Fundamental behaviors emerge from simulations of a living minimal cell.

We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.

Biodiversity patterns diverge along geographic temperature gradients.

Models applying space-for-time substitution, including those projecting ecological responses to climate change, generally assume an elevational and latitudinal equivalence that is rarely tested. However, a mismatch may lead to different capacities for providing climatic refuge to dispersing species. We compiled community data on zooplankton, ectothermic animals that form the consumer basis of most aquatic food webs, from over 1200 mountain lakes and ponds across western North America to assess biodiversity along geographic temperature gradients spanning nearly 3750 m elevation and 30° latitude. Species richness, phylogenetic relationships, and functional diversity all showed contrasting responses across gradients, with richness metrics plateauing at low elevations but exhibiting intermediate latitudinal maxima. The nonmonotonic/hump-shaped diversity trends with latitude emerged from geographic interactions, including weaker latitudinal relationships at higher elevations (i.e. in alpine lakes) linked to different underlying drivers. Here, divergent patterns of phylogenetic and functional trait dispersion indicate shifting roles of environmental filters and limiting similarity in the assembly of communities with increasing elevation and latitude. We further tested whether gradients showed common responses to warmer temperatures and found that mean annual (but not seasonal) temperatures predicted elevational richness patterns but failed to capture consistent trends with latitude, meaning that predictions of how climate change will influence diversity also differ between gradients. Contrasting responses to elevation- and latitude-driven warming suggest different limits on climatic refugia and likely greater barriers to northward range expansion.

Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning.

Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over visited molecular configurations - microstates. However, to obtain convergence, we need a sufficiently long record of visited microstates, which translates to the high-computational cost of the molecular simulations. In this work, we show how to use a point cloud-based deep learning strategy to rapidly predict the structural properties of liquids from a single molecular configuration. We tested our approach using three homogeneous liquids with progressively more complex entities and interactions: Ar, NO, and H2O under varying pressure and temperature conditions within the liquid state domain. Our deep neural network architecture allows rapid insight into the liquid structure, here probed by the radial distribution function, and can be used with molecular/atomistic configurations generated by either simulation, first-principle, or experimental methods.

Common Photo-oxidative Decarboxylation Mechanism in Iron Hydroxy Carboxylate Complexes.

Photochemical oxidation of dissolved organic matter is a crucial component of carbon cycling in surface waters. Photo-oxidation of iron(III)-carboxylate complexes is of particular interest because complexation with iron(III) can sensitize this functional group to photodecarboxylation. The photo-oxidation mechanism of ferrioxalate has been extensively characterized, but it is unclear whether the mechanism or timing is similar for other more complex carboxylates. In this study, we use time-resolved infrared spectroscopy to demonstrate that Fe(III)-citrate, an aliphatic carboxylate, and Fe(III)-salicylate, an aromatic carboxylate, follow the same photo-oxidation kinetics as ferrioxalate. Hence the data suggest a common mechanism for decarboxylation of iron hydroxy carbonates. Differences in the CO2 yield within 50 ps are qualitatively similar to the long-time-scale quantum yield for Fe(II) production.

Application of modern coexistence theory to rare plant restoration provides early indication of restoration trajectories.

Restoration ecology commonly seeks to re-establish species of interest in degraded habitats. Despite a rich understanding of how succession influences re-establishment, there are several outstanding questions that remain unaddressed: are short-term abundances sufficient to determine long-term re-establishment success, and what factors contribute to unpredictable restorations outcomes? In other words, when restoration fails, is it because the restored habitat is substandard, because of strong competition with invasive species, or alternatively due to changing environmental conditions that would equally impact established populations? Here, we re-purpose tools developed from modern coexistence theory to address these questions, and apply them to an effort to restore the endangered Contra Costa goldfields (Lasthenia conjugens) in constructed ("restored") California vernal pools. Using 16 years of data, we construct a population model of L. conjugens, a species of conservation concern due primarily to habitat loss and invasion of exotic grasses. We show that initial, short-term appearances of restoration success from population abundances is misleading, as year-to-year fluctuations cause long-term population growth rates to fall below zero. The failure of constructed pools is driven by lower maximum growth rates compared with reference ("natural") pools, coupled with a stronger negative sensitivity to annual fluctuations in abiotic conditions that yield decreased maximum growth rates. Nonetheless, our modeling shows that fluctuations in competition (mainly with exotic grasses) benefit L. conjugens through periods of competitive release, especially in constructed pools of intermediate pool depth. We therefore show how reductions in invasives and seed addition in pools of particular depths could change the outcome of restoration for L. conjugens. By applying a largely theoretical framework to the urgent goal of ecological restoration, our study provides a blueprint for predicting restoration success, and identifies future actions to reverse species loss.

