Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations

Single-molecule force spectroscopy is a powerful tool for studying protein folding. Over the last decade, a key question has emerged: how are changes in intrinsic biomolecular dynamics altered by attachment to μm-scale force probes via flexible linkers? Here, we studied the folding/unfolding of α₃D using atomic force microscopy (AFM)–based force spectroscopy. α₃D offers an unusual opportunity as a prior single-molecule fluorescence resonance energy transfer (smFRET) study showed α₃D’s configurational diffusion constant within the context of Kramers theory varies with pH. The resulting pH dependence provides a test for AFM-based force spectroscopy’s ability to track intrinsic changes in protein folding dynamics. Experimentally, however, α₃D is challenging. It unfolds at low force (<15 pN) and exhibits fast-folding kinetics. We therefore used focused ion beam–modified cantilevers that combine exceptional force precision, stability, and temporal resolution to detect state occupancies as brief as 1 ms. Notably, equilibrium and nonequilibrium force spectroscopy data recapitulated the pH dependence measured using smFRET, despite differences in destabilization mechanism. We reconstructed a one-dimensional free-energy landscape from dynamic data via an inverse Weierstrass transform. At both neutral and low pH, the resulting constant-force landscapes showed minimal differences (∼0.2 to 0.5 k_BT) in transition state height. These landscapes were essentially equal to the predicted entropic barrier and symmetric. In contrast, force-dependent rates showed that the distance to the unfolding transition state increased as pH decreased and thereby contributed to the accelerated kinetics at low pH. More broadly, this precise characterization of a fast-folding, mechanically labile protein enables future AFM-based studies of subtle transitions in mechanoresponsive proteins.

Single-molecule force spectroscopy (SMFS) has been remarkably successful across broad classes of biological molecules (RNA, DNA, and proteins) (1–5). A particularly fruitful data acquisition regime probes multiple back-and-forth folding/unfolding transitions at near-equilibrium and equilibrium conditions (6–9). This methodology efficiently yields numerous transitions and therefore a wealth of kinetic data, one-dimensional (1D) free-energy landscape parameters, and even a full 1D projection of the free-energy landscape along the stretching axis (10, 11). The standard SMFS assay has the molecule of interest tethered via a flexible linker to the force probe, such as an optically trapped bead or an atomic force microscopy (AFM) cantilever (Fig. 1A). These micrometer-sized force probes are the primary measurement (x_meas) but have finite response time and are therefore coupled to, but do not precisely track, molecular dynamics (x_prot) (Fig. 1B) (12–14). Additionally, the flexible linker’s compliance modifies this coupling between the molecule and the force probe. Linkers stretched at a finite force (F) can even create an entropic barrier not present in the absence of applied force (15, 16). More generally, there is an expanding set of theoretical and experimental studies (12–30) investigating how such instrumental and assay parameters affect the underlying biomolecular dynamics and whether the measured dynamics are dominated by the instrument used to measure them.Open in a separate windowFig. 1.Probing the folding and unfolding dynamics of a globular protein by SMFS. (A) Cartoon showing a polyprotein consisting of a single copy of α₃D (blue) and two copies of NuG2 (red) stretched with an atomic force microscope. At low forces, the mechanically labile α₃D repeatedly unfolds and refolds as detected by a change in cantilever deflection. (B) A conceptual two-dimensional free-energy landscape shows the underlying protein extension (x_prot) and the experimentally measured extension (x_meas). The macroscopic force probe has finite temporal resolution, and the application of force can introduce an entropic barrier between resolved states. (C) The sum of the equilibrium folding and unfolding rates for α₃D in a strong denaturant (5 to 6 M urea) as a function of pH as determined in a prior smFRET study (37). (D) A conceptual sketch of α₃D’s 1D free-energy landscape deduced by a combination of smFRET and molecular dynamics studies based on Ref. 37. The dramatic increase in α₃D’s kinetics at low pH shown in panel C was explained as increased configurational diffusion along a smooth rather than a rough energy landscape.AFM characterization of proteins is widely used (1–5) and therefore is an important experimental regime to explore, distinct from numerous studies investigating instrumental effects on nucleic acid hairpins measured with optical traps (17, 18, 23, 24, 26, 31). Historically, limited force precision and stability coupled with the slow response of the force probe has made it challenging to perform AFM-based equilibrium and near-equilibrium studies (32) and thereby difficult to quantify the role of instrumental artifacts. Recent work using a standard gold-coated cantilever concluded that the equilibrium dynamics of the fast-folding protein gpW were dominated by the dynamics of the cantilever diffusing on a force-induced entropic barrier (29). Such results raise significant concerns about interpreting rates or landscapes measured in AFM studies of globular protein folding and thereby motivate the following question: How do variations in intrinsic protein folding dynamics manifest in AFM-based studies, particularly in an experimental regime dominated by an instrument-induced entropic barrier?Here, we address this question by directly modulating a globular protein’s underlying folding dynamics without significantly changing the height of the barrier or the free-energy difference between the states. To do so, we studied α₃D using AFM-based force spectroscopy (Fig. 1A). The dynamics and energetics of α₃D, a computationally designed, fast-folding three-helix bundle of 73 amino acids (33, 34), have been studied by traditional ensemble (33) and single-molecule fluorescence resonance energy transfer (smFRET) (35–39) assays. Equilibrium smFRET studies in chemical denaturants showed accelerated folding/unfolding kinetics as pH was reduced (35). A subsequent landmark paper (37) combined state-of-the-art smFRET and microsecond-long, all-atom molecular dynamics simulations to show that this acceleration resulted from suppression of nonnative contacts changing the local roughness of the 1D landscape (Fig. 1 C and D) rather than a change in the height or the overall shape of the barrier between states. In the context of Kramers theory (40), this roughness manifests as a change in D, the conformational diffusion coefficient along the 1D landscape. The authors concluded that most, if not all, of the 14-fold change in folding kinetics came from an increase in D. This pH-dependent change in kinetics serves as a benchmark of α₃D’s dynamics in the absence of the force probe and associated linker. In other words, we will leverage conditions known to modulate the rate of folding along the molecular coordinate (x_prot) while measuring the consequence of that change on the measured coordinate (x_meas) (Fig. 1B).While α₃D provides a conceptually attractive means to modulate intrinsic molecular dynamics, it presents significant experimental challenges. Like gpW (28, 29), α₃D unfolds at a low force (< 15 pN) by AFM standards (2, 3, 41) and exhibits even faster folding kinetics under force. Thus, spatiotemporal resolution is critical, and instrumentation limitations are expected to be even more pronounced. Force drift is also a critical issue, particularly for extended assays (>1 to 100 s) because standard gold-coated cantilevers exhibit significant force drift (42); yet, equilibrium assays of structured RNA (6) and proteins (9) are sensitive to sub-pN changes in F. We therefore used focused ion beam (FIB)–modified cantilevers (32, 43) that combine sub-pN stability over 100 s (43, 44) with a ∼13-fold improvement in spatiotemporal precision compared with the standard cantilever used in the aforementioned AFM study characterizing gpW (29). This stability in conjunction with a newly designed polyprotein construct allowed us to measure an individual α₃D unfold and fold over 5,000 times and for periods up to 1 h using both constant velocity (v) and equilibrium (v = 0) data acquisition protocols. Rates derived from both the equilibrium and dynamic data recapitulated α₃D’s pH-dependent kinetics from smFRET. However, the reconstructed 1D folding-energy landscape was consistent with the predicted entropic barrier and therefore encodes no information about α₃D’s folding landscape beyond ΔG₀, the thermodynamic stability of α₃D. Importantly, rate analysis yielded the expected asymmetric distance to the transition state from the folded and unfolded state and revealed a significant increase in the distance to the unfolding transition state as pH was lowered. These studies demonstrate that AFM-force spectroscopy can track changes in intrinsic protein dynamics with high precision, even in mechanically labile, fast-folding systems.     

