Stable metal anodes enabled by a labile organic molecule bonded to a reduced graphene oxide aerogel

Metallic anodes (lithium, sodium, and zinc) are attractive for rechargeable battery technologies but are plagued by an unfavorable metal–electrolyte interface that leads to nonuniform metal deposition and an unstable solid–electrolyte interphase (SEI). Here we report the use of electrochemically labile molecules to regulate the electrochemical interface and guide even lithium deposition and a stable SEI. The molecule, benzenesulfonyl fluoride, was bonded to the surface of a reduced graphene oxide aerogel. During metal deposition, this labile molecule not only generates a metal-coordinating benzenesulfonate anion that guides homogeneous metal deposition but also contributes lithium fluoride to the SEI to improve Li surface passivation. Consequently, high-efficiency lithium deposition with a low nucleation overpotential was achieved at a high current density of 6.0 mA cm⁻². A Li|LiCoO₂ cell had a capacity retention of 85.3% after 400 cycles, and the cell also tolerated low-temperature (−10 °C) operation without additional capacity fading. This strategy was applied to sodium and zinc anodes as well.

Rechargeable batteries based on metal anodes including lithium (Li), sodium (Na), and zinc (Zn) show great promise in achieving high energy density (1–3). Unfortunately, the electrochemical interface of the metal anodes is not favorable for metal deposition. Metal nucleation is inhomogeneous at the surface, leading to the growth of metal dendrites (4–7) and the formation of an unstable solid–electrolyte interphase (SEI) that is incapable of protecting metals from the side reactions with the electrolyte (8–12).Substantial efforts have been devoted to stabilizing the interface of metal anodes, especially for Li metal. These include the design of artificial protective layers (13–17), alternative electrolytes (18–24), and sacrificial additives (25–30) to stabilize the metal–electrolyte interface, the development of mechanically robust coatings (31–34) to block Li dendrite growth, and the use of structured scaffolds to host dendrite-free Li deposition by reducing local current densities (35–43). However, the performance of metal anodes remains poor under high-current or low-temperature conditions. This is because the inhomogeneous Li nucleation and unstable SEI problems have not been well addressed, and these problems at the interface are even exacerbated under critical operating conditions, especially high-current densities and low temperatures (5, 6, 44).Toward this end, we report a simple molecular approach for regulating the electrochemical interface of metal anodes, which enables even Li deposition and stable SEI formation in a conventional electrolyte. This was realized by bonding a labile organic molecule, benzenesulfonyl fluoride (BSF), to a reduced graphene oxide (rGO) aerogel surface as the Li anode host (Fig. 1A). During Li deposition, BSF molecules electrochemically decompose at the interface and generate benzenesulfonate anions bonded to the rGO aerogel (Fig. 1B). The conjugated anions have a strong binding affinity for Li, serving as lithiophilic sites on the rGO surface to synergistically induce homogeneous Li nucleation of Li on the rGO surface. At the same time, BSF molecules contribute LiF to the SEI layer, which facilitates Li surface passivation (Fig. 1C). As a result, high-efficiency (99.2%) Li deposition was achieved at a Li deposition amount of 6.0 mAh cm⁻² and a current density of 6.0 mA cm⁻²; the barrier to Li nucleation was markedly reduced, as evidenced by the low nucleation overpotentials at high-current density (6.0 mA cm⁻²) or at a low temperature (−10 °C). A 400-cycle life with a capacity retention of 83.6% was achieved for a Li|LiCoO₂ (LCO) cell in a conventional carbonate electrolyte. Moreover, with the organic molecule-tuned interface, the Li|LCO cell can be stably cycled at a low operating temperature (−10 °C). This approach was applied to Na and Zn metal anodes as well.Open in a separate windowFig. 1.Illustration of a stable interface for Li deposition using a labile organic molecule, benzenesulfonyl fluoride (BSF). (A) Covalently bonded BSF on the rGO aerogel surface. (B) In situ generation of a lithiophilic conjugated anion (benzenesulfonate) and LiF on the surface during Li deposition. (C) Li nucleation preferentially occurs at the conjugated anion sites owing to the strong Li binding affinity, which leads to uniform Li deposition. In addition, the LiF that is formed is in the SEI layer and passivates the Li surface.     

From the Cover: Historic Yangtze flooding of 2020 tied to extreme Indian Ocean conditions

Heavy monsoon rainfall ravaged a large swath of East Asia in summer 2020. Severe flooding of the Yangtze River displaced millions of residents in the midst of a historic public health crisis. This extreme rainy season was not anticipated from El Niño conditions. Using observations and model experiments, we show that the record strong Indian Ocean Dipole event in 2019 is an important contributor to the extreme Yangtze flooding of 2020. This Indian Ocean mode and a weak El Niño in the Pacific excite downwelling oceanic Rossby waves that propagate slowly westward south of the equator. At a mooring in the Southwest Indian Ocean, the thermocline deepens by a record 70 m in late 2019. The deepened thermocline helps sustain the Indian Ocean warming through the 2020 summer. The Indian Ocean warming forces an anomalous anticyclone in the lower troposphere over the Indo-Northwest Pacific region and intensifies the upper-level westerly jet over East Asia, leading to heavy summer rainfall in the Yangtze Basin. These coupled ocean-atmosphere processes beyond the equatorial Pacific provide predictability. Indeed, dynamic models initialized with observed ocean state predicted the heavy summer rainfall in the Yangtze Basin as early as April 2020.

Summer is the rainy season for East Asia. A northeastward-slanted rain band—called Mei-yu in China and Baiu in Japan—extends from the Yangtze River valley of China to the east of Japan during early summer (early June to mid-July). The Yangtze is the longest river of Asia, flowing from the eastern Tibetan Plateau and exiting into the ocean in Shanghai. Approximately one-third of the population of China live in the river basin. The Mei-yu rain band displays marked interannual variability with great socioeconomic impacts on the densely populated region, including agriculture production, water availability, food security, and economies (1–5).During June through July 2020, the Mei-yu rain band intensified markedly, with rainfall exceeding the 1981 to 2010 mean of ∼300 mm by ∼300 mm over the Yangtze River valley (Fig. 1A). This corresponds to an excess of up to 4 SDs (Fig. 1B). By 12 July 2020, the Yangtze floods caused 141 deaths, 28,000 homes were flattened, and 3.53 million hectares of crops were affected, with the direct economic loss at 82.23 billion yuan (11.76 billion US dollars) (6). South of the Mei-yu rain band, negative rainfall anomalies (−60 mm/month) extended over a broad region from the Bay of Bengal to tropical Northwest Pacific (Fig. 1A). This meridional dipole of rainfall anomalies is known as the recurrent Pacific–Japan pattern (7).Open in a separate windowFig. 1.Atmospheric dynamics of the Yangtze flooding of 2020. June through July averaged anomalies of (A) rainfall (shading, mm/month), SLP (contours at ±0.3, ±0.6, ±1.2, and ±1.8 hPa), and 850 hPa wind (vector, displayed with speed > 0.3 m/s); (C) column-integrated moisture transport (vector, displayed with magnitude > 15 kg ⋅ m⁻¹ ⋅ s⁻¹) and 500 hPa omega (shading, Pa/s, and negative values for ascent motions); and (D) 500 hPa horizontal temperature advection (shading, K/s) and wind (vector, displayed with speed > 0.5 m/s). Blue solid curves denote the Yangtze and Yellow Rivers. Black dashed curves (2,000 m isoline of topography) denote the Tibetan Plateau and surrounding mountains. SLP anomalies over and north of Tibetan Plateau are masked out for clarity. (B) June through July averaged rainfall anomalies (mm/month) over the Yangtze River Valley (26° to 33°N, 105° to 122°E) during 1979 to 2020, with one SD of 35 mm/month. Major El Niño events are marked.In June through July 2020, an anomalous anticyclone with depressed rainfall dominates the lower troposphere over the tropical and subtropical Northwest Pacific through the South China Sea (Fig. 1A). The easterly wind anomalies on the south flank of the anomalous anticyclone extend into the North Indian Ocean, while the anomalous southwesterlies on the northwest flank transport water vapor from the south to feed the enhanced Mei-yu rainband (Fig. 1C). In the mid-troposphere, the westerlies intensify over midlatitude East Asia, and the anomalous mid-tropospheric warm advection from Tibet (Fig. 1D) adiabatically induce upward motions (Fig. 1C) to enhance Mei-yu rainfall. The resultant anomalous diabatic heating reinforces the anomalous vertical motion, forming a positive feedback (8–12). This is consistent with the empirical relationship known to Chinese forecasters between the 500 hPa geopotential height and the Mei-yu rain band.On the interannual timescale, El Niño-Southern Oscillation (ENSO) has been identified as the dominant forcing of Mei-yu rainfall variability (3–5, 13). Mei-yu rainfall in the Yangtze Basin tends to increase (decrease) in post-El Niño (La Niña) summer. A Northwest Pacific anomalous anticyclone often develops rapidly during an El Niño winter (14), interacting with local sea surface temperature (SST) (15, 16) and modulated by the background annual cycle (17). The anomalous anticyclone cools the tropical Northwest Pacific on the southeastern flank by strengthening the northeast trade winds and surface evaporation. The ocean cooling suppresses atmospheric convection, reinforcing the anomalous anticyclone with a Rossby wave response. El Niño also causes the tropical Indian Ocean to warm. The Indo-western Pacific Ocean capacitor refers to the following interbasin positive feedback in summer between the Indian Ocean warming and the Northwest Pacific anomalous anticyclone. The tropical Indian Ocean warming excites a Matsuno-Gill-type (18, 19) response in tropospheric temperature, with a Kelvin response that penetrates eastward and induces northeasterly surface wind anomalies in the tropical Northwest Pacific. The resultant Ekman divergence suppresses convection and induces the anomalous anticyclone (20). The anomalous anticyclone in turn feeds back to the North Indian Ocean warming by weakening the background southwest monsoon and suppressing surface evaporation (21–23).The above ocean-atmospheric coupling processes work well for major El Niño events and provide predictability for Mei-yu rainfall over East Asia (Fig. 1B). A robust Northwest Pacific anomalous anticyclone developed during the summers of 1998 and 2016, each following a major El Niño. A strong anomalous anticyclone and excessive Mei-yu rainfall were not expected for 2020 summer, however, since in the 2019/20 winter (November to January), the Niño3.4 index was marginal at only 0.5 °C (SI Appendix, Fig. S1) as compared to 2.4 °C and 2.6 °C in 1997/98 and 2015/16 winters, respectively. SST anomalies in the equatorial central Pacific (Niño4) were positive and nearly constant in magnitude during May 2018 to May 2020 (SI Appendix, Fig. S1), but the Northwest Pacific anomalous anticyclone did not develop in 2019 summer. Then what caused the pronounced anomalous anticyclone during the 2020 summer? Was it due to unpredictable atmospheric internal dynamics as in August 2016 (24, 25), or did some predictable SST anomalies play a role?     