Ab initio modeling of H2S dissociative chemisorption on Ag(100).

Natural sulfidation of silver nanomaterials can passivate the surface, while preserving desirable optical and electrical properties, which is beneficial for limiting Ag+ release and cytotoxicity. But little is known at the atomic scale about silver sulfidation mechanisms, particularly on different crystallographic terminations. Using density functional theory (DFT) calculations, we examined the process of H2S sorption and reaction on Ag(100) surfaces relevant to Ag nanowires (AgNWs). DFT energy minimizations predict a strong dissociative chemisorption of H2S on the surface yielding co-adsorbed sulfide and hydrogen atoms in specific surface sites. However, nudged elastic band (NEB) calculations suggest relatively large activation energies for both the first and second dissociation steps, due in part to overcoming the energy to cleave the S-H bond and attendant site migration from an on-top Ag site position to a hollow site position of the bound S atom. The large barriers associated with the dissociative chemisorption reaction for gas-phase H2S points to the importance of including thermochemical contributions and the influence of other components in more complex environmental media such as air or water to help complete the mechanistic picture of silver sulfidation and passivation for realistic systems.

Applying modern coexistence theory to priority effects.

Modern coexistence theory is increasingly used to explain how differences between competing species lead to coexistence versus competitive exclusion. Although research testing this theory has focused on deterministic cases of competitive exclusion, in which the same species always wins, mounting evidence suggests that competitive exclusion is often historically contingent, such that whichever species happens to arrive first excludes the other. Coexistence theory predicts that historically contingent exclusion, known as priority effects, will occur when large destabilizing differences (positive frequency-dependent growth rates of competitors), combined with small fitness differences (differences in competitors' intrinsic growth rates and sensitivity to competition), create conditions under which neither species can invade an established population of its competitor. Here we extend the empirical application of modern coexistence theory to determine the conditions that promote priority effects. We conducted pairwise invasion tests with four strains of nectar-colonizing yeasts to determine how the destabilizing and fitness differences that drive priority effects are altered by two abiotic factors characterizing the nectar environment: sugar concentration and pH. We found that higher sugar concentrations increased the likelihood of priority effects by reducing fitness differences between competing species. In contrast, higher pH did not change the likelihood of priority effects, but instead made competition more neutral by bringing both fitness differences and destabilizing differences closer to zero. This study demonstrates how the empirical partitioning of priority effects into fitness and destabilizing components can elucidate the pathways through which environmental conditions shape competitive interactions.

Ion exchange selectivity in clay is controlled by nanoscale chemical-mechanical coupling.

Ion exchange in nanoporous clay-rich media plays an integral role in water, nutrient, and contaminant storage and transport. In montmorillonite (MMT), a common clay mineral in soils, sediments, and muds, the swelling and collapse of clay particles through the addition or removal of discrete molecular layers of water alters cation exchange selectivities in a poorly understood way. Here, we show that ion exchange is coupled to the dynamic delamination and restacking of clay layers, which creates a feedback between the hydration state of the exchanging cation and the composition of the clay interlayer. Particles with different hydration states are distinct phases with unique binding selectivities. Surprisingly, equilibrium achieved through thermal fluctuations in cation concentration and hydration state leads to the exchange of both ions and individual MMT layers between particles, a process we image directly with high-resolution transmission electron microscopy at cryogenic conditions (cryo-TEM). We introduce an exchange model that accounts for the binding selectivities of different phases, which is likely applicable to many charged colloidal or macromolecular systems in which the structural conformation is correlated with the activities of water and counterions within spatially confined compartments.

Crumpling of silver nanowires by endolysosomes strongly reduces toxicity.