Lipoteichoic acid polymer length is determined by competition between free starter units

Carbohydrate polymers exhibit incredible chemical and structural diversity, yet are produced by polymerases without a template to guide length and composition. As the length of carbohydrate polymers is critical for their biological functions, understanding the mechanisms that determine polymer length is an important area of investigation. Most Gram-positive bacteria produce anionic glycopolymers called lipoteichoic acids (LTA) that are synthesized by lipoteichoic acid synthase (LtaS) on a diglucosyl-diacylglycerol (Glc₂DAG) starter unit embedded in the extracellular leaflet of the cell membrane. LtaS can use phosphatidylglycerol (PG) as an alternative starter unit, but PG-anchored LTA polymers are significantly longer, and cells that make these abnormally long polymers exhibit major defects in cell growth and division. To determine how LTA polymer length is controlled, we reconstituted Staphylococcus aureus LtaS in vitro. We show that polymer length is an intrinsic property of LtaS that is directly regulated by the identity and concentration of lipid starter units. Polymerization is processive, and the overall reaction rate is substantially faster for the preferred Glc₂DAG starter unit, yet the use of Glc₂DAG leads to shorter polymers. We propose a simple mechanism to explain this surprising result: free starter units terminate polymerization by displacing the lipid anchor of the growing polymer from its binding site on the enzyme. Because LtaS is conserved across most Gram-positive bacteria and is important for survival, this reconstituted system should be useful for characterizing inhibitors of this key cell envelope enzyme.

All cell surfaces are rich in carbohydrate polymers that act as structural components, scaffolds for other molecules, and participants in signaling processes (1). The biological functions of a carbohydrate polymer are often greatly affected by its length. For example, depending on molecular weight, hyaluronic acid polymers can promote cell migration, differentiation, and inflammation or can inhibit these processes (2, 3). Similarly, the number of repeat units in bacterial O-antigen has a profound effect on complement activation and host cell uptake (4, 5). Unlike protein and nucleic acid polymers, which are assembled on a template that determines both length and composition, carbohydrate polymers are assembled without the use of a template. Template-independent length regulation is not as precise as template-directed polymerization, but physiological lengths of carbohydrate polymers typically fall into a defined range that is important for function (6). How different polymerases achieve length control is a fundamental question in the field.Several mechanisms for carbohydrate polymer length determination have been described. Some polymerases include a “molecular ruler” domain that measures the polymer against a portion of the enzyme (7), some use a dedicated “termination enzyme” to control length (8), and others rely on repeat unit concentration to control polymerization (9). These mechanisms are not mutually exclusive and can act together to control length (10, 11). The degree to which a polymerase is processive also influences product length. Processivity, a fundamental property of polymerases, refers to the number of elongation steps that occur without release of the growing polymer (12). A polymerase may be partially processive, in that more than one monomer addition occurs while the polymer is bound to the enzyme, but the polymer can be released and then rebind to continue elongation. A polymerase may also act in a distributive manner, where the growing polymer is released after each round of monomer addition. While some general mechanisms and aspects of length control for carbohydrate polymerases are known, here we describe a previously unknown mechanism for length regulation of a common type of lipoteichoic acid (LTA), a cell surface polymer that is crucially important to the physiology of most Gram-positive bacteria (13, 14).In the Gram-positive pathogen Staphylococcus aureus (Sa), LTA is a membrane-anchored poly(glycerol-phosphate) polymer involved in virulence (15–19), regulation of cell size and division (20–23), and osmotic stability (24, 25) (Fig. 1A). Sa LTA is assembled by the conserved lipoteichoic acid synthase (LtaS) on the cell surface using glucose(β1,6)-glucose(β1,3)-diacylglycerol (Glc₂DAG) as the membrane-anchored “starter unit” (20, 26). The polymer elongates in a process that involves the repeated transfer of phosphoglycerol units from phosphatidylglycerol (PG) to a catalytic threonine in LtaS (T300) and then to the tip of the growing polymer (Fig. 1B) (27–29). Repeat units may be modified by D-alanyl esters or, less commonly, GlcNAc moieties (24, 30). Because LTA is so important for Sa survival (13, 14, 21, 22), LtaS is a proposed target for antibiotics, and understanding its behavior may facilitate inhibitor development.Open in a separate windowFig. 1.LTA is a lipid-anchored polymer assembled from Glc₂DAG and PG on the bacterial cell surface. (A) Chemical structure of LTA from Sa. Phosphoglycerol repeat units may be modified with D-alanine esters or GlcNAc moieties. (B) Mechanism of LTA synthesis by LtaS. Phosphoglycerol units are transferred from PG to residue T300 to form a covalent intermediate, releasing DAG. Phosphoglycerol is then transferred to a Glc₂DAG starter unit to form GroP-Glc₂DAG. Additional repeat units are added to the glycerol tip of the polymer. (C) In Sa, PgcA and GtaB synthesize UDP-glucose from glucose-6-phosphate. UgtP uses UDP-glucose and DAG to make Glc₂DAG. LtaA exports Glc₂DAG to the cell surface. LtaS transfers phosphoglycerol units derived from PG to T300, releasing DAG for recycling. (D) Anti-LTA Western blot of Sa RN4220 wild-type (wt) or ΔugtP lysates. ΔugtP mutants lack Glc₂DAG, and LTA is instead polymerized directly on PG (20).Glc₂DAG, the starter unit for LTA polymerization, is biosynthesized on the cytoplasmic leaflet of the membrane by the sequential action of three enzymes: the phosphoglucose mutase PgcA, the UTP-glucose-1-phosphate uridylyltransferase GtaB, and the diacylglycerol β-glucosyltransferase UgtP (also called YpfP) (15, 20). Glc₂DAG is exported to the cell surface by the flippase LtaA (Fig. 1C) (15). An interesting feature of LtaS is that it can use PG as an alternative starter unit if Glc₂DAG synthesis or export is blocked (20). However, polymers formed on this alternative starter unit (PG-LTA) are significantly longer than polymers formed on Glc₂DAG (Glc₂DAG-LTA, Fig. 1D) (15, 23), and cells that make these longer polymers have cell division defects (20, 23), are much less virulent (15, 16), and are more sensitive to beta-lactam antibiotics and other cell envelope stresses (23). Whether the shorter polymers assembled on Glc₂DAG reflect the intrinsic behavior of LtaS or the action of other cellular factors is an important question that cannot be definitively answered with genetic approaches.Here we used in vitro reconstitution to test whether the identity of the LTA membrane anchor determines the length of the polymers that LtaS synthesizes. We show that the length differences observed between wild-type and mutant cells lacking Glc₂DAG are recapitulated in a proteoliposome system that contains only purified LtaS, PG, and either Glc₂DAG or an alternative anchor. Based on our studies, we propose a model for how polymer length can be controlled in polymerases that operate without a template.     