A switch to feeding on cycads generates parallel accelerated evolution of toxin tolerance in two clades of Eumaeus caterpillars (Lepidoptera: Lycaenidae)

We assembled a complete reference genome of Eumaeus atala, an aposematic cycad-eating hairstreak butterfly that suffered near extinction in the United States in the last century. Based on an analysis of genomic sequences of Eumaeus and 19 representative genera, the closest relatives of Eumaeus are Theorema and Mithras. We report natural history information for Eumaeus, Theorema, and Mithras. Using genomic sequences for each species of Eumaeus, Theorema, and Mithras (and three outgroups), we trace the evolution of cycad feeding, coloration, gregarious behavior, and other traits. The switch to feeding on cycads and to conspicuous coloration was accompanied by little genomic change. Soon after its origin, Eumaeus split into two fast evolving lineages, instead of forming a clump of close relatives in the phylogenetic tree. Significant overlap of the fast evolving proteins in both clades indicates parallel evolution. The functions of the fast evolving proteins suggest that the caterpillars developed tolerance to cycad toxins with a range of mechanisms including autophagy of damaged cells, removal of cell debris by macrophages, and more active cell proliferation.

The genus Eumaeus Hübner (Lycaenidae, Theclinae) arguably contains the most aposematically colored caterpillars and butterflies among the ∼4,000 Lycaenidae in the world (1–6). The brilliant red and gold gregarious caterpillars (Fig. 1) sequester cycasin from the leaves of their cycad food plants (Zamiaceae), which deters predators (3–9). Other secondary metabolites in cycads (e.g., 10‒11) may also deter predators. Eumaeus adults have a bright orange-red abdomen and an orange-red hindwing spot (except for one species) (Fig. 2). Blue and green iridescent markings are especially conspicuous on a black ground color. Eumaeus adults are among the largest lycaenids and have more rounded wings and a slower, more gliding flight than most Theclinae (1). Cycads are among the most primitive extant seed-plants (9), and the “plethora of aposematic attributes suggests a very ancient association between Eumaeus and the cycad host plants” (3).Open in a separate windowFig. 1.Caterpillars and pupae of Theorema eumenia (Top) and Eumaeus godartii (Bottom) in Costa Rica. Clockwise from Upper Left, second or third instar (length, ∼13 mm), fourth (final) instar (∼20 mm), pupa (∼18 mm), pupa (∼24 mm), fourth (final) instar (∼27 mm), second or third instar (∼20 mm). (Images from authors W.H. and D.H.J.).Open in a separate windowFig. 2.Adult wing uppersides and undersides. Eumaeus childrenae (two Upper Left images), E. atala (two Upper Right images), Theorema eumenia (two Lower Left images), and Mithras nautes (two Lower Right images). Scale bar, 1 cm.Eumaeus has been classified as a separate family (12–14), a genus in the Riodinidae (15‒16), or a monotypic subfamily or tribe of the Lycaenidae (17–20). Alternatively, others called it a typical member of the Neotropical Lycaenidae (21‒22). The evolutionary question behind this discordant taxonomic history is whether Eumaeus is a phylogenetically isolated lineage long associated with cycads (3) or an embedded clade in which a recent food plant shift to cycads resulted in the rapid evolution of aposematism. Recent molecular evidence for a limited number of taxa suggested the latter (23). To answer this question definitively, we analyzed genomic sequences of Eumaeus and its relatives.To trace the evolution of cycad feeding, we report the caterpillar food plants of the genera most closely related to Eumaeus and illustrate their immature stages (Fig. 1 and SI Appendix). This natural history information combined with analyses of genome sequences is the foundation for investigating the subsequent evolutionary impact on the Eumaeus genome of the switch to eating cycads.     

Heading perception depends on time-varying evolution of optic flow

There is considerable support for the hypothesis that perception of heading in the presence of rotation is mediated by instantaneous optic flow. This hypothesis, however, has never been tested. We introduce a method, termed “nonvarying phase motion,” for generating a stimulus that conveys a single instantaneous optic flow field, even though the stimulus is presented for an extended period of time. In this experiment, observers viewed stimulus videos and performed a forced-choice heading discrimination task. For nonvarying phase motion, observers made large errors in heading judgments. This suggests that instantaneous optic flow is insufficient for heading perception in the presence of rotation. These errors were mostly eliminated when the velocity of phase motion was varied over time to convey the evolving sequence of optic flow fields corresponding to a particular heading. This demonstrates that heading perception in the presence of rotation relies on the time-varying evolution of optic flow. We hypothesize that the visual system accurately computes heading, despite rotation, based on optic acceleration, the temporal derivative of optic flow.

James Gibson first remarked that the instantaneous motion of points on the retina (Fig. 1A) can be formally described as a two-dimensional (2D) field of velocity vectors called the “optic flow field” (or “optic flow”) (1). Such optic flow, caused by an observer’s movement relative to the environment, conveys information about self-motion and the structure of the visual scene (1–15). When an observer translates in a given direction along a straight path, the optic flow field radiates from a point in the image with zero velocity, or singularity, called the focus of expansion (Fig. 1B). It is well known that under such conditions, one can accurately estimate one’s “heading” (i.e., instantaneous direction of translation in retinocentric coordinates) by simply locating the focus of expansion (SI Appendix). However, if there is angular rotation in addition to translation (by moving along a curved path or by a head or eye movement), the singularity in the optic flow field will be displaced such that it no longer corresponds to the true heading (Fig. 1 C and D). In this case, if one estimates heading by locating the singularity, the estimate will be biased away from the true heading. This is known as the rotation problem (14).Open in a separate windowFig. 1.Projective geometry, the rotation problem, time-varying optic flow, and the optic acceleration hypothesis. (A) Viewer-centered coordinate frame and perspective projection. Because of motion between the viewpoint and the scene, a 3D surface point traverses a path in 3D space. Under perspective projection, the 3D path of this point projects onto a 2D path in the image plane (retina), the temporal derivative of which is called image velocity. The 2D velocities associated with all visible points define a dense 2D vector field called the optic flow field. (B–D) Illustration of the rotation problem. (B) Optic flow for pure translation (1.5-m/s translation speed, 0° heading, i.e., heading in the direction of gaze). Optic flow singularity (red circle) corresponds to heading (purple circle). (C) Pure rotation, for illustrative purposes only and not corresponding to any experimental condition (2°/s rightward rotation). (D) Translation + rotation (1.5 m/s translation speed, 0° heading, 2°/s rightward rotation). Optic flow singularity (red circle) is displaced away from heading (purple circle). (E) Three frames from a video depicting movement along a circular path with the line-of-sight initially perpendicular to a single fronto-parallel plane composed of black dots. (F) Time-varying evolution of optic flow. The first optic flow field reflects image motion between the first and second frames of the video. The second optic flow field reflects image motion between the second and third frames of the video. For this special case (circular path), the optic flow field evolves (and the optic flow singularity drifts) only due to the changing depth of the environment relative to the viewpoint. (G) Illustration of the optic acceleration hypothesis. Optic acceleration is the derivative of optic flow over time (here, approximated as the difference between the second and first optic flow fields). The singularity of the optic acceleration field corresponds to the heading direction. Acceleration vectors autoscaled for visibility.Computer vision researchers and vision scientists have developed a variety of algorithms that accurately and precisely extract observer translation and rotation from optic flow, thereby solving the rotation problem. Nearly all of these rely on instantaneous optic flow (i.e., a single optic flow field) (4, 9, 16–25) with few exceptions (26–29). However, it is unknown whether these algorithms are commensurate with the neural computations underlying heading perception.The consensus of opinion in the experimental literature is that human observers can estimate heading (30, 31) from instantaneous optic flow, in the absence of additional information (5, 10, 15, 32–34). Even so, there are reports of systematic biases in heading perception (11); the visual consequences of rotation (eye, head, and body) can bias heading judgments (10, 15, 35–37), with the amount of bias typically proportional to the magnitude of rotation. Other visual factors, such as stereo cues (38, 39), depth structure (8, 10, 40–43), and field of view (FOV) (33, 42–44) can modulate the strength of these biases. Errors in heading judgments have been reported to be greater when eye (35–37, 45, 46) or head movements (37) are simulated versus when they are real, which has been taken to mean that observers require extraretinal information, although there is also evidence to the contrary (10, 15, 33, 40, 41, 44, 47–50). Regardless, to date no one has tested whether heading perception (even with these biases) is based on instantaneous optic flow or on the information available in how the optic flow field evolves over time. Some have suggested that heading estimates rely on information accumulated over time (32, 44, 51), but no one has investigated the role of time-varying optic flow without confounding it with stimulus duration (i.e., the duration of evidence accumulation).In this study, we employed an application of an image processing technique that ensured that only a single optic flow field was available to observers, even though the stimulus was presented for an extended period of time. We called this condition “nonvarying phase motion” or “nonvarying”: The phases of two component gratings comprising each stationary stimulus patch shifted over time at a constant rate, causing a percept of motion in the absence of veridical movement (52). Phase motion also eliminated other cues that may otherwise have been used for heading judgments, including image point trajectories (15, 32) and their spatial compositions (i.e., looming) (53, 54). For nonvarying phase motion, observers exhibited large biases in heading judgments in the presence of rotation. A second condition, “time-varying phase motion,” or “time-varying,” included acceleration by varying the velocity of phase motion over time to match the evolution of a sequence of optic flow fields. Doing so allowed observers to compensate for the confounding effect of rotation on optic flow, making heading perception nearly veridical. This demonstrates that heading perception in the presence of rotation relies on the time-varying evolution of optic flow.     

