contributing to the proper functioning of photosynthesis, particularly under elevated light intensities.