Geometrical manipulation of complex supramolecular tessellations by hierarchical assembly of amphiphilic platinum(II) complexes

Here we report complex supramolecular tessellations achieved by the directed self-assembly of amphiphilic platinum(II) complexes. Despite the twofold symmetry, these geometrically simple molecules exhibit complicated structural hierarchy in a columnar manner. A possible key to such an order increase is the topological transition into circular trimers, which are noncovalently interlocked by metal···metal and π–π interactions, thereby allowing for cofacial stacking in a prismatic assembly. Another key to success is to use the immiscibility of the tailored hydrophobic and hydrophilic sidechains. Their phase separation leads to the formation of columnar crystalline nanostructures homogeneously oriented on the substrate, featuring an unusual geometry analogous to a rhombitrihexagonal Archimedean tiling. Furthermore, symmetry lowering of regular motifs by design results in an orthorhombic lattice obtained by the coassembly of two different platinum(II) amphiphiles. These findings illustrate the potentials of supramolecular engineering in creating complex self-assembled architectures of soft materials.

Tessellation in two dimensions (2D) is a very old topic in geometry on how one or more shapes can be periodically arranged to fill a Euclidean plane without any gaps. Tessellation principles have been extensively applied in decorative art since the early times. In natural sciences, there has been a growing attention on creating ordered structures with increasingly complex architectures inspired by semi-regular Archimedean tilings (ATs) and quasicrystalline textures on account of their intriguing physical properties (1–5) and biological functions (6). Recent advances in this regard have been achieved in various fields of supramolecular science, including the programmable self-assembly of DNA molecules (7), coordination-driven assembly (8–10), supramolecular interfacial engineering (11–13), crystallization of organic polygons (14, 15), colloidal particle superlattices (16), and other soft-matter systems (17–20). Moreover, tessellation in 2D can overcome the topological frustration to generate complex semi- or non-regular patterns by using geometrically simple motifs. As exemplified by the self-templating assembly of spherical soft microparticles (21), a vast array of 2D micropatterns encoding non-regular tilings, such as rectangular, rhomboidal, hexagonal, and herringbone superlattices were obtained by layer-by-layer strategy at a liquid–liquid interface. Tessellation principles have also been extended to the self-assembly of giant molecules in three dimensions (3D). Superlattices with high space-group symmetry (Im3¯m, Pm3¯n, and P4₂/mnm) were reported in dendrimers and dendritic polymers by Percec and coworkers (22–24). Recently, Cheng and coworkers identified the highly ordered Frank–Kasper phases obtained from giant amphiphiles containing molecular nanoparticles (25–28). Despite such advancements made in the field of soft matter, an understanding of how structural ordering in supramolecular materials is influenced by the geometric factors of its constituent molecules has so far remained elusive.In light of these developments and the desire to explore the supramolecular systems, square-planar platinum(II) (Pt^II) polypyridine complexes may serve as an ideal candidate for model studies not only because of their intriguing spectroscopic and luminescence properties (29, 30), but also because of their propensity to form supramolecular polymers or oligomers via noncovalent Pt···Pt and π–π interactions (31–39). Although rod-shaped and lamellar structures are the most commonly observed in the self-assembly of planar Pt^II complexes (34–39), 2D-ordered nanostructures, such as the hexagonally packed columns (31, 40) and honeycomb-like networks (41–43), were recently first demonstrated by us.Herein, we report a serendipitous discovery of a C_2h-symmetric Pt^II amphiphile (Fig. 1A) that can hierarchically self-assemble into a 3D-ordered nanostructure with hexagonal geometry. Interestingly, this structurally anisotropic molecule possibly undergoes topological transition and interlocks to form its circular trimer by noncovalent Pt···Pt and π–π interactions (Fig. 1B). The resultant triangular motif is architecturally stabilized and preorganized for one-dimensional (1D) prismatic assembly (Fig. 1C). Together with the phase separation of the tailored hydrophobic and hydrophilic sidechains, an unusual and unique 3D hexagonal lattice is formed (Fig. 1D), in which the Pt centers adopt a rare rhombitrihexagonal AT-like order. Finally, the nanoarchitecture develops in a hierarchical manner on the substrate due to the homogeneous nucleation (Fig. 1E).Open in a separate windowFig. 1.Hierarchical self-assembly of Pt^II amphiphile into hexagonal ordering. (A) Space-filling (CPK) model of a C_2h-symmetric Pt^II amphiphile (1). All of the hydrogen atoms and counterions are omitted for clarity. (B) CPK representations of possible models of regular triangular, tetragonal, pentagonal, and hexagonal motifs formed with Pt···Pt and π–π stacking. These motifs possess a hydrophilic core (red) with various diameters wrapped by a hydrophobic shell comprising long alkyl chains (gray). (C) CPK representation of a 1D prismatic structure consisting of circular trimers with long-range Pt···Pt and π–π stacking. (D) CPK representation of a 3D columnar lattice constructed by the prismatic assemblies adopting a rare rhombitrihexagonal AT-like order. With the assistance of the phase separation, the hydrophobic domain serves as a discrete column associated with six prismatic neighbors. (E) Schematic representation of the nanoarchitecture with homogeneous orientation.     