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid–peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

The rich, highly efficient, and specific biochemistry in living cells is orchestrated by molecules belonging to a small number of families, primarily nucleic acids, proteins, fatty acids, and sugars. Many fundamental cellular and viral functions, including replication and translation, are facilitated by synergistic activity in complexes of these molecules, very often involving nucleic acids (DNA, RNA, or their constituent nucleotides/nucleobases) and proteins (or peptides/amino acids). Among the most important examples of such complexes are the nucleosome (which comprises DNA packaging units in eukaryotes), the ribosome (which translates RNA sequences into proteins), and amino acid–charged transfer RNA (t-RNA) conjugates (which are exploited during translation) (1–4). In order to harness such synergistic activity in synthetic materials, several groups (including the authors) have recently studied the coassembly of nucleic acids with (often) positively charged peptides or the self-assembly of premade nucleic-acid–peptide (NA–pep) chimeras (5–12). It is expected that such assemblies could produce new materials for various applications, such as autocatalysis, electron transfer, tissue scaffolding, and (drug) delivery (13–18). Intriguingly, the NA–pep assemblies combine “digital” molecular information for the hybridization of nucleic acids with “analog” instructions that affect peptide aggregation and, as such, are expected to show superior behavior in comparison with related nucleic-acid–only or peptide-only assemblies (19–21).We now propose that alongside the development of NA–pep conjugate assemblies for new materials, an analysis of the formation of chimeras within complex mixtures, and particularly the selection of specific sequences through replication processes, will offer insight into their emergence in the early chemical evolution. Indeed, several studies have indicated that evolution in prebiotic environments, toward the origin of life, must have involved cooperative interactions among diverse classes of molecules (22–25). Other studies, including the seminal works of Eigen (26) and Kauffman (27), have revealed the possible emergence of synergistic activity in prebiotic autocatalytic networks and, as a consequence, phase transitions toward beneficial cooperative and/or selective behavior (28, 29). Importantly, while it has been shown that highly complex functions emerge by wiring together multiple pathways—driving, for example, elaborate feedback loops—our studies, as well as others, have indicated that multiple unique dynamic features (30–36), including chemical computation (37), can be developed in relatively small networks.Despite strong evidence for prebiotic pathways that yield nucleobases and peptides—suggesting that molecules of both families were indeed present in early chemical evolution—prebiotic chemistry research has focused largely on studying each class of molecule separately (38). This approach has led to incomplete discussions on the “RNA World,” the “Peptide World,” or the “Metabolism-First World,” with minimal overlap between the different domains. In particular, studies on replicating molecules and replication networks have investigated discrete systems affected only by a single class of molecule—whether nucleic acids, peptides, lipid amphiphiles, or small organic molecules (39–41). Herein, we propose to blur the limits between families of replicators by combining nucleic-acid molecular genetic information with peptide-based assembly “phenotypes.” To this end, we sought to reveal the self-organization and selection processes taking place in mixtures containing short complementary nucleopeptide conjugates (designated R^AA and R^TT, Fig. 1). Experimental and simulation analyses of the template-directed replication processes within these networks clearly demonstrate that product formation is governed both by nucleobase hybridization and by the formation of unique supramolecular architectures by each of the nucleopeptide conjugates. Unequal assembly-dependent replication capacity induces selectivity toward the formation of R^AA. By studying the system in a flow reactor, namely, at far-from-equilibrium conditions, we show how this selectivity can be influenced and maximized—through changes in the physical (flow) and chemical (template and inhibition) conditions—to the point of almost complete extinction of R^TT, the weaker replicator. We suggest that, prior to the origin of life, processes such as these may have led to the emergence of simple functional NA–pep assemblies (42), which could facilitate further structural development into the current cellular NA–pep assemblies.Open in a separate windowFig. 1.Nucleopeptide replication networks. (A and B) NCL reactions forming the R^AA and R^TT conjugates from their respective electrophile and nucleophile precursors and time-dependent formation of these conjugates in template-free (bg), autocatalytic (ac), and cross-catalytic (cc) reactions. Note that at pH 7.4, the Glu side chain carboxylic acids would be in their deprotonated anionic form. Reactions were carried out with 100 µM E^AA or E^TT and 100 µM N, either in the absence of a template (bg) or when seeded with the designated amount of template at initiation (ac/cc). Insets show the early stages of the background reactions, highlighting the lag phase typical of product formation through autocatalysis (Top insets) and the rate enhancement (percent) in cross-catalytic reactions seeded with 60 or 30 µM template or in autocatalytic reactions seeded with 60 µM template (Bottom insets). (C and D) A time-dependent analysis of the replicator-assisted product formation of the conjugates R^AA (green) and R^TT (red) in network reactions initiated with E^AA (50 µM), E^TT (50 µM), and N (100 µM) and seeded with 20 (dashed lines) or 60 μM (solid lines) R^TT (C) or R^AA (D). HPLC chromatograms (Top) indicate the increase in R^AA and R^TT product over time in representative reactions seeded with 60 μM R^TT (C) or 60 μM R^AA (D); note that R^TT and R^AA peaks have initial intensity due to seeding (in C and D, respectively), and the * symbols denote minor (≥15%) branched product peaks, removed for clarity (see also SI Appendix, Fig. S20). All reactions were carried out in duplicate, in Hepes buffer (pH 7.4), in the presence of TCEP as a reducing agent (5 mM) and with ABA (30 μM) as the internal standard. Data were acquired by HPLC analysis of aliquots collected at the designated times (SI Appendix, Figs. S17–S20).     

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

Evolution is driven by a complex interplay of deterministic and stochastic forces whose relative importance is a matter of debate (1). Being largely a historical process, we have limited ability to experimentally test for the predictability of evolution in its full complexity (i.e., in natural environments) (2). Distinct lineages that independently adapted to similar conditions by similar phenotype (termed parallel,” considered synonymous to “convergent” here) can provide invaluable insights into the issue (3, 4). An improved understanding of the probability of parallel evolution in nature may inform on constraints on evolutionary change and provide insights relevant for predicting the evolution of pathogens (5–7), pests (8, 9), or species in human-polluted environments (10, 11). Although the past few decades have seen an increasing body of work supporting the parallel emergence of traits by the same genes and even alleles, we know surprisingly little about what makes parallel evolution more likely and, by extension, what factors underlie evolutionary predictability (1, 12).A wealth of literature describes the probability of “genetic” parallelism, showing why certain genes are involved in parallel adaptation more often than others (13). There is theoretical and empirical evidence for the effect of pleiotropic constraints, availability of beneficial mutations or position in the regulatory network all having an impact on the degree of parallelism at the level of a single locus (3, 13–18). In contrast, we know little about causes underlying “genomic” parallelism (i.e., what fraction of the genome is reused in adaptation and why). Individual case studies demonstrate large variation in genomic parallelism, ranging from absence of any parallelism (19), similarity in functional pathways but not genes (20, 21), and reuse of a limited number of genes (22–24) to abundant parallelism at both gene and functional levels (25, 26). Yet, there is little consensus about what determines variation in the degree of gene reuse (fraction of genes that repeatedly emerge as selection candidates) across investigated systems (1).Divergence (the term used here to consistently describe both intra- and interspecific genetic differentiation) between the compared instances of parallelism appears as a potential driver of the variation in gene reuse (14, 27, 28). Phenotype-oriented meta-analyses suggest that both phenotypic convergence (28) and genetic parallelism underlying phenotypic traits (14) decrease with increasing time to the common ancestor. Although a similar targeted multiscale comparison is lacking at the genomic level, our brief review of published studies (29 cases, Dataset S1) suggests that also gene reuse tends to scale with divergence (Fig. 1A and SI Appendix, Fig. S1). Moreover, allele reuse (repeated sweep of the same haplotype that is shared among populations either via gene flow or from standing genetic variation) frequently underlies parallel adaptation between closely related lineages (29–32), while parallelism from independent de novo mutations at the same locus dominates between distantly related taxa (13). Similarly, previous studies reported a decreasing probability of hemiplasy (apparent convergence resulting from gene tree discordance) with divergence in phylogeny-based studies (33, 34). This suggests that the degree of allele reuse may be the primary factor underlying the hypothesized divergence-dependency of parallel genome evolution, possibly reflecting either weak hybridization barriers, widespread ancestral polymorphism between closely related lineages (35), or ecological reasons (lower niche differentiation and geographical proximity) (36, 37). However, the generally restricted focus of individual studies of genomic parallelism on a single level of divergence does not lend itself to a unified comparison across divergence scales. Although different ages of compared lineages affect a variety of evolutionary–ecological processes such as diversification rates, community structure, or niche conservatism (37), the hypothesis that genomic parallelism scales with divergence has not yet been systematically tested, and the underlying evolutionary processes remain poorly understood.Open in a separate windowFig. 1.Hypotheses regarding relationships between genomic parallelism and divergence and the Arabidopsis system used to address these hypotheses. (A) Based on our literature review, we propose that genetically closer lineages adapt to a similar challenge more frequently by gene reuse, sampling suitable variants from the shared pool (allele reuse), which makes their adaptive evolution more predictable. Color ramp symbolizes rising divergence between the lineages (∼0.02 to 18 Mya in this study); the symbols denote different divergence levels tested here using resequenced genomes of 22 Arabidopsis populations (circles) and meta-analysis of candidates in Brassicaceae (asterisks). (B) Spatial arrangement of lineages of varying divergence (neutral F_ST; bins only aid visualization; all tests were performed on a continuous scale) encompassing parallel alpine colonization within the two Arabidopsis outcrossers from central Europe: A. arenosa (diploid: aVT; autotetraploid: aNT, aZT, aRD, and aFG) and A. halleri (diploid: hNT and hFG). Note that only two of the ten between-species pairs (dark green) are shown to aid visibility. The color scale corresponds to the left part of the color ramp used in A. (C) Photos of representative alpine and foothill habitat. (D) Representative phenotypes of originally foothill and alpine populations grown in common garden demonstrating phenotypic convergence. Scale bar corresponds to 4 cm. (E) Morphological differentiation among 223 A. arenosa individuals originating from foothill (black) and alpine (gray) populations from four regions after two generations in a common garden. Principal component analysis was run using 16 morphological traits taken from ref. 45.Here, we aimed to test this hypothesis and investigate whether allele reuse is a major factor underlying the relationship. We analyzed replicated instances of adaptation to a challenging alpine environment, spanning a range of divergence from populations to tribes within the plant family Brassicaceae (38–43) (Fig. 1A). First, we took advantage of a unique naturally multireplicated setup in the plant model genus Arabidopsis that was so far neglected from a genomic perspective (Fig. 1B). Two predominantly foothill-dwelling Arabidopsis outcrossers (A. arenosa, A. halleri) exhibit scattered, morphologically distinct alpine occurrences at rocky outcrops above the timberline (Fig. 1C). These alpine forms are separated from the widespread foothill population by a distribution gap spanning at least 500 m of elevation. Previous genetic and phenotypic investigations and follow-up analyses presented here showed that the scattered alpine forms of both species represent independent alpine colonization in each mountain range, followed by parallel phenotypic differentiation (Fig. 1 D and E) (44–46). Thus, we sequenced genomes from seven alpine and adjacent foothill population pairs, covering all European lineages encompassing the alpine ecotype. We discovered a suite of 151 genes from multiple functional pathways relevant to alpine stress that were repeatedly differentiated between foothill and alpine populations. This points toward a polygenic, multifactorial basis of parallel alpine adaptation.We took advantage of this set of well-defined parallel selection candidates and tested whether the degree of gene reuse decreases with increasing divergence between the compared lineages (Fig. 1A). By extending our analysis to five additional alpine Brassicaceae species, we further tested whether there are limits to gene reuse above the species level. Finally, we inquired about possible underlying evolutionary processes by estimating the extent of allele reuse using a designated modeling approach. Overall, our empirical analysis provides a perspective to the ongoing discussion about the variability in the reported magnitude of parallel genome evolution and identifies allele reuse as an important evolutionary process shaping the extent of genomic parallelism between populations, species, and genera.     

Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

As anthropogenic activities rapidly transform the environment, a fundamental question is whether wild populations have the capacity to adapt and evolve fast enough in response (1–3). Phenotypic change can result from phenotypic plasticity, but emerging examples of genomic change over only a few generations have made clear that rapid evolution is also possible (4–6). In the literature, one of the most dramatic and widely cited cases involves the declining age and size at maturation of Atlantic cod (Gadus morhua) following several generations of high fishing pressure (3, 7–10). Fisheries produce some of the fastest rates of phenotypic change ever observed in wild populations (2, 11), but the extent to which fisheries-induced evolution has occurred in the wild and the degree to which it is reversible remain strongly debated (12).The hypothesis that evolution underlies these phenotypic changes is supported by a range of observations. For example, theory on the selective nature of many fisheries reveals that higher rates of harvesting will—with only a few exceptions—favor earlier sexual maturation, greater investment in reproduction, and slower growth (13). In addition, experiments in the laboratory that selectively remove large or small individuals from a population reveal rapid evolution of body size and maturation time in only a few generations, as well as substantial impacts on fishery yields (14–16). Fisheries-induced evolution experiments in the laboratory also reveal selective sweeps through dramatic shifts in allele frequencies, loss of genetic diversity, and increases in linkage disequilibrium at specific locations in the genome (15, 17, 18).However, translating these findings to wild populations has been substantially more difficult. One concern is that phenotypic plasticity, gene flow, or spatial shifts in populations can also explain the substantial phenotypic and limited genotypic changes reported from the wild to date (10, 13, 19–23). The magnitude and rate of fisheries-induced evolution may also be quite small in the wild (19). While theory provides strong evidence that fishing can be a potent driver of evolutionary changes, a clear empirical demonstration of fisheries-induced evolution would require evidence that the observed change is genetic (13). Whether and to what extent the widespread genomic reorganization observed in experiments also occurs in wild-harvested populations therefore remain unknown.Genomic analyses of temporal samples before and after selective events have provided key opportunities to test for rapid adaptive evolution from standing genetic variation in wild populations by identifying unusually strong shifts in allele frequencies over time (4, 5). In addition, the history of genomic research with Atlantic cod (24, 25) provides a unique opportunity to test for genomic signatures of fisheries-induced evolution in particular. Archival samples collected by fisheries scientists decades or even centuries ago represent a valuable source of historical genomic material that can provide rare insight into the genetic patterns of the past (26). Here, we obtained whole-genome sequence data from well-preserved archives of Atlantic cod scales and otoliths (ear bones) that were originally collected from two populations on either side of the Atlantic Ocean: the northeast Arctic population sampled near Lofoten, Norway in 1907 and the Canadian northern cod population sampled near Twillingate, Newfoundland in 1940 (Fig. 1A and SI Appendix, Table S1). The Canadian northern population collapsed from overfishing in the early 1990s, while the northeast Arctic population experienced high fishing rates but smaller declines in biomass (10, 27, 28). Both populations have shown marked reductions in age at maturation, though with slight increases in maturation age in northeast Arctic cod after 2005 (Fig. 1B). We compared these historical genomes with modern data from the same locations (Fig. 1A and SI Appendix, Table S2). In total, we analyzed 113 individual genomes (Methods) from these two unique populations that had independently experienced intensive fishing during the last century (7, 10). We found a marked lack of large genomic changes or selective sweeps through time, suggesting instead that phenotypic plasticity or, potentially, highly polygenic evolution can explain the observed changes in phenotype.Open in a separate windowFig. 1.Spatiotemporal population structure based on genome-wide data in Atlantic cod. (A) In total, 113 modern and historical specimens were analyzed from northern cod collected in Newfoundland, Canada (1940, yellow; 2013, dark yellow) and from northeast Arctic cod collected in the Lofoten archipelago, Norway (1907, orange; modern: 2011, red; 2014, dark red). (B) Age at 50% maturity over time in each population. (C) PCA as implemented in PCAngsd. Velicier’s minimum average partial (MAP) test identified a single significant PC and only one PC is shown. Individuals are colored according to A. (D) Model-based ADMIXTURE ancestry components for historical (1907, 1940) and modern (2013, 2014) populations (k = 2; NGSadmix). Each individual is represented by a column colored to show the proportion of each ancestry component for Canada (dark yellow) and Norway (orange). Population differentiation based on pairwise weighted F_ST is also shown. (E) The correlation between the allele frequencies in historical and modern populations. Colors reflect the relative density of points, from darker (more density) to lighter (less density). R², coefficient of correlation.     

A modular toolkit to inhibit proline-rich motif–mediated protein–protein interactions

Small-molecule competitors of protein–protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principle, we developed a small, selective, peptidomimetic inhibitor of Ena/VASP EVH1 domain interactions. Highly invasive MDA MB 231 breast-cancer cells treated with this ligand showed displacement of VASP from focal adhesions, as well as from the front of lamellipodia, and strongly reduced cell invasion. General applicability of our strategy is illustrated by the design of an ErbB4-derived ligand containing two ProM-1 fragments, targeting the yes-associated protein 1 (YAP1)-WW domain with a fivefold higher affinity.Proline-rich segments (PRSs) belong to the most abundant sequence motifs of the proteome (1), interacting frequently with PRS-recognizing domains (PRDs), such as EVH1, SH3, GYF, and WW. Although exhibiting different tertiary structures, PRDs expose clusters of aromatic residues, forming a shallow, corrugated binding groove with a hydrogen bond-donating residue (W, Y) in the central position. In the bound state, PRSs often show a conformation closely related to the ideal left-handed polyproline II (PPII) helix characterized by backbone angles of Φ = −78° and Ψ = +146° (2). As a consequence of the axial symmetry of PPII helices, two different types of consensus motifs occur: one containing PxxP specifically recognized by the EVH1 and SH3 domains, the other comprising xPPx, typical for motifs binding at WW and GYF domains. The conserved prolines represent the core of the consensus motifs and interact intimately with the exposed aromatic side chains. They cannot be replaced by any other natural amino acid without complete loss of affinity (2, 3). On the other hand, the core motif alone binds only very weakly to its PRD. Further interactions of flanking residues located outside the core motif contribute substantially to both affinity and specificity. Incorporation of nonnatural amino acids in place of such specificity-determining residues is therefore often beneficial for binding (4–9). However, peptide ligands display a number of disadvantages when used as competitors, among them metabolic instability and often low cell permeability. Cell-permeable small molecules that grant the ability to modulate the function of PRDs are still not available.Here, we present a modular concept for the systematic development of such low-molecular weight compounds. It is based on molecular building blocks that can replace the conserved prolines within the core motif without any loss of affinity. Combinations of such building blocks allow complete replacement of the proline-rich core motifs. They may be supplemented with organic scaffolds addressing the flanking epitopes to obtain peptidomimetic inhibitors of PRDs, highly desirable for functional analysis of PRS-mediated protein–protein interactions.As proof of concept, we developed a peptidomimetic inhibitor targeting the enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) family Ena/VASP homology 1 (EVH1) domains. This protein family is involved in modulation of the actin cytoskeleton, a complex and highly regulated process, which is the driving force of directed cell migration (10, 11) and plays important roles in disease-relevant processes like tumor metastasis (12, 13). The Ena/VASP family proteins [i.e., VASP, enabled homolog (EnaH), and Ena-VASP–like (EVL) (14–16)] are notably localized at focal adhesions and lamellipodia. Single Ena/VASP protein deletions are mostly compensated for the other members of the family (17); however, triple knock-out mice are embryonic lethal (18, 19). The proteins comprise EVH1 and Ena/VASP homology 2 (EVH2) domains, separated by a proline-rich region. Although EVH2 binds to the barbed ends of actin filaments, EVH1 interacts with proteins, like zyxin or lamellipodin (Lpd also called RAPH1), that contain the class 1 EVH1 consensus motif [FYWL]P.ϕP (ϕ is an aliphatic amino acid) (2, 20–22). Using our peptidomimetic inhibitor, we show that inhibition of the Ena/VASP family EVH1 domains strongly influences both cellular localization of VASP as well as cell migration.     

From the Cover: Neurophysiological coordination of duet singing

Coordination of behavior for cooperative performances often relies on linkages mediated by sensory cues exchanged between participants. How neurophysiological responses to sensory information affect motor programs to coordinate behavior between individuals is not known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use acoustic feedback to coordinate extraordinary duet performances in which females and males rapidly take turns singing. We made simultaneous neurophysiological recordings in a song control area “HVC” in pairs of singing wrens at a field site in Ecuador. HVC is a premotor area that integrates auditory feedback and is necessary for song production. We found that spiking activity of HVC neurons in each sex increased for production of its own syllables. In contrast, hearing sensory feedback produced by the bird’s partner decreased HVC activity during duet singing, potentially coordinating HVC premotor activity in each bird through inhibition. When birds sang alone, HVC neurons in females but not males were inhibited by hearing the partner bird. When birds were anesthetized with urethane, which antagonizes GABAergic (γ-aminobutyric acid) transmission, HVC neurons were excited rather than inhibited, suggesting a role for GABA in the coordination of duet singing. These data suggest that HVC integrates information across partners during duets and that rapid turn taking may be mediated, in part, by inhibition.

Animals routinely rely on sensory feedback for the control of their own behavior. In cooperative performances, such sensory feedback can include cues produced by other participants (1–8). For example, in interactive vocal communication, including human speech, individuals take turns vocalizing. This “turn taking” is a consequence of each participant responding to auditory cues from a partner (4–6, 9, 10). The role of such “heterogenous” (other-generated) feedback in the control of vocal turn taking and other cooperative performances is largely unknown.Plain-tailed wrens (Pheugopedius euophrys) are neotropical songbirds that cooperate to produce extraordinary duet performances but also sing by themselves (Fig. 1A) (4, 10, 11). Singing in plain-tailed wrens is performed by both females and males and used for territorial defense and other functions, including mate guarding and attraction (1, 11–16). During duets, female and male plain-tailed wrens take turns, alternating syllables at a rate of between 2 and 5 Hz (Fig. 1A) (4, 11).Open in a separate windowFig. 1.Neural control of solo and duet singing in plain-tailed wrens. (A) Spectrogram of a singing bout that included male solo syllables (blue line, top) followed by a duet. Solo syllables for both sexes (only male solo syllables are shown here) are sung at lower amplitudes than syllables produced in duets. Note that the smeared appearance of wren syllables in spectrograms reflects the acoustic structure of plain-tailed wren singing. (B and C) Each bird has a motor system that is used to produce song and sensory systems that mediate feedback. (B) During solo singing, the bird hears its own song, which is known as autogenous feedback (orange). (C) During duet singing, each bird hears both its own singing and the singing of its partner, known as heterogenous feedback (green). The key difference between solo and duet singing is heterogenous feedback that couples the neural systems of the two birds. This coupling results in changes in syllable amplitude and timing in both birds.There is a categorical difference between solo and duet singing. In solo singing, the singing bird receives only autogenous (hearing its own vocalization) feedback (Fig. 1B). The partner may hear the solo song if it is nearby, a heterogenous (other-generated) cue. In duet singing, birds receive both heterogenous and autogenous feedback as they alternate syllable production (Fig. 1C). Participants use heterogenous feedback during duet singing for precise timing of syllable production (4, 11). For example, when a male temporarily stops participating in a duet, the duration of intersyllable intervals between female syllables increases (4), showing an effect of heterogenous feedback on the timing of syllable production.How does the brain of each wren integrate heterogenous acoustic cues to coordinate the precise timing of syllable production between individuals during duet performances? To address this question, we examined neurophysiological activity in HVC, a nucleus in the nidopallium [an analogue of mammalian cortex (17, 18)]. HVC is necessary for song learning, production, and timing in species of songbirds that do not perform duets (19–24). Neurons in HVC are active during singing and respond to playback of the bird’s own learned song (25–27). In addition, recent work has shown that HVC is also involved in vocal turn taking (19).To examine the role of heterogenous feedback in the control of duet performances, we compared neurophysiological activity in HVC when female or male wrens sang solo syllables with syllables sung during duets. Neurophysiological recordings were made in awake and anesthetized pairs of wrens at the Yanayacu Biological Station and Center for Creative Studies on the slopes of the Antisana volcano in Ecuador. We found that heterogenous cues inhibited HVC activity during duet performances in both females and males, but inhibition was only observed in females during solo singing.     

Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters

ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K⁺ channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease.

ATP binding cassette (ABC) proteins are a large family of membrane proteins found in all kingdoms of life (1, 2). ABC proteins have a core structure composed of two transmembrane (TM) domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2) (Fig. 1A and SI Appendix, Fig. S1A) (3–5). Through ATP binding and hydrolysis at the NBDs, ABC proteins actively transport solutes across cell membranes, regulate activities of other proteins, or function as channels (1, 2). Thus, ABC proteins are involved in many biological processes, including lipid homeostasis, cellular metal trafficking, and antigen peptide transport. Mutations in human ABC proteins cause diseases such as Tangier disease, adenoleukodystrophy, cystic fibrosis, Dubin–Johnson syndrome, and pseudoxanthoma elasticum (PXE) (1, 2). Furthermore, the export of a wide range of cancer chemotherapeutics, antibiotics, and anti-fungal drugs by ABC transporters confers multidrug resistance to tumor cells, bacteria, and fungal pathogens, respectively (1, 2, 6, 7).Open in a separate windowFig. 1.Ycf1p structure. (A) Ycf1p domain arrangement. TMD, transmembrane domain; L0, L0 linker; NBD, nucleotide binding domain; and R, regulatory (R) region. The Pep4p proteolytic digestion site within the luminal loop 6 of TMD1 is denoted by a pink “*.” Phosphorylation sites in the L0 linker (S251) and R region (S908 and T911) are depicted with a “P” circled in red. (B) Cryo-EM density of Ycf1p with domains colored as in A. (C) Example of the atomic model for individual TM helices in TMD0 and the R region fit into the corresponding map densities. (D) Schematic ribbon diagram of Ycf1p colored as in A and B and with the proteolytic digestion site denoted by a pink “*.”Human ABC proteins are divided into seven subfamilies (A to G) based in part on the sequence of their NBDs and TMDs in the core ABC structure (1, 2). The C-subfamily is the most diverse and includes the cystic fibrosis transmembrane conductance regulator (CFTR), the sulphonylurea receptors that form regulatory subunits in ATP-sensitive K⁺ (K_ATP) channels, and the multidrug resistance proteins (MRPs). In addition to the ABC core, ABCC proteins contain an N-terminal extension that is either composed of an additional TM domain (TMD0) and L0 linker (Fig. 1A, orange and tan, respectively, and SI Appendix, Fig. S1A) or just an L0 tail (5, 8). A TMD0, but not L0 linker, is also found in some ABCB proteins (3, 5). These N-terminal extensions are involved in trafficking, endosomal recycling, protein interactions, and/or regulation of ABC activity (9–18). The existence of disease-causing mutations in TMD0 and the L0 linker of different ABCC proteins (8, 13, 18) indicates that these regions play important roles in protein function when present.High-resolution structural information for TMD0 is available only for the atypical ABCC protein SUR1 (19, 20), which is part of the large hetero-octameric K_ATP channel complex. In contrast, structures of monomeric ABC transporters showed only low-resolution density for TMD0 that was insufficient for building a full atomic model or lacked density for the domain altogether (14, 21–24). The vacuolar ABCC protein yeast cadmium factor 1 (Ycf1p) from Saccharomyces cerevisiae is a close homolog of human MRPs and a model for ABCC proteins that function as monomers. Ycf1p transports glutathione-conjugated heavy metals, such as Cd²⁺, from the cytosol into the vacuole, detoxifying the cell (25, 26). Human MRP1 can rescue Cd²⁺ transport activity in a YCF1 deletion strain (27).Like other ABCC proteins, Ycf1p contains a relatively long and mostly disordered linker that connects NBD1 and TMD2 (25, 28, 29) (Fig. 1A and SI Appendix, Fig. S1A). This linker contains stimulatory phosphorylation sites (25, 28), similar to the phospho-regulatory (R) region in the ABCC protein CFTR (30–32). Ycf1p also contains an inhibitory phosphorylation site in the L0 linker (33). However, how the R region interacts with the ABCC core and how its phosphorylation modulates protein function remain poorly understood for most ABCC proteins. Structural studies of Ycf1p presented here reveal how TMD0 and the R region exert their regulatory functions in MRP-like ABCC proteins.     

A new sea-level record for the Neogene/Quaternary boundary reveals transition to a more stable East Antarctic Ice Sheet

Sea-level rise resulting from the instability of polar continental ice sheets represents a major socioeconomic hazard arising from anthropogenic warming, but the response of the largest component of Earth’s cryosphere, the East Antarctic Ice Sheet (EAIS), to global warming is poorly understood. Here we present a detailed record of North Atlantic deep-ocean temperature, global sea-level, and ice-volume change for ∼2.75 to 2.4 Ma ago, when atmospheric partial pressure of carbon dioxide (pCO₂) ranged from present-day (>400 parts per million volume, ppmv) to preindustrial (<280 ppmv) values. Our data reveal clear glacial–interglacial cycles in global ice volume and sea level largely driven by the growth and decay of ice sheets in the Northern Hemisphere. Yet, sea-level values during Marine Isotope Stage (MIS) 101 (∼2.55 Ma) also signal substantial melting of the EAIS, and peak sea levels during MIS G7 (∼2.75 Ma) and, perhaps, MIS G1 (∼2.63 Ma) are also suggestive of EAIS instability. During the succeeding glacial–interglacial cycles (MIS 100 to 95), sea levels were distinctly lower than before, strongly suggesting a link between greater stability of the EAIS and increased land-ice volumes in the Northern Hemisphere. We propose that lower sea levels driven by ice-sheet growth in the Northern Hemisphere decreased EAIS susceptibility to ocean melting. Our findings have implications for future EAIS vulnerability to a rapidly warming world.

The instability of polar continental ice sheets in a warmer future is an issue of major societal concern (1–5). Based on linear extrapolation of recent sea-level rise (2), mean global sea level could increase by 65 ± 12 cm by 2100 relative to the 2005 baseline, consistent with Intergovernmental Panel on Climate Change projections (1) of a ∼30- to 100-cm increase by 2100. Further, satellite observations (4) document substantial mass loss of both the Greenland Ice Sheet (GIS) and the West Antarctic Ice Sheet (WAIS) over the past decade—the two ice sheets that are most susceptible to global warming because of rapidly rising Arctic air temperatures (1) (GIS) and vulnerability to ocean-atmospheric warming (5, 6) (WAIS). The mass balance of the much larger EAIS and its contribution to ongoing sea-level change, however, remain poorly constrained (1).The role of atmospheric partial pressure of carbon dioxide (pCO₂) as a driver of long-term changes in ice volume and sea level over the Cenozoic Era (past ∼66 My) is widely documented (7–9) and there is compelling evidence (6, 10–12) of East Antarctic Ice Sheet (EAIS) retreat during warm intervals of the Pliocene epoch between ∼5.3 and 3.3 Ma when pCO₂ levels (13, 14) last reached values close to the present day (∼400 parts per million volume [ppmv]; Fig. 1 A and B and see SI Appendix, section S1). However, there is disagreement over EAIS behavior under pCO₂ levels (13) similar to those of preindustrial Quaternary times (<280 ppmv). A compilation of marine geochemical paleo-sea-level and pCO₂ records suggests that the EAIS was stable under these conditions (7). In contrast, while the amplitudes of change are controversial (15) (SI Appendix, section S2), sea-level reconstructions from paleoshorelines (16) and benthic geochemical data (9, 17, 18) (Fig. 2) imply EAIS melting during the Quaternary “super-interglacials” of Marine Isotope Stage (MIS) 11 (∼400 ka) and 31 (∼1.07 Ma) under relatively low pCO₂ conditions. Supporting evidence for EAIS retreat during the most recent “super-interglacial” MIS 11 comes from isotope measurements in mineral deposits recording past changes in subglacial East Antarctic waters (19), as well as records of ice-rafted debris (IRD) and detrital sediment neodymium isotopes from offshore the Wilkes Subglacial Basin (20). The latter records (20) also indicate EAIS retreat during the last interglacial MIS 5e (∼120 ka). Melting of the EAIS as inferred in the late Quaternary was likely driven by ocean–atmosphere warming around Antarctica and grounding-line retreat in response to ice–ocean interactions (19, 20).Open in a separate windowFig. 1.Neogene to Quaternary climate and sea-level evolution. (A) LR04 stack (21) for the past 5 My; arrow indicates the iNHG (∼3.6 to 2.4 Ma) and its culmination (thick-arrowed interval) (22); green line indicates the benthic δ¹⁸O level associated with MIS 101. (B) Atmospheric pCO₂ estimates of refs. 13 (blue) and 23 (purple) for the past 5 My; the late Quaternary glacial–interglacial pCO₂ range (1) is indicated as preindustrial pCO₂ band. Yellow shading in A and B highlights the study interval (∼2.75 to 2.4 Ma). (C and D) Site U1313 benthic δ¹⁸O and Mg/Ca raw data, respectively. (E) Site U1313 deep-sea temperature. (F) Site U1313 δ¹⁸O_sw-based sea level relative to present (black line); blue shading: 95% probability interval from Monte Carlo simulations (2σ); red line: threshold (11.6 msle) above which a smaller-than-present EAIS is signaled (24–26); m = marine part of EAIS, t = terrestrial part of EAIS. Glacials are highlighted in gray.Open in a separate windowFig. 2.Implication of different sea-level-δ¹⁸O_sw conversions for estimates of interglacial ice-volume loss. y axis shows lower-than-modern δ¹⁸O_sw values (∆δ¹⁸O_sw) and the x axis (log-scale) the corresponding sea-level increase for commonly used conversion factors (27–29) (0.011 [black], 0.010 [purple], and 0.008 ‰⋅m⁻¹ [red]) and those for Antarctica only (11) (0.014 ‰⋅m⁻¹) ignoring (yellow) and incorporating (brown) the impact of its marine-based ice sheets. Stars mark ∆δ¹⁸O_sw for interglacials of this study and corresponding sea-level equivalents in dependence of the conversion applied. Orange, blue, and purple diamonds show the same for MIS 31, 11 (18), and 5e (17), respectively. Vertical lines indicate the sea-level increase resulting from complete melting of the GIS (+7.3 m), WAIS (+4.3 m), and EAIS (+53.3 m) (24–26).To further investigate past EAIS response to climate forcing we studied the Neogene/Quaternary transition when mean pCO₂ (13, 23) fell from levels similar to the anthropogenically perturbed values of today into the Quaternary range, leading to progressive high-latitude cooling and the intensification of Northern Hemisphere Glaciation (21, 30–33) (iNHG; Fig. 1 A and B). Our approach is based on a simple approximation that, once estimated past global sea level exceeds 11.6 m sea-level equivalent (msle) above modern, which corresponds to the complete melting of the present-day GIS [7.3 msle (24, 25)] and the marine- and land-based WAIS [3.4 and 0.9 msle (25, 26), respectively], EAIS instability (i.e., a retreat from its present-day size) can be inferred (see SI Appendix, section S4.1 for details). We quantified sea-level and ice-volume changes for the interval ∼2.75 to 2.4 Ma (MIS G7 to 95) by measuring the oxygen-isotope composition (δ¹⁸O) and Mg/Ca ratio in well-preserved benthic foraminiferal calcite (Oridorsalis umbonatus) from Integrated Ocean Drilling Program (IODP) Site U1313 [41°0′N, 32°57′W; 3,426-m water depth (34)] in the North Atlantic Ocean (Fig. 1 C and D). Using this approach we reconstructed changes in seawater δ¹⁸O (δ¹⁸O_sw), a proxy for global sea level and continental ice volume (35). This was done by 1) calculating bottom-water temperatures (BWT) derived from Mg/Ca (36) (Fig. 1E), 2) combining Mg/Ca-derived BWTs with δ¹⁸O to determine δ¹⁸O_sw (37) (Fig. 1F), and 3) converting δ¹⁸O_sw to sea level using a relationship between changes in sea level and δ¹⁸O_sw of 0.011 ‰⋅m⁻¹ (27) (Materials and Methods and Fig. 1F). Ninety-five percent probability intervals calculated through Monte Carlo simulations for individual sea-level data points yield an average uncertainty for our sea-level estimates of ± 28 m (∼2σ [SD]) (Materials and Methods and Fig. 1F), roughly equivalent to the decay/growth of ice four times greater than the GIS. Our approach was validated by reconstructing δ¹⁸O_sw for the recent (∼0 to 7 ka) at IODP Site U1313 and for late Holocene core-top (multicorer) samples from a neighboring site (MSM58) which are indistinguishable from the observed modern-day values (see Materials and Methods and SI Appendix, section S4.2.8 for details).     