Fibrous particles interact with cells and organisms in complex ways that can lead to cellular dysfunction, cell death, inflammation, and disease. The development of conductive transparent networks (CTNs) composed of metallic silver nanowires (AgNWs) for flexible touchscreen displays raises new possibilities for the intimate contact between novel fibers and human skin. Here, we report that a material property, nanowire-bending stiffness that is a function of diameter, controls the cytotoxicity of AgNWs to nonimmune cells from humans, mice, and fish without deterioration of critical CTN performance parameters: electrical conductivity and optical transparency. Both 30- and 90-nm-diameter AgNWs are readily internalized by cells, but thinner NWs are mechanically crumpled by the forces imposed during or after endocytosis, while thicker nanowires puncture the enclosing membrane and release silver ions and lysosomal contents to the cytoplasm, thereby initiating oxidative stress. This finding extends the fiber pathology paradigm and will enable the manufacture of safer products incorporating AgNWs.

Floquet Prethermalization with Lifetime Exceeding 90 s in a Bulk Hyperpolarized Solid.

We report the observation of long-lived Floquet prethermal states in a bulk solid composed of dipolar-coupled ^{13}C nuclei in diamond at room temperature. For precessing nuclear spins prepared in an initial transverse state, we demonstrate pulsed spin-lock Floquet control that prevents their decay over multiple-minute-long periods. We observe Floquet prethermal lifetimes T_{2}^{'}≈90.9 s, extended >60 000-fold over the nuclear free induction decay times. The spins themselves are continuously interrogated for ∼10 min, corresponding to the application of ≈5.8×10^{6} control pulses. The ^{13}C nuclei are optically hyperpolarized by lattice nitrogen vacancy centers; the combination of hyperpolarization and continuous spin readout yields significant signal-to-noise ratio in the measurements. This allows probing the Floquet thermalization dynamics with unprecedented clarity. We identify four characteristic regimes of the thermalization process, discerning short-time transient processes leading to the prethermal plateau and long-time system heating toward infinite temperature. This Letter points to new opportunities possible via Floquet control in networks of dilute, randomly distributed, low-sensitivity nuclei. In particular, the combination of minutes-long prethermal lifetimes and continuous spin interrogation opens avenues for quantum sensors constructed from hyperpolarized Floquet prethermal nuclei.

Physiology underlies the assembly of ecological communities.

Trait-based community ecology promises an understanding of the factors that determine species abundances and distributions across habitats. However, ecologists are often faced with large suites of potentially important traits, making generalizations across ecosystems and species difficult or even impossible. Here, we hypothesize that key traits structuring ecological communities may be causally dependent on common physiological mechanisms and that elucidating these mechanisms can help us understand the distributions of traits and species across habitats. We test this hypothesis by investigating putatively causal relationships between physiological and behavioral traits at the species and community levels in larvae of 17 species of dragonfly that co-occur at the landscape scale but segregate among lakes. We use tools borrowed from phenotypic selection analyses to show that physiological traits underlie activity rate, which has opposing effects on foraging and predator avoidance behaviors. The effect of activity on these behaviors ultimately shapes species distributions and community composition in habitats with either large-bodied fish or invertebrates as top predators. Remarkably, despite the inherent complexity of ecological communities, the expression of just two biomolecules accounts for a high proportion of the variation in behavioral traits and hence, dragonfly community composition between habitats. We suggest that causal relationships among traits can drive species distributions and community assembly.

Supercritical CO2 uptake by nonswelling phyllosilicates.

Interactions between supercritical (sc) CO2 and minerals are important when CO2 is injected into geologic formations for storage and as working fluids for enhanced oil recovery, hydraulic fracturing, and geothermal energy extraction. It has previously been shown that at the elevated pressures and temperatures of the deep subsurface, scCO2 alters smectites (typical swelling phyllosilicates). However, less is known about the effects of scCO2 on nonswelling phyllosilicates (illite and muscovite), despite the fact that the latter are the dominant clay minerals in deep subsurface shales and mudstones. Our studies conducted by using single crystals, combining reaction (incubation with scCO2), visualization [atomic force microscopy (AFM)], and quantifications (AFM, X-ray photoelectron spectroscopy, X-ray diffraction, and off-gassing measurements) revealed unexpectedly high CO2 uptake that far exceeded its macroscopic surface area. Results from different methods collectively suggest that CO2 partially entered the muscovite interlayers, although the pathways remain to be determined. We hypothesize that preferential dissolution at weaker surface defects and frayed edges allows CO2 to enter the interlayers under elevated pressure and temperature, rather than by diffusing solely from edges deeply into interlayers. This unexpected uptake of CO2, can increase CO2 storage capacity by up to ∼30% relative to the capacity associated with residual trapping in a 0.2-porosity sandstone reservoir containing up to 18 mass % of illite/muscovite. This excess CO2 uptake constitutes a previously unrecognized potential trapping mechanism.