Cingulo-opercular control network and disused motor circuits joined in standby mode

Whole-brain resting-state functional MRI (rs-fMRI) during 2 wk of upper-limb casting revealed that disused motor regions became more strongly connected to the cingulo-opercular network (CON), an executive control network that includes regions of the dorsal anterior cingulate cortex (dACC) and insula. Disuse-driven increases in functional connectivity (FC) were specific to the CON and somatomotor networks and did not involve any other networks, such as the salience, frontoparietal, or default mode networks. Censoring and modeling analyses showed that FC increases during casting were mediated by large, spontaneous activity pulses that appeared in the disused motor regions and CON control regions. During limb constraint, disused motor circuits appear to enter a standby mode characterized by spontaneous activity pulses and strengthened connectivity to CON executive control regions.

Disuse is a powerful paradigm for inducing plasticity that has uncovered key organizing principles of the human brain (1–4). Monocular deprivation—prolonged covering of one eye—revealed that multiple afferent inputs can compete for representational territory in the primary visual cortex (1). Similar competition between afferents also shapes the somatomotor system. Manipulations such as peripheral nerve deafferentation, whisker trimming, and limb constraint all drive plasticity in the primary somatosensory and motor cortex (2–4). Most plasticity studies to date have used focal techniques, such as microelectrode recordings, to study local changes in brain function. As a result, little is known about how behavior and experience shape the brain-wide functional networks that support complex cognitive operations (5).The brain is composed of networks of regions that cooperate to perform specific cognitive functions (5–8). These functional networks show synchronized spontaneous activity while the brain is at rest, a phenomenon known as resting-state functional connectivity (FC) (9–11). FC can be measured noninvasively in humans using resting-state functional MRI (rs-fMRI) and has been used to parse the brain into canonical functional networks (12, 13), including visual, auditory, and somatomotor networks (14, 15); ventral and dorsal attention networks (8, 16); a default mode network with roles in internally directed cognition and episodic memory (7, 11); a salience network thought to assess the homeostatic relevance of external stimuli (17); a frontoparietal control network supporting error processing and moment-to-moment adjustments in behavior (18–20); and a cingulo-opercular control network (CON), which maintains executive control during goal-directed behavior (18, 19, 21). Each functional network likely carries out a variety of additional functions.A more recent advance in human neuroscience has been the recognition of individual variability in network organization (22–25). Most early rs-fMRI studies examined central tendencies in network organization using group-averaged FC measurements (10, 12, 13). Recent work has demonstrated that functional networks can be identified in an individual-specific manner if sufficient rs-fMRI data are acquired, an approach termed precision functional mapping (PFM) (22, 23, 26–30). PFM respects the unique functional anatomy of each person and avoids averaging together functionally distinct brain regions across individuals.We recently demonstrated that PFM can be used to follow the time course of disuse-driven plasticity in the human brain (31). Three adult participants (Nico, Ashley, and Omar) were scanned at the same time of day for 42 to 64 consecutive days (30 min of rs-fMRI per day) before, during, and after 2 wk of dominant upper-extremity casting (Fig. 1 A and B). Casting caused persistent disuse of the dominant upper extremity during daily behaviors and led to a marked loss of strength and fine motor skill in all participants. During casting, the upper-extremity regions of the left primary somatomotor cortex (L-SM1_ue) and right cerebellum (R-Cblm_ue) functionally disconnected from the remainder of the somatomotor network. Disused motor circuits also exhibited large, spontaneous pulses of activity (Fig. 1C). Disuse pulses did not occur prior to casting, started to occur frequently within 1 to 2 d of casting, and quickly waned after cast removal.Open in a separate windowFig. 1.Experimental design and spontaneous activity pulses. (A) Three participants (Nico, Ashley, and Omar) wore casts covering the entire dominant upper extremity for 2 wk. (B) Participants were scanned every day for 42 to 64 consecutive days before, during, and after casting. All scans included 30 min of resting-state functional MRI. (C) During the Cast period, disused somatomotor circuits exhibited large pulses of spontaneous activity. (C, Left) Whole-brain ANOVA showing which brain regions contained disuse-driven pulses. (C, Right) Time courses of all pulses recorded from the disused primary somatomotor cortex.Somatomotor circuits do not function in isolation. Action selection and motor control are thought to be governed by complex interactions between the somatomotor network and control networks, including the CON (18). Prior studies of disuse-driven plasticity, including our own, have focused solely on somatomotor circuits. Here, we leveraged the whole-brain coverage of rs-fMRI and the statistical power of PFM to examine disuse-driven plasticity throughout the human brain.     

Elementary mechanisms of calmodulin regulation of NaV1.5 producing divergent arrhythmogenic phenotypes

In cardiomyocytes, Na_V1.5 channels mediate initiation and fast propagation of action potentials. The Ca²⁺-binding protein calmodulin (CaM) serves as a de facto subunit of Na_V1.5. Genetic studies and atomic structures suggest that this interaction is pathophysiologically critical, as human mutations within the Na_V1.5 carboxy-terminus that disrupt CaM binding are linked to distinct forms of life-threatening arrhythmias, including long QT syndrome 3, a “gain-of-function” defect, and Brugada syndrome, a “loss-of-function” phenotype. Yet, how a common disruption in CaM binding engenders divergent effects on Na_V1.5 gating is not fully understood, though vital for elucidating arrhythmogenic mechanisms and for developing new therapies. Here, using extensive single-channel analysis, we find that the disruption of Ca²⁺-free CaM preassociation with Na_V1.5 exerts two disparate effects: 1) a decrease in the peak open probability and 2) an increase in persistent Na_V openings. Mechanistically, these effects arise from a CaM-dependent switch in the Na_V inactivation mechanism. Specifically, CaM-bound channels preferentially inactivate from the open state, while those devoid of CaM exhibit enhanced closed-state inactivation. Further enriching this scheme, for certain mutant Na_V1.5, local Ca²⁺ fluctuations elicit a rapid recruitment of CaM that reverses the increase in persistent Na current, a factor that may promote beat-to-beat variability in late Na current. In all, these findings identify the elementary mechanism of CaM regulation of Na_V1.5 and, in so doing, unravel a noncanonical role for CaM in tuning ion channel gating. Furthermore, our results furnish an in-depth molecular framework for understanding complex arrhythmogenic phenotypes of Na_V1.5 channelopathies.