From the Cover: Aquatic biodiversity enhances multiple nutritional benefits to humans

Humanity depends on biodiversity for health, well-being, and a stable environment. As biodiversity change accelerates, we are still discovering the full range of consequences for human health and well-being. Here, we test the hypothesis—derived from biodiversity–ecosystem functioning theory—that species richness and ecological functional diversity allow seafood diets to fulfill multiple nutritional requirements, a condition necessary for human health. We analyzed a newly synthesized dataset of 7,245 observations of nutrient and contaminant concentrations in 801 aquatic animal taxa and found that species with different ecological traits have distinct and complementary micronutrient profiles but little difference in protein content. The same complementarity mechanisms that generate positive biodiversity effects on ecosystem functioning in terrestrial ecosystems also operate in seafood assemblages, allowing more diverse diets to yield increased nutritional benefits independent of total biomass consumed. Notably, nutritional metrics that capture multiple micronutrients and fatty acids essential for human well-being depend more strongly on biodiversity than common ecological measures of function such as productivity, typically reported for grasslands and forests. Furthermore, we found that increasing species richness did not increase the amount of protein in seafood diets and also increased concentrations of toxic metal contaminants in the diet. Seafood-derived micronutrients and fatty acids are important for human health and are a pillar of global food and nutrition security. By drawing upon biodiversity–ecosystem functioning theory, we demonstrate that ecological concepts of biodiversity can deepen our understanding of nature’s benefits to people and unite sustainability goals for biodiversity and human well-being.

Species losses and range shifts because of climate change, harvesting, and other human activities are altering aquatic biodiversity locally and globally (1–5). In aquatic ecosystems, not only are some species severely depleted because of overfishing or habitat loss (3, 6–8), the ecosystem-level dimensions of biodiversity such as the total number of species and their functional diversity have also changed (9). Beyond the loss of particular species, changes in ecosystem-level dimensions of biodiversity threaten numerous ecosystem services to humans, which include the cultural, economic, or health benefits people derive from nature (10–13). In many regions, such as tropical coastal systems, the cumulative impacts of human activities are severe and associated with strong declines in taxonomic and ecological functional diversity (6) and coincide with regions with a high dependence of people upon wild-caught seafood for food and nutrition (14). In temperate regions, where some coastal communities depend on local wild seafood harvests to meet their nutritional needs (15, 16), species richness may be increasing as species recover from exploitation and warmer oceans allow species to expand their ranges into new territory (1, 2, 17).There is growing concern that biodiversity change leads to changes in human health and well-being (10, 13, 18). Specific and quantitative links between aquatic biodiversity and human health that distinguish contributions of species diversity from those of biomass, as predicted by biodiversity–ecosystem functioning theory, have not been established. At a time of unprecedented global change and increasing reliance on seafood to meet nutritional demands (19), there is an urgent need to understand how changing aquatic ecosystem structure may alter the provisioning of seafood-derived human nutrition.Seafood, consisting of wild-caught marine and freshwater finfish and invertebrates, provides an important source of protein and calories to humans. Additionally, unlike staple foods such as rice or other grains, seafood can address multiple dimensions of food and nutritional security simultaneously by providing essential micronutrients, such as vitamins, minerals, and polyunsaturated essential fatty acids critical to human health (19–22). Given the multiple attributes of seafood that are valuable to human health, it is possible that the diversity of an aquatic assemblage, distinct from the inclusion of any particularly nutritious species, could support human well-being consistent with a large body of evidence for biodiversity’s major contributions to ecological functions (11, 23–26). Dietary diversity is a basic tenet of a nutritious diet (27) and it is widely appreciated that diets composed of more food groups and more species are more nutritious (28–31). Ecological measures of dietary diversity (diet diversity, species richness, functional diversity, and Simpson’s index of evenness) have been associated with the nutritional value of diets in a range of contexts (27, 29, 32–38). These studies rely on relationships between species included in the diet (or other food intake measures) and nutritional adequacy of reported diets. However, a simple correlation between dietary diversity and a measure of dietary benefits provides only partial support for a claim that biodiversity benefits human well-being, consistent with the same ecological processes by which biodiversity supports numerous ecosystem functions and services (23, 26). We build upon this foundation of empirical relationships between diet diversity and diet quality by placing this question in the quantitative ecological theoretical framework that relates biodiversity to function (24, 25), thereby laying the groundwork for additional development of links between biodiversity science and our understanding of human well-being.Ecological theory predicts that biodiversity can be ecologically and economically important, apart from the importance of total biomass or the presence of particular species (23, 39). According to theory and over 500 explicit experimental tests (23, 40, 41), diversity in ecological communities and agricultural systems enhances ecosystem functioning by two mechanisms: 1) more diverse assemblages may outperform less diverse assemblages of the same density or biomass of individuals because more diverse assemblages will include more of the possible species and are therefore more likely to include high-performing species, assuming random processes of including species from the species pool (a selection effect), or 2) more diverse assemblages of a given density (or biomass) contain species with complementary functional traits, allowing them to function more efficiently (a complementarity effect) (25, 39). For aquatic animals, increased diversity enhances productivity of fish biomass (42) and also enhances temporal stability of biomass production and total yields (43, 44), providing economic and nutritional benefits to humans related to increased stability of harvests and production of biomass for consumption (43). However, when considering aquatic species from the perspective of human nutrition, functions other than biomass production become relevant because total seafood biomass consumption is not predictive of micronutrient benefits from seafood (45, 46).Here, we test a hypothesis central to ecological theory in the 21st century: whether biodiversity per se (species richness and ecological functional diversity), distinct from the identities and abundance of species, enhances human well-being (Fig. 1). We chose a measure of human well-being distinct from provision of protein, calories, or total yields—the micronutrient and essential fatty acid benefits of seafood. For increasing biodiversity per se (as opposed to increasing total seafood consumption) to enhance nutritional benefits as predicted by biodiversity–ecosystem functioning theory (25, 47), the amounts of various nutrients within edible tissues must differ among species, and furthermore, nutrient concentrations must trade off among species, such that species that have relatively high concentrations of some nutrients also have relatively low concentrations of others (25). Specifically, a “biodiversity effect” (sensu ref. 25) on nutritional benefits requires that concentrations of multiple nutrients are negatively correlated with each other, or uncorrelated, when compared among species, creating a complementary distribution of nutrients across species. In contrast, if nutrient concentrations in edible tissue are positively correlated for multiple nutrients across species such that, for example, a species containing high amounts of iron also has a high essential fatty acid concentration, thereby containing multiple nutrients in high concentrations simultaneously, seafood species or ecological functional diversity in the diet would not be important. In the case of positive correlations among nutrient concentrations, the ecosystem service of nutritional benefits would be enhanced by consuming more fish biomass or by selecting a few highly nutritious species, without considering species richness or ecological functional diversity.Open in a separate windowFig. 1.Aquatic biodiversity increases human well-being because edible species have distinct and complementary multinutrient profiles (A) and differ in mean micro- and macronutrient content (shown here relative to 10 and 25% thresholds of recommended dietary allowance, RDA, guidelines) for representative finfish (Abramis brama, Mullus surmuletus), mollusc (Mytilus galloprovincialis), and crustacean species (Nephrops norvegicus). Biodiversity–ecosystem functioning theory predicts that nutritional benefits, including the number of nutrient RDA targets met per 100 g portion (NT; i, iii) and minimum portion size (P_min; ii, iv) (B and E), are enhanced with increasing seafood species richness. Orange dots in B and E correspond to potential diets of high and low biodiversity levels. Seafood consumers with limited access to seafood each day may not reach RDA targets if diets are low in diversity (D–F versus A–C; gray shading indicates proportion of population that meets nutrient requirements). DHA: docosahexaenoic acid, EPA: eicosapentaenoic acid.We aimed to bridge two distinct theoretical frameworks—the biodiversity–ecosystem functioning theory and human nutrition science—by quantitatively testing for effects of aquatic species richness and ecological functional diversity (48, 49) in seafood diets on nutritional benefits via complementarity or selection effects. We used the public health measure of recommended dietary allowance (RDA) index to quantify nutritional benefits. RDAs are nutrient-based reference values that indicate the average daily dietary intake level that is sufficient to meet the nutrient requirement of nearly all (97 to 98%) healthy individuals in a particular life stage and gender group (50). Here, we used the RDA for females aged 19 to 50 y (SI Appendix, Tables S1 and S2; see SI Appendix, Table S1 for definitions of key terms). We measured nutritional value in terms of concentrations relative to RDAs, and we refer to these recommended amounts (or portions thereof) as “RDA targets” (SI Appendix, Tables S1 and S2 and Metrics). We quantified nutritional value in two ways: 1) the minimum amount of seafood tissue (in grams) required to meet given RDA targets (either for a single nutrient or the five micronutrients and fatty acids simultaneously; referred to as “minimum portion size required,” P_min [SI Appendix, Table S1, Eq. A1, and Metrics]) and 2) the number of nutrients that meet an RDA target in a single 100 g seafood portion (NT, SI Appendix, Table S1, Eq. A2). By considering nutritional value per unit biomass in both metrics, we avoided confounding diversity of seafood consumed with the total amount consumed (Metrics). We first tested two hypotheses: 1) seafood species richness increases NT because of complementarity in nutrient concentrations among species, and 2) seafood species richness increases the nutritional value of a 100 g edible portion of seafood, thereby lowering the minimum portion size, P_min, and improving the efficiency with which seafood consumers reach nutritional targets (Fig. 1). Following biodiversity–ecosystem functioning theory, we predicted that increased species richness is correlated with ecological functional diversity (51) in potential seafood diets and that ecological functional diversity is related to diversity in the concentration of essential elements and fatty acids that have nutritional value to human consumers, such that species and ecological functional diversity yields increased nutritional benefits. We also tested the hypothesis that seafood diversity increases total intake of heavy metal contaminants because some aquatic animals are known to bioaccumulate toxic metals in their tissues. For this reason, variation in bioaccumulation among species could lead to a biodiversity effect on contaminant intake that is detrimental to human health.In a global analysis of over 5,040 observations of nutrient concentrations in 547 aquatic species (SI Appendix, Fig. S1), we considered the provision of nutritional benefits to human consumers. To assess whether the relationships between biodiversity and human nutrition benefits depend on the geographic extent (global or local) over which seafood are harvested or accessed (11), we tested whether seafood species richness is associated with higher nutritional value at local scales (versus global scale) in traditional Indigenous seafood diets in North America (SI Appendix, Methods 1.4). Seafood is critical for Indigenous groups, who on average consume seafood at a rate that is 15 times higher than the global average per capita consumption rate (16). To test our hypotheses at the geographic scale of local consumer communities, we complemented our global analysis with additional analyses of 25 to 57 species in 14 geographically constrained groups of species consumed together as part of traditional Indigenous diets (SI Appendix, Methods 1.4).     