Deconstructing the Impact of Malaria Vector Diversity on Disease Risk.

AbstractRecent years have seen significant progress in understanding the impact of host community assemblage on disease risk, yet diversity in disease vectors has rarely been investigated. Using published malaria and mosquito surveys from Kenya, we analyzed the relationship between malaria prevalence and multiple axes of mosquito diversity: abundance, species richness, and composition. We found a net amplification of malaria prevalence by vector species richness, a result of a strong direct positive association between richness and prevalence alongside a weak indirect negative association between the two, mediated through mosquito community composition. One plausible explanation of these patterns is species niche complementarity, whereby less competent vector species contribute to disease transmission by filling spatial or temporal gaps in transmission left by dominant vectors. A greater understanding of vector community assemblage and function, as well as any interactions between host and vector biodiversity, could offer insights to both fundamental and applied ecology.

Ecological and Evolutionary Stochasticity Shape Natural Selection.

The distribution of biodiversity depends on the combined and interactive effects of ecological and evolutionary processes. The joint contribution of these processes has focused almost exclusively on deterministic effects, even though mechanisms that increase the importance of random ecological processes are expected to also increase the importance of random evolutionary processes. Here we manipulate the sizes of old field fragments to generate correlated sampling effects for a focal population (a gall maker) and its enemy community. Traits and communities were more variable in smaller patches. However, because of the preference of some enemies for some trait values (gall sizes), random variation in population mean trait values exacerbated differences in community composition. The random distribution of traits and interactions created predictable but highly variable patterns of natural selection. Our study highlights how stochastic processes can affect ecological and evolutionary processes structuring the strength and direction of selection locally and at larger scales.

Species Differences in Phenology Shape Coexistence.

Ecological theory produces opposing predictions about whether differences in the timing of life-history transitions, or "phenology," promote or limit coexistence. Phenological separation is predicted to create temporal niche differences, increasing coexistence, yet phenological separation could also competitively favor one species, increasing fitness differences and hindering coexistence. We experimentally manipulated relative germination timing, a critical phenological event, of two annual grass species, Vulpia microstachys and V. octoflora, to test these contrasting predictions. We parameterized a competition model to estimate within-season niche differences, fitness differences, and coexistence and to estimate coexistence when year-to-year fluctuations of germination timing occur. Increasing germination separation caused parallel changes in niche and fitness differences, with the net effect of weakening within-year coexistence. Both species experienced a competitive advantage by germinating earlier, and a 4-day head start allowed the generally inferior competitor to exclude the otherwise superior competitor. The overall consequence of germination separation was to limit coexistence within a given year, although year-to-year variation in the relative timing of germination was sufficient to support long-term coexistence. Our results clarify how phenological differences structure competitive interactions and highlight the need to quantify year-to-year variation in these differences to better understand species coexistence.

Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity.

Human-assisted introductions of exotic species are a leading cause of anthropogenic change in biodiversity; however, context dependencies and interactions with co-occurring stressors impede our ability to predict their ecological impacts. The legacy of historical sportfish stocking in mountainous regions of western North America creates a unique, natural quasiexperiment to investigate factors moderating invasion impacts on native communities across broad geographic and environmental gradients. Here we synthesize fish stocking records and zooplankton relative abundance for 685 mountain lakes and ponds in the Cascade and Canadian Rocky Mountain Ranges, to reveal the effects of predatory sportfish introduction on multiple taxonomic, functional and phylogenetic dimensions of prey biodiversity. We demonstrate an innovative analytical approach, combining exploratory random forest machine learning with confirmatory multigroup analysis using multivariate partial least-squares structural equation models, to generate and test hypotheses concerning environmental moderation of stocking impacts. We discovered distinct effects of stocking across different dimensions of diversity, including negligible (nonsignificant) impacts on local taxonomic richness (i.e. alpha diversity) and trophic structure, in contrast to significant declines in compositional uniqueness (i.e. beta diversity) and body size. Furthermore, we found that stocking impacts were moderated by cross-scale interactions with climate and climate-related land-cover variables (e.g. factors linked to treeline position and glaciers). Interactions with physical morphometric and lithological factors were generally of lesser importance, though catchment slope and habitat size constraints were relevant in certain dimensions. Finally, applying space-for-time substitution, a strong antagonistic (i.e. dampening) interaction between sportfish predation and warmer temperatures suggests redundancy of their size-selective effects, meaning that warming will lessen the consequences of introductions in the future and stocked lakes may be less impacted by subsequent warming. While both stressors drive biotic homogenization, our results have important implications for fisheries managers weighing the costs/benefits of stocking-or removing established non-native populations-under a rapidly changing climate.