Voltage-gated sodium channels (Na_V) are responsible for the initiation and spatial propagation of action potentials (AP) in excitable cells (1, 2). Na_V channels undergo rapid activation that underlie the AP upstroke while ensuing inactivation permits AP repolarization. The Na_V1.5 channel constitutes the predominant isoform in cardiomyocytes, whose pore-forming α-subunit is encoded by the SCN5A gene. Na_V1.5 dysfunction underlies diverse forms of cardiac disease including cardiomyopathies, arrhythmias, and sudden death (3–6). Human mutations in Na_V1.5 are associated with two forms of inherited arrhythmias–congenital long QT syndrome 3 (LQTS3) and Brugada syndrome (BrS) (7). LQTS3 stems from delayed or incomplete inactivation of Na_V1.5 that causes persistent Na influx that prolongs AP repolarization—a “gain-of-function” phenotype (7–9). BrS predisposes patients to sudden death and is associated with a reduction in the peak Na current that may slow cardiac conduction or cause region-specific repolarization differences—a “loss-of-function” phenotype (10, 11). Genetic studies have identified an expanding array of mutations in multiple Na_V1.5 domains, including the channel carboxy-terminus (CT) that is a hotspot for mutations linked to both LQTS3 and BrS (12, 13). This domain interacts with the Ca²⁺-binding protein calmodulin (CaM), suggesting that altered CaM regulation of Na_V1.5 may be a common pathophysiological mechanism (12, 14–16). More broadly, human mutations in the homologous regions of neuronal Na_V1.1 (17, 18), Na_V1.2 (19, 20), and Na_V1.6 (21) as well as skeletal muscle Na_V1.4 (22) are linked to varied clinical phenotypes including epilepsy, autism spectrum disorder, neurodevelopmental delay, and myotonia (23). Taken together, a common Na_V mechanistic deficit—defective CaM regulation—may underlie these diverse diseases.CaM regulation of Na_V channels is complex, isoform specific, and mediated by multiple interfaces within the channel (14–16). The Na_V CT consists of a dual vestigial EF hand segment and a canonical CaM-binding “IQ” (isoleucine–glutamine) domain (24, 25) (Fig. 1A). The IQ domain of nearly all Na_V channels binds to both Ca²⁺-free CaM (apoCaM) and Ca²⁺/CaM, similar to Ca_V channels (26–31). As CaM is typically a Ca²⁺-dependent regulator, much attention has been focused on elucidating Ca²⁺-dependent changes in Na_V gating. For skeletal muscle Na_V1.4, transient elevation in cytosolic Ca²⁺ causes a dynamic reduction in the peak current, a process reminiscent of Ca²⁺/CaM-dependent inactivation of Ca_V channels (32). Cardiac Na_V1.5 by comparison exhibits no dynamic effect of Ca²⁺ on the peak current (32–34). Instead, sustained Ca²⁺ elevation has been shown to elicit a depolarizing shift in Na_V1.5 steady-state inactivation (SSI or h_∞), although the magnitude and the presence of a shift have been debated (32, 35). Additional CaM-binding sites have been identified in the channel amino terminus domain (36) and the III-IV linker near the isoleucine, phenylalanine, and methionine (IFM) motif that is well recognized for its role in fast inactivation (35, 37). However, recent cryogenic electron microscopy structures, biochemical, and functional analyses suggest that both the III-IV linker and the Domain IV voltage-sensing domain might instead interact with the channel CT in a state-dependent manner (38–43).Open in a separate windowFig. 1.Absence of dynamic Ca²⁺/CaM effects on WT Na_V1.5 SSI. (A, Left) Structure of Na_V1.5 transmembrane domain (6UZ3) (70) juxtaposed with that of Na_V1.5 CT–apoCaM complex (4OVN) (28). (Right) Arrhythmia-linked CT mutations highlighted in Na_V1.5 CT–apoCaM structure (LQTS3, blue; BrS, magenta; mixed syndrome, purple). (B) Dynamic Ca²⁺-dependent changes in Na_V1.5 SSI probed using Ca²⁺ photouncaging. Na currents specifying h_∞ at ∼100 nM (Left) and ∼4 μM Ca²⁺ step (Right). (C) Population data for Na_V1.5 SSI under low (black, Left) versus high (red, Right) intracellular Ca²⁺ reveal no differences (P = 0.55, paired t test). Dots and bars are mean ± SEM (n = 8 cells). (D) FRET two-hybrid analysis of Cerulean-tagged apoCaM interaction with various Venus-tagged Na_V1.5 CT (WT, black; IQ/AA, red; S[1904]L, blue). Each dot is FRET efficiency measured from a single cell. Solid line fits show 1:1 binding isotherm.Beyond Ca²⁺-dependent effects, the loss of apoCaM binding to the Na_V1.5 IQ domain increases persistent current (34, 44), suggesting that apoCaM itself may be pathophysiologically relevant. Indeed, Na_V1.5 mutations in the apoCaM-binding interface are associated with LQTS3 and atrial fibrillation (7), as well as a loss-of-function BrS phenotype and a mixed-syndrome phenotype whereby some patients present with BrS while others with LQTS3 (Fig. 1A) (13, 45). How alterations in CaM binding paradoxically elicits both gain-of-function and loss-of-function effects is not fully understood, though important to delineate pathophysiological mechanisms and for personalized therapies.Here, using single- and multichannel recordings, we show that apoCaM binding elicits two distinct effects on Na_V1.5 gating: 1) an increase in the peak channel open probability (P_O/peak) and 2) a reduction in the normalized persistent channel open probability (R_persist), consistent with previous studies (34, 44). The two effects may explain how mixed-syndrome mutations in the Na_V1.5 CT produce either BrS or LQTS3 phenotypes. On one hand, the loss of apoCaM association may diminish P_O/peak and induce BrS by shunting cardiac AP. On the other hand, increased R_persist may prevent normal AP repolarization, resulting in LQTS3. Analysis of elementary mechanisms suggests that these changes relate to a switch in the state dependence of channel inactivation. Furthermore, dynamic changes in Ca²⁺ can inhibit persistent current for certain mutant Na_V1.5 owing to enhanced Ca²⁺/CaM binding that occurs over the timescale of a cardiac AP. This effect may result in beat-to-beat variability in persistent Na current for some mutations. In all, these findings explain how a common deficit in CaM binding can contribute to distinct arrhythmogenic mechanisms.     