Herbivory and warming interact in opposing patterns of covariation between arctic shrub species at large and local scales

A major challenge in predicting species’ distributional responses to climate change involves resolving interactions between abiotic and biotic factors in structuring ecological communities. This challenge reflects the classical conceptualization of species’ regional distributions as simultaneously constrained by climatic conditions, while by necessity emerging from local biotic interactions. A ubiquitous pattern in nature illustrates this dichotomy: potentially competing species covary positively at large scales but negatively at local scales. Recent theory poses a resolution to this conundrum by predicting roles of both abiotic and biotic factors in covariation of species at both scales, but empirical tests have lagged such developments. We conducted a 15-y warming and herbivore-exclusion experiment to investigate drivers of opposing patterns of covariation between two codominant arctic shrub species at large and local scales. Climatic conditions and biotic exploitation mediated both positive covariation between these species at the landscape scale and negative covariation between them locally. Furthermore, covariation between the two species conferred resilience in ecosystem carbon uptake. This study thus lends empirical support to developing theoretical solutions to a long-standing ecological puzzle, while highlighting its relevance to understanding community compositional responses to climate change.

A readily observable phenomenon in nature is the tendency for the distributions of potentially competing species to covary positively at large spatial scales but negatively at small scales (1, 2). This scale dependence in patterns of species covariation is a defining phenomenon in ecology (3), and a classic illustration of it derives from MacArthur’s observations of Dendroica sp. warblers in mixed forests of the northeastern United States (1) and related theoretical work (4, 5). However, while opposing patterns of species covariation at large and local scales are ubiquitous, assigning causality to interacting drivers of such patterns in natural systems is challenging. Originally, theory explained this phenomenon as a product of distinct types of drivers of species abundance and distribution at large versus local scales. According to this framework, regional factors, such as climate, determine species’ distributions over large scales, while biotic interactions such as exploitation and interference determine presence, absence, and relative abundances of species at local scales (5–10). Hence, species with similar resource demands should, and often do, overlap spatially (covary positively) at broad scales as their distributions track abiotic niche requirements such as favorable climatic conditions (11). Meanwhile, the same species should, and often do, covary negatively at smaller spatial scales, where local biotic interactions such as competition, interference, niche complementarity, or exploitation by consumers or pathogens promote exclusion or segregation (5, 12–14). More recent theoretical developments have, however, highlighted the potential for roles of both types of drivers in patterns at both scales (7, 15, 16). Understanding whether, and how, climate and biotic interactions simultaneously influence species’ covariation at large and local scales has been repeatedly identified as a key challenge in improving predictions of species’ distributional and biodiversity responses to climate change (15, 17, 18).In contrast to progress in theory, field experimental tests of such potential interactions between biotic and abiotic factors in opposing patterns of species covariation at large and local scales have been lacking (14), in part because of the challenges inherent in conducting sufficiently controlled field experiments over suitably long time scales (19, 20). Consequently, novel empirical support for the role of, for example, biotic interactions in large scale patterns of species covariation has been strictly observational (21). Application of more robust empirical tests of predictions deriving from recent theory on this topic may also improve understanding of the consequences of patterns of species covariation at opposing spatial scales for important aspects of ecosystem function (22), including carbon exchange (23–26). Here, we present results of a 15-y warming and herbivore-exclusion experiment conducted at a remote arctic field site aimed at investigating influences of both drivers on patterns of covariation between two dominant shrub species at local and large spatial scales. The experimental design targets temperature as the abiotic limiting factor and herbivory (and associated ancillary effects) as the biotic limiting factor (Methods).The two focal shrub species in this study, dwarf birch (Betula nana) and gray willow (Salix glauca), hereafter “birch” and “willow,” respectively, are the most abundant plant species at our study site in low-arctic Greenland (27), and their functional role in ecosystem CO₂ exchange far exceeds that of any other vascular plant species at the site (28, 29). Furthermore, the two species are codominant across much of the Arctic (Fig. 1) (30, 31), but some experimental evidence indicates that Betula has the capacity to outcompete Salix at local scales in the Arctic due to its greater developmental plasticity and ability to invest rapidly in stem growth (32). Hence, although annual sampling throughout the duration of our experiment has assessed aboveground dynamics of all components of the plant community (Methods), our focus here is on patterns of covariation between birch and willow. Although birch is generally more common than willow across the study site (SI Appendix), the two species share similar distributions across the site, occur mainly on low to mid elevation slopes and plateaus, and predictably avoid arid steep slopes and stagnant mesic or saturated lowlands and fens (Fig. 1B). Each of the two species readily forms monospecific “shrub islands” at the local scale (Fig. 1C and SI Appendix, Fig. S3).Open in a separate windowFig. 1.(A) Circum-Arctic distributions of the two focal shrub species, dwarf birch (B. nana) and gray willow (S. glauca). Shaded polygons were derived from published range maps (30, 65). Point locations were derived from occurrence records (66–68) and the GBIF data portal (www.gbif.org). (B and C) Landscape and local scale views of patterns of covariation between the two species at the study site near Kangerlussuaq, Greenland. (B) South-facing hillside and lowland plains at the study site illustrating cooccurrence of dwarf birch (B. nana) and gray willow (S. glauca) at the landscape scale. (C) Monospecific shrub islands of each species are evident at smaller plot scales at the study site. In both photographs, birch appears dark or olive green, while willow appears lighter green. Image credit: E.P.     

A conformational switch driven by phosphorylation regulates the activity of the evolutionarily conserved SNARE Ykt6

Ykt6 is a soluble N-ethylmaleimide sensitive factor activating protein receptor (SNARE) critically involved in diverse vesicular fusion pathways. While most SNAREs rely on transmembrane domains for their activity, Ykt6 dynamically cycles between the cytosol and membrane-bound compartments where it is active. The mechanism that regulates these transitions and allows Ykt6 to achieve specificity toward vesicular pathways is unknown. Using a Parkinson’s disease (PD) model, we found that Ykt6 is phosphorylated at an evolutionarily conserved site which is regulated by Ca²⁺ signaling. Through a multidisciplinary approach, we show that phosphorylation triggers a conformational change that allows Ykt6 to switch from a closed cytosolic to an open membrane-bound form. In the phosphorylated open form, the spectrum of protein interactions changes, leading to defects in both the secretory and autophagy pathways, enhancing toxicity in PD models. Our studies reveal a mechanism by which Ykt6 conformation and activity are regulated with potential implications for PD.