Temperature-dependence of the dielectric relaxation of water using non-polarizable water models.

Key physical and chemical properties of aqueous fluids are determined by the structure and dynamics of the hydrogen bond network of water but we lack adequate models for the linkages between hydrogen bonding and aqueous chemistry, particularly in non-ambient conditions or in confinement. Dielectric relaxation spectroscopy (DRS) provides a sensitive approach for probing water dynamics but sound interpretation of DRS data requires molecular simulation and associated computational methods capable of accurately representing aqueous fluids and their frequency dependent, complex permittivity. Here, we test the accuracy of dielectric spectra of bulk liquid water calculated from molecular dynamics simulations using 19 non-polarizable water models at 298 K. In contrast to prior studies, the simulation size, time-step and duration allow calculation of the dielectric function from 107-1012 Hz without assuming an analytical form. The accuracy of the prediction of the low-frequency (static) dielectric constant at room temperature is related to the water molecule dipole moment, specifically models with µ ≥ 2.4 D give ε(0) with a relative error lower than 5%. However, no water model tested can fully reproduce the complex dielectric spectra of water. For a subset of models, calculations of the dielectric response from -5 to 60 °C reproduces the experimental trend in water dynamics with temperature but the characteristic relaxation time is always underestimated. The calculated water dipole relaxation time and hydrogen-bond lifetime are both exponentially decaying functions of temperature, and exhibit a linear correlation very close to equality. The comparison provides new computational support for the concept that the Debye relaxation of liquid water is determined by the dynamics of the hydrogen-bond network, and that both are ensemble properties.

Experimental dispersal reveals characteristic scales of biodiversity in a natural landscape.

Ecological theory posits that dispersal among habitat patches links local communities and is a key "regional" process that maintains biological diversity. However, manipulations required to experimentally test regional processes are infeasible for most systems, and thus more work is needed to detect the scales at which regional processes manifest and their overall effect on diversity. In a Californian grassland, a hotspot for global biodiversity, we used a seed vacuum to increase dispersal at spatial scales varying from 1 m to 10 km while maintaining a realistic spatial structure of species pools and environmental conditions. We found that dispersal limitation has a profound influence on diversity; species richness increased with the spatial scale of seed mixing, doubling in plots that received seed from large (≥5 km) compared with small (≤5 m) scales. This increase in diversity corresponded to an increase in how well species distributions were explained by environmental conditions, from modest at small scales (R2 = 0.34) to strong at large scales (R2 = 0.52). Responses to the spatial scale of seed mixing were nonlinear, with no differences below 5 m or above 5 km. Nonlinearities were explained by homogeneity of environmental conditions below 5 m and by a lack of additional variation in the species pool above 5 km. Our approach of manipulating natural communities at different spatial scales reveals (i) nonlinear transitions in the importance of environmental sorting and dispersal, and (ii) the negative effects of dispersal limitation on local diversity, consistent with previous research suggesting that large numbers of species are headed toward regional extinction.

Indirect Interactions Shape Selection in a Multispecies Food Web.

Species do not live, interact, or evolve in isolation but are instead members of complex ecological communities. In ecological terms, complex multispecies interactions can be understood by considering indirect effects that are mediated by changes in traits and abundances of intermediate species. Interestingly, traits and abundances are also central to our understanding of phenotypic selection, suggesting that indirect effects may be extended to understand evolution in complex communities. Here we explore indirect ecological effects and their evolutionary corollary in a well-understood food web comprising a plant, its herbivores, and enemies that select for opposite defensive phenotypes in one of the herbivores. We show that ecological indirect interactions are mediated by changes to both the traits and the abundances of intermediate species and that these changes ultimately reduce enemy attack and weaken selection. We discuss the generality of the link between indirect effects and selection. We go on to argue that local adaptation and eco-evolutionary feedback may be less likely in complex multispecies food webs than in simpler food chains (e.g., coevolution). Overall, considering selection in complex interaction networks can facilitate the rapprochement of community ecology and evolution.