Appraisal of sedimentary alkenones for the quantitative reconstruction of phytoplankton biomass

Marine primary productivity (PP) is the driving factor in the global marine carbon cycle. Its reconstruction in past climates relies on biogeochemical proxies that are not considered to provide an unequivocal signal. These are often based on the water column flux of biogenic components to sediments (organic carbon, biogenic opal, biomarkers), although other factors than productivity are posited to control the sedimentary contents of the components, and their flux is related to the fraction of export production buried in sediments. Moreover, most flux proxies have not been globally appraised. Here, we assess a proxy to quantify past phytoplankton biomass by correlating the concentration of C₃₇ alkenones in a global suite of core-top sediments with sea surface chlorophyll-a (SSchla) estimates over the last 20 y. SSchla is the central metric to calculate phytoplankton biomass and is directly related to PP. We show that the global spatial distribution of sedimentary alkenones is primarily correlated to SSchla rather than diagenetic factors such as the oxygen concentration in bottom waters, which challenges previous assumptions on the role of preservation on driving concentrations of sedimentary organic compounds. Moreover, our results suggest that the rate of global carbon export to sediments is not regionally constrained, and that alkenones producers play a dominant role in the global export of carbon buried in the seafloor. This study shows the potential of using sedimentary alkenones to estimate past phytoplankton biomass, which in turn can be used to infer past PP in the global ocean.

Global carbon distribution between the ocean and the atmosphere regulates global climate on Earth. This distribution is primarily controlled by marine primary productivity (PP) and phytoplanktonic organisms, which transforms atmospheric CO₂ into organic matter. Only a fraction of this produced organic matter is exported to the deep ocean. Global models estimate that 48 PgC·y⁻¹ are produced in ocean surface waters (1), while 6 PgC·y⁻¹ (2) are exported out from the photic zone and 0.15 PgC·y⁻¹ are buried in sediments (3). Exported organic carbon is out of contact with the atmosphere on decadal-to-millennial timescales or longer once is buried in the seafloor, which exerts a major control on global climate by regulating the partial pressure of atmospheric CO₂ (4). Hence, estimating marine PP, export, and burial productivity changes during past key climatic periods (e.g., glacial–interglacial transitions) is essential to understand our present climate and predict its evolution in the future.To infer past PP, a range of proxies based on the fluxes of biogenic components are available (5–7). As flux proxies, they are related to changes in past export productivity, which are assumed to be proportional to surface PP in paleoreconstructions. However, depositional factors such as oxygen or ballasting effect are thought to be important in controlling organic matter export from the upper water column to sediments (8–10), and thus, sedimentary organic proxies concentration. The relative weights of the factors that control the spatial variability of organic matter concentration in sediments are still unconstrained, which leads to some uncertainty on the applicability of organic matter proxies to infer PP (7). Consequently, available proxies are sometimes interpreted to infer either changes in PP or depositional conditions (11).One of the common approaches to reconstruct PP relies on the measurement of C₃₇ di- and tri- unsaturated methyl ketones (i.e., C₃₇ alkenones) concentrations or fluxes in sediments (12–18). These organic molecules are biomarkers of the ubiquitous coccolithophore Emiliania huxleyi, which is the principal source of alkenones and the most abundant coccolithophore in the modern pelagic ocean (19–24). Geophyrocapsa oceanica and other coccolithophoral species from the same genera are also considered important alkenones producers nowadays (20).In this study, we evaluate the potential use of sedimentary C₃₇ alkenones content to infer past phytoplankton biomass at a global scale through the comparison of their spatial variability in a global compilation of core-top sediments with sea surface chlorophyll-a (SSchla) (Fig. 1). This is the primary pigment of photosynthesis and is present in all photosynthetic phytoplankton species. Its concentration in surface waters is commonly used as an indicator of phytoplankton biomass and to infer PP (25, 26). On a global scale, its concentration in surface waters is estimated by remote sensing (27). We also assess the effect of oxygen on the spatial accumulation of alkenones in sediments by comparing its concentration in bottom waters with alkenones abundance on a global scale.Open in a separate windowFig. 1.Global core-top sediments distribution. Lines delineate distinct biogeochemical regions defined on the basis of phytoplankton community, temperature, and nutrient concentration (44). SA, subarctic; SO, Southern Ocean; ST, subtropics; T, tropics.     

De novo biosynthesis of a nonnatural cobalt porphyrin cofactor in E. coli and incorporation into hemoproteins

Enzymes that bear a nonnative or artificially introduced metal center can engender novel reactivity and enable new spectroscopic and structural studies. In the case of metal-organic cofactors, such as metalloporphyrins, no general methods exist to build and incorporate new-to-nature cofactor analogs in vivo. We report here that a common laboratory strain, Escherichia coli BL21(DE3), biosynthesizes cobalt protoporphyrin IX (CoPPIX) under iron-limited, cobalt-rich growth conditions. In supplemented minimal media containing CoCl₂, the metabolically produced CoPPIX is directly incorporated into multiple hemoproteins in place of native heme b (FePPIX). Five cobalt-substituted proteins were successfully expressed with this new-to-nature cobalt porphyrin cofactor: myoglobin H64V V68A, dye decolorizing peroxidase, aldoxime dehydratase, cytochrome P450 119, and catalase. We show conclusively that these proteins incorporate CoPPIX, with the CoPPIX making up at least 95% of the total porphyrin content. In cases in which the native metal ligand is a sulfur or nitrogen, spectroscopic parameters are consistent with retention of native metal ligands. This method is an improvement on previous approaches with respect to both yield and ease-of-implementation. Significantly, this method overcomes a long-standing challenge to incorporate nonnatural cofactors through de novo biosynthesis. By utilizing a ubiquitous laboratory strain, this process will facilitate spectroscopic studies and the development of enzymes for CoPPIX-mediated biocatalysis.