Membrane fusion represents the final stage in vesicle trafficking and is largely driven by the soluble N-ethylmeleimide sensitive factor activating protein receptor (SNARE) proteins, which contribute to the specificity of the trafficking event (1, 2). Ykt6 is an essential R-SNARE and one of the most highly conserved SNAREs in all eukaryotes (3, 4). Ykt6 plays a key role in numerous vesicular transport pathways in yeast and in mammalian cells: 1) the secretory pathways, which are endoplasmic reticulum (ER) to the Golgi apparatus (Golgi), intra-Golgi, Golgi–ER retrieval pathways, and in the constitutive transport from the Golgi to the plasma membrane (3, 5, 6); 2) the endocytic pathways, which are between the Golgi and the vacuole/lysosome (7, 8) and endosomes to exosomes (9); and 3) the macroautophagy pathway (hereafter referred to as autophagy) (10–12). To date, the mechanism(s) underlying Ykt6 recruitment to distinct vesicular pathways remains unresolved.Unlike most SNAREs, Ykt6 contains a C-terminal lipid anchor motif which can be reversibly either palmitoylated (7, 13, 14) or geranylgeranylated (15) at cysteine 194 and permanently farnesylated at cysteine 195 (16). The reversible nature of palmitoylation and/or geranylgeranylation has been proposed as a mechanism to regulate Ykt6 membrane association, allowing it to cycle between the cytosol and membrane-bound compartments (14, 17). While lipid modifications are crucial to regulate Ykt6 membrane association, NMR and crystallography studies demonstrated that activation of Ykt6 is far more complex (18). When in the cytosol, Ykt6 forms a closed conformation whereby the N-terminal regulatory longin domain folds back onto the SNARE domain stabilized by hydrophobic interactions (18–20). Deletion of the longin domain, or substitution of a hydrophobic residue to a negatively charged one within the Ykt6 longin domain (F42E), causes the longin domain to dissociate from the SNARE domain and relocalize Ykt6 to both the plasma membrane and Golgi (14, 18). These data have led to a model whereby, for Ykt6 to be active and membrane associated, the longin and SNARE domains must separate to facilitate the open conformation. Once in the open conformation, Ykt6 can be palmitoylated, providing its membrane stability and interactions with its SNARE partners (14, 19). Whether this is the molecular mechanism that activates Ykt6, as well as the in vivo physiological triggers, remains to be shown.Misfolding of α-synuclein (α-syn) is the pathological hallmark of both familial and sporadic Parkinson’s disease (PD) (21–24). α-Syn triggers high levels of cytosolic Ca²⁺ and the activation of calcineurin (CaN), a Ca²⁺-dependent phosphatase (25, 26). Using an unbiased phosphoproteomic approach in a yeast model for α-syn toxicity, we previously found endogenous Ykt6 phosphorylated and regulated by CaN (27) (Fig. 1A). Ykt6 itself has been implicated in α-syn pathobiology as Ykt6 overexpression overcomes the secretory trafficking deficits caused by α-syn and protects against cell death (28, 29). Whether Ykt6 regulation by phosphorylation contributes to Ykt6 deficits under α-syn toxicity remains to be determined.Open in a separate windowFig. 1.Evolutionarily conserved phosphorylation site within human Ykt6 SNARE domain (S174) is sensitive to calcineurin, evolutionarily conserved in yeast and in humans, and is a critical determinant for its intracellular localization. (A) Fold phosphorylation of the indicated peptide from endogenous yeast Ykt6 detected by shotgun phosphoproteomics after correction for protein abundance from control yeast cells and yeast cells with high levels of Ca²⁺ (driven by overexpression of α-syn) with either WT or knockout for calcineurin (∆CaN) and knockout for the modulator of calcineurin (∆FKBP12). The identified phosphorylation sites are highlighted in red. Data from triplicate samples were pulled together for illustrated analysis (28). Data from ref. 27. (B) Alignment of Ykt6 sequences across species. Highlighted in pink is the identified phosphorylation site conserved across evolution. Arrows depicted represent Ykt6 zero-layer arginine (white) and additional CaN-sensitive sites identified in phosphoproteomic screen (red is human, black is yeast). (C) Fold phosphorylation of the indicated human Ykt6 peptide from HEK293T cells as detected by iTRAQ MS. Prior to GFP-Ykt6 immunoprecipitation, cells were treated for 30 min with the Ca²⁺ ionophore ionomycin (1 μM) and cotreated with calcineurin-specific inhibitor tacrolimus (1 μM). (D) Representative IF images of transiently transfected HeLa cells with GFP-tagged wild-type (WT) or phosphomimetic mutant of Ykt6 (S174D). Cells were treated with ionomycin (1 μM) and/or tacrolimus (1 μM) for 30 min. Nuclei (blue) are stained with DAPI. (Scale bar, 10 μm.) (E) Quantification of cells with GFP plasma membrane localization as shown in A. n = 3; *P < 0.05, ***P < 0.001, ****P < 0.0001. One-way ANOVA, uncorrected Fisher’s least significance difference (LSD) test. (F) Quantification of Ykt6 on membrane fractions (Na⁺K+)/Ykt6 on cytosol fractions (tubulin) from Western blots after cell fractionation (see Dataset S1); n = 3. (G, H) Quantification of GFP-WT Ykt6 (G) or GFP-S174D Ykt6 (H) on PM fraction (see Materials and Methods for details) of HEK293T cotransfected with the indicated Flag-tagged kinases. (I) Quantification of endogenous Ykt6 membrane (Na⁺K+)/Ykt6 cytosol (tubulin) fraction from Western blots after cell fractionation of HEK293T cells transfected with the indicated Flag-tagged kinases; n = 3 (see SI Appendix, Fig. S5D). Stats for (F–I) **P < 0.05, ***P < 0.001, ****P < 0.0001. One-way ANOVA, uncorrected Fisher’s LSD test. All comparisons to dimethyl sulfoxide (dmso) control of Flag-transfected dmso. (J) 40× confocal images after IF for YKT6 (green) and FLAG-tagged candidate kinases (red) of HEK293T cells cotransfected with GFP-WT-Ykt6 and the indicated Flag-tagged kinase. Single Z-frame images were channel merged and background subtracted before processed for quantitative analysis. Individual representative cells were chosen from each condition to better present changes in intracellular localization of YKT6. (Scale bar, 10 μm.) n = 3; ∼600 cells total.Here, we report that phosphorylation at the evolutionarily conserved site S174 within the Ykt6 SNARE domain drives an intramolecular rearrangement mediating the conversion from a closed cytosolic to an open membrane-bound state. Using an unbiased high-content kinase screening assay, we found that protein kinase C iota type (PRKCi) regulates Ykt6 phosphorylation and membrane association. Furthermore, we demonstrate that phosphorylation is sensitive to CaN and a key determinant of the binding affinity and specificity for various protein interactions. Phospho-dependent interactions of Ykt6 have functional consequences in two cellular activities in which Ykt6 has been shown to play a role: the secretory and autophagy pathways. Moreover, we show the biological importance of the evolutionarily conserved phosphosite under physiological and α-syn toxic conditions in yeast and Caenorhabditis elegans models of PD. Taken together, our results provide a mechanistic insight into the regulation of Ykt6 and its cellular activities with implications for PD, wherein malfunctions in Ykt6, autophagy, and the secretory pathway have been attributed (28–30).     

High-resolution multicontrast tomography with an X-ray microarray anode–structured target source

Multicontrast X-ray imaging with high resolution and sensitivity using Talbot–Lau interferometry (TLI) offers unique imaging capabilities that are important to a wide range of applications, including the study of morphological features with different physical properties in biological specimens. The conventional X-ray TLI approach relies on an absorption grating to create an array of micrometer-sized X-ray sources, posing numerous limitations, including technical challenges associated with grating fabrication for high-energy operations. We overcome these limitations by developing a TLI system with a microarray anode–structured target (MAAST) source. The MAAST features an array of precisely controlled microstructured metal inserts embedded in a diamond substrate. Using this TLI system, tomography of a Drum fish tooth with high resolution and tri-contrast (absorption, phase, and scattering) reveals useful complementary structural information that is inaccessible otherwise. The results highlight the exceptional capability of high-resolution multicontrast X-ray tomography empowered by the MAAST-based TLI method in biomedical applications.

Adding phase and scattering/darkfield contrast to the conventional absorption contrast in X-ray microscopy is a rapidly expanding research field because it offers tremendous advantages in a wide range of applications. The different contrast mechanisms are highly complementary, as they feature different sample–beam interactions that fingerprint different material properties. For example, the real and imaginary parts of the refractive index exhibit very significant differences in their absolute values (SI Appendix, Fig. S1) and represent the phase shift and attenuation of the X-ray, respectively (1–7). This has major implications for biomedical imaging, e.g., mammography (6, 8, 9), lung pathology (10–13), and industrial applications such as the structural investigation of carbon-reinforced polymer composites (14, 15). With this motivation, a variety of X-ray phase-contrast imaging (XPCI) techniques have been developed (2, 5–7, 9, 16), and there is a strong emphasis on achieving the phase-contrast efficiently and quantitatively (17–20). Among all these methods, grating-based XPCI (GXPCI), especially the Talbot–Lau interferometry (TLI) (3), is a leading contender for bringing XPCI into widespread adoption. Its unique advantages include 1) the compatibility with conventional, low-brilliance laboratory X-ray sources (3), 2) high sensitivity at high X-ray energy (20), and 3) desirable spatial resolution down to the micrometer level (21). Furthermore, it simultaneously provides three different contrast mechanisms: attenuation, refraction (differential phase-shift), and scattering (dark-field) in a single GXPCI dataset. The multicontrast modalities of TLI can offer valuable and complementary information for better discrimination of different structural components with different physical properties (4, 19). The GXPCI-enabled scattering contrast corresponds to the ultra-small-angle scattering strength of a material and offers excellent sensitivity to the morphological features that are much finer than the nominal spatial resolution (22–24). The phase-contrast component, on the other hand, quantitatively reconstructs the spatial distribution of the electron density, which is a fundamental material property that has different implications in different applications (20, 25). For example, the electron density of a battery cathode material fingerprints its state of charge and evolves as the battery is charged and discharged (26). Therefore, the three-dimensional (3D) electron density map of a battery electrode can be used to quantify the reaction heterogeneity, which is critical to the battery performance. The extraordinary potential of TLI tomography is reflected by the broad interest in applying this method to biological and medical imaging (5, 6, 8, 9, 12, 13), nondestructive testing (14, 27), materials science (19), and security screening (28). There are, however, key limitations of this technique that have yet to be addressed.A main advantage of TLI is its compatibility with a high-power laboratory X-ray source, which could largely improve the throughput of the experiment (3). In a conventional TLI setup, an absorption source grating (G0) is utilized to formulate a structured illumination pattern (Fig. 1A). G0 is inserted near the exit window of the X-ray tube for improving the spatial coherence and for reinforcing a geometrical constraint that matches the configuration of the downstream optics (SI Appendix, Fig. S2). The drawback of using the source grating G0 is that more than half of the X-ray’s source flux is wasted, significantly jeopardizing the efficiency of the imaging system. To increase the imaging sensitivity, one needs to use G0 gratings with fine periods as small as a few micrometers (29). Meanwhile, to ensure a sufficient X-ray transmission contrast, the thickness of the G0 grating lines has to reach several tens of micrometers, manifesting a desire for a high aspect ratio (AR) that is technically very challenging (30). To overcome this issue, Thüring et al. tilted the gratings with respect to the beam to effectively increase the AR. This approach, however, significantly reduces the useful field of view (FOV), compromising the practicality of this technique (30). Additionally, a G0 with large AR collimates the X-ray beam, which is another reason for the diminished FOV (∝AR⁻¹) (SI Appendix, Fig. S3) (21). We acknowledge that curved and tiled gratings can potentially be fabricated to alleviate this issue; however, they are associated with great challenges in microfabrication, particularly when targeting high a AR and small radius (21, 31). Several approaches have been introduced to circumvent the use of G0 and its associated limitations. One demonstrated approach involves fabricating grooves on an anode target for structured illumination. However, this method has a rather limited FOV because the spatial coherence property changes as a function of the target position (32). Morimoto et al. developed a TLI with a transmission grating by using a structured X-ray source. They demonstrated two-dimensional imaging results with a rather low spatial resolution and at a low working energy (20 kV) (33, 34). Despite the tremendous research efforts devoted to this field, the aforementioned challenges have hindered the broad adoption of TLI as a standard tool for high-resolution structural investigations with high-energy X-rays.Open in a separate windowFig. 1.Schematic comparison of the conventional TLI setup and our approach with a MAAST source is shown in A. SEM images of the MAAST pattern with etched grooves (B) and with W-MMIs embedded in the polycrystalline diamond substrate (C).To tackle these challenges, we developed a TLI system with a microarray anode–structured target (MAAST) X-ray source. We overcome the limitations of the conventional configuration with an extended source and a G0 grating by designing and incorporating the illumination pattern into the MAAST source as a built-in feature. Our approach significantly improves the efficiency in the use of source X-rays for imaging at high resolution and with high sensitivity. We further present correlative tri-contrast tomography on a Drum fish tooth specimen and demonstrate a clear separation of biological features with different physical properties. Our results highlight the exceptional imaging capability empowered by the MAAST-based TLI method. Our approach also features a compact and robust setup that can potentially be made broadly available to academia research and industrial applications.