The identity of a metal center often defines enzymatic activity, and swapping the native metal for an alternative one or introducing a new metal center has profound effects. More generally, the chemical utility of natural cofactors has inspired decades of study into synthetic analogs with distinct properties, and researchers have subsequently sought straightforward ways to put these novel cofactors back into proteins (1). Substituted metalloenzymes constitute one of the simplest cases. Changing the identity of the metal ion in metalloproteins has enabled powerful spectroscopic and functional studies of these proteins (2–10) in addition to new biocatalytic activities (11–20). However, most methods for producing such proteins with new-to-nature cofactors are limited by the inability to produce the novel protein–cofactor complex in vivo.Hemoproteins, in particular, have been studied through metal substitution because of their important biological functions and utility as biocatalysts. Heme is a ubiquitous and versatile cofactor in biology, and heme-dependent proteins serve essential gas sensing functions (21), metabolize an array of xenobiotic molecules (22), and perform synthetically useful oxygen activation and radical-based chemistry (23). Metal-substituted hemoproteins have enabled key spectroscopic studies of hemoprotein function and the development of biocatalysts with novel reactivity. For example, electron paramagnetic resonance (EPR) studies on cobalt-substituted sperm whale myoglobin (CoMb) enabled detailed characterization of the paramagnetic CoMbO₂ complex (3, 4, 24, 25). In analogous oxygen-binding studies in CoMb and cobalt-substituted hemoglobin (5, 6, 26), resonance Raman was used to identify the O–O stretching mode because cobalt-substituted proteins exhibit enhancement of this vibrational mode compared to the native iron proteins.Metal substitution has a profound effect on catalytic activity of hemoproteins, enabling numerous synthetic applications. Substitution of the native iron for cobalt in several hemoproteins, including a thermostable cytochrome c variant, enabled the reduction of water to H₂ under aerobic, aqueous conditions (27–29). Reconstitution of apoprotein with selected metalloporphyrins has been used to generate metal-substituted myoglobin and cytochrome P450s variants. These enzymes were effective as biocatalysts for C–H activation and carbene insertion reactions (11–14). In a tour de force of directed evolution, which required purification and cofactor reconstitution of each individual variant, Hartwig and coworkers generated a cytochrome P450 variant that utilizes a nonnative Ir(Me)mesoporphyrin cofactor to perform desirable C–H activation chemistry (14). These activities may not be unique to the Ir-substituted protein, as synthetic cobalt porphyrin complexes have been shown to mediate a variety of Co(III)-aminyl and -alkyl radical transformations, including C–H activation (30–32). Indeed, a number of cobalt porphyrin carbene complexes display significant carbon-centered radical character (33–35), whereas the corresponding Fe-porphyrin complexes are closed shell species (36, 37), indicating that cobalt porphyrins may possess distinct, complementary modes of reactivity (38–40).Inspired by these applications, researchers have sought strategies for generating metal-substituted hemoproteins. For many metalloproteins, metal substitution is carried out by removal of the native metal with a chelator and replacement with an alternate metal of similar coordination preference. This method is inapplicable to hemoproteins, as porphyrins do not readily exchange metal ions. Consequently, diverse methods have been employed to make metal-substituted hemoproteins (41–46). Early on, copper, cobalt, nickel, and manganese-substituted horseradish peroxidase (HRP) were prepared by a multistep process that subjected protein to strong acid and organic solvents (41, 42). Variations of this method have been used repeatedly (24, 43, 47–49). However, this method is applicable only to a narrow range of hemoproteins that tolerate the harsh treatment. With the advent of overexpression methods, significant improvement of metalloporphyrin-substituted protein yield was achieved by direct expression of the apoprotein and reconstitution with the desired metalloporphyrin in lysate prior to purification (50). Although this approach has many virtues, direct expression of apoprotein is ineffective for many hemoproteins, again limiting the utility of this method.As an alternative to the above in vitro approaches, researchers have pursued systems for direct in vivo expression of metal substituted hemoproteins. Two specialty strains of Escherichia coli (E. coli) were engineered to incorporate metalloporphyrin analogs from the growth medium into hemoproteins during protein expression. The engineered RP523 strain cannot biosynthesize heme and bears an uncharacterized heme permeability phenotype. Together, these two features enable this strain to assimilate and incorporate various metalloporphyrins into overexpressed hemoproteins with no background heme incorporation (44, 51–53). However, heme auxotrophy makes RP523 cells exceedingly sensitive to O₂, and, in many situations, RP523 cultures must be grown anaerobically. An alternative BL21(DE3)-based engineered strain harbors a plasmid bearing the heme transporter ChuA, which facilitates import of exogenous heme analogs (45). Production of metalloporphyrin-substituted protein with this ChuA-containing strain relies on growth in iron-limited minimal media, thereby diminishing heme biosynthesis. This method was used successfully to express metal-substituted versions of the heme domain of cytochrome P450 BM3 (45) and several myoglobin variants (11, 12). Because these cells biosynthesize a small quantity of their own heme, they are far more robust than the RP523 cells. Unfortunately, this advantage comes at the cost of increased heme contamination in the product protein (2 to 5%) (45).A set of intriguing papers reported the production of cobalt-substituted human cystathionine β-synthase (CoCBS) that relies on the de novo biosynthesis of CoPPIX from CoCl₂ and δ-aminolevulinic acid (δALA), a biosynthetic precursor to heme (46, 54). This method yielded significant amounts of CoCBS—albeit with modest heme contamination (7.4%)—sufficient for spectroscopic and functional characterization of the CoPPIX-substituted protein (8, 46). As cobalt is known to be toxic to E. coli, the researchers passaged the CBS expression strain through cobalt-containing minimal media for 12 d, enabling the cells to adapt to high concentrations of cobalt prior to protein expression. It is plausible that this serial passaging alters the E. coli cells, enabling the biosynthesis of CoPPIX and in vivo production of metal-substituted protein. The adaptation process is slow (>10 d), and it is unknown how genomic instability under these mutagenic conditions affects the reproducibility of this passaging approach.The possibility of facile CoPPIX production is particularly attractive for future biocatalysis efforts. As described above, synthetic cobalt porphyrins have been shown to perform a range of radical-mediated reactions. The ability to produce a CoPPIX center in vivo may enable engineering these unusual reactivities via directed evolution in addition to spectroscopic applications. We therefore set out to explore the unusual phenotype of CoPPIX production by E. coli and to ascertain whether it was possible to efficiently biosynthesize cobalt-containing hemoproteins in vivo from a single “generalist” cell line. Our goal was to achieve an efficient and facile method of cobalt-substituted hemoprotein production with minimal contamination of the native cofactor. Herein, we report the surprising discovery that native E. coli BL21(DE3) can biosynthesize a new-to-nature CoPPIX cofactor (Fig. 1). We use this insight to produce cobalt-substituted hemoproteins in vivo without requirement for complex expression methods or specialized strains.Open in a separate windowFig. 1.Chemical structures of iron protoporphyrin IX (FePPIX or heme b), cobalt protoporphyrin IX (CoPPIX), and free base protoporphyrin IX (H₂PPIX).     

Interventions can shift the thermal optimum for parasitic disease transmission

Temperature constrains the transmission of many pathogens. Interventions that target temperature-sensitive life stages, such as vector control measures that kill intermediate hosts, could shift the thermal optimum of transmission, thereby altering seasonal disease dynamics and rendering interventions less effective at certain times of the year and with global climate change. To test these hypotheses, we integrated an epidemiological model of schistosomiasis with empirically determined temperature-dependent traits of the human parasite Schistosoma mansoni and its intermediate snail host (Biomphalaria spp.). We show that transmission risk peaks at 21.7 °C (T_opt), and simulated interventions targeting snails and free-living parasite larvae increased T_opt by up to 1.3 °C because intervention-related mortality overrode thermal constraints on transmission. This T_opt shift suggests that snail control is more effective at lower temperatures, and global climate change will increase schistosomiasis risk in regions that move closer to T_opt. Considering regional transmission phenologies and timing of interventions when local conditions approach T_opt will maximize human health outcomes.

Temperature is important to the transmission of most infectious diseases, but the effects of temperature variability on parasite and host traits and their interactive effects on infection dynamics are poorly understood across many host–parasite systems (1–3). The variable responses of host and parasite traits to altered thermal regimes (i.e., thermal trait variation) could also impact intervention efficacy if the mortality of temperature-sensitive life stages is greater than the relative contribution of natural, temperature-dependent constraints on parasite transmission. For example, anthelminthic drugs decrease parasite transmission but likely have little effect on temperature-dependent transmission dynamics because adult parasites are buffered from environmental temperature in endothermic hosts. In contrast, vector control measures and water sanitation cause vector and parasite mortality, respectively, that is independent of ecophysiological constraints and irrespective of environmental temperature (4–6).If interventions override natural temperature-dependent constraints on transmission, they could cause shifts in the thermal optimum (T_opt) of parasite transmission, which could theoretically alter seasonal disease dynamics and render interventions less effective at certain times of the year and with global warming. This, in turn, would affect risk assessments and intervention planning for various disease systems (7, 8), especially under global climate change. Nevertheless, the hypotheses of intervention-related shifts to the T_opt of transmission and the resulting knock-on effects on disease phenology and intervention efficacy have never been proposed or tested.Human schistosomiasis, which affects more than 200 million people worldwide, is a major source of human morbidity and mortality in sub-Saharan Africa (9) and represents an ideal system to test these hypotheses. Schistosoma mansoni, an important causative parasite species, is transmitted through two aquatic larval stages (Fig. 1). Miracidia infect intermediate snail hosts (Biomphalaria spp.), and cercariae are released from snails to infect humans (10). Because free-living parasite larvae and snails are ectotherms, aquatic transmission is influenced by temperature (11, 12), with warm temperatures decreasing miracidial (13, 14) and cercarial survival (15) and reducing the odds of infection (13, 16). Although several Schistosoma parasite and snail traits are temperature-dependent (17–21), many models assume temperature-invariant transmission (12, 22, 23). Additionally, schistosomiasis interventions either target temperature-sensitive transmission stages, such as molluscicides, snail removal, and water sanitation, or temperature-insensitive stages, such as anthelmintic drugs provided to endothermic hosts. These interventions might impact T_opt differently and thus transmission phenology in areas where S. mansoni is endemic.Open in a separate windowFig. 1.The schistosomiasis transmission cycle spans the endothermic human body and aquatic environment. Parameters representing temperature-dependent traits investigated in this study are highlighted in purple. Parameters pertaining to disease control interventions are highlighted in orange. Parameter definitions are given in the main text and SI Appendix, Table S6.The objectives of this study were to: 1) quantify temperature-dependent S. mansoni and Biomphalaria spp. traits; 2) derive temperature-specific R₀ (i.e., estimated number of secondary cases from one infected human) predictions and thus a T_opt for schistosome transmission; 3) evaluate how R₀ and T_opt are affected by three interventions targeting distinct components of the parasite life cycle; and 4) explore the effects of temperature and interventions on transmission with regard to spatial and temporal surface water temperature variation.We predicted that 1) parasite and snail traits would exhibit unimodal responses to temperature, allowing for the identification of a T_opt for each trait; 2) transmission (i.e., R₀) would decrease in response to all interventions; 3) T_opt of R₀ would only change in response to interventions targeting ectothermic parasite and host life stages; and 4) this in turn would alter transmission phenology in geographically and temporally dependent manners based on the proximity of local conditions to T_opt.     

Nonadiabatic coupling of the dynamical structure to the superconductivity in YSr2Cu2.75Mo0.25O7.54 and Sr2CuO3.3

A crucial issue in cuprates is the extent and mechanism of the coupling of the lattice to the electrons and the superconductivity. Here we report Cu K edge extended X-ray absorption fine structure measurements elucidating the internal quantum tunneling polaron (iqtp) component of the dynamical structure in two heavily overdoped superconducting cuprate compounds, tetragonal YSr₂Cu_2.75Mo_0.25O_7.54 with superconducting critical temperature, T_c = 84 K and hole density p = 0.3 to 0.5 per planar Cu, and the tetragonal phase of Sr₂CuO_3.3 with T_c = 95 K and p = 0.6. In YSr₂Cu_2.75Mo_0.25O_7.54 changes in the Cu-apical O two-site distribution reflect a sequential renormalization of the double-well potential of this site beginning at T_c, with the energy difference between the two minima increasing by ∼6 meV between T_c and 52 K. Sr₂CuO_3.3 undergoes a radically larger transformation at T_c, >1-Å displacements of the apical O atoms. The principal feature of the dynamical structure underlying these transformations is the strongly anharmonic oscillation of the apical O atoms in a double-well potential that results in the observation of two distinct O sites whose Cu–O distances indicate different bonding modes and valence-charge distributions. The coupling of the superconductivity to the iqtp that originates in this nonadiabatic coupling between the electrons and lattice demonstrates an important role for the dynamical structure whereby pairing occurs even in a system where displacements of the atoms that are part of the transition are sufficiently large to alter the Fermi surface. The synchronization and dynamic coherence of the iqtps resulting from the strong interactions within a crystal would be expected to influence this process.

More than 30 y after the discovery of unconventional superconductivity in cuprates (1) and subsequently in analogous materials its underlying mechanism and in particular the role of the lattice are still under debate. Proposed microscopic theories range from purely electronic Mott–Hubbard and t-J approaches at one extreme to Bose–Einstein condensates of bipolarons at the other (2–4). Experimentally, however, anomalous isotope effects (5), resonant ultrasound (6), angle-resolved photoemission spectroscopy (7–9), femtosecond optical pump terahertz (10)/megaelectron-volt transmission electron microscopy probe (11), infrared pump (12), and so on have demonstrated that specific phonons not only couple to the superconductivity but correlate directly with the gap energy and may even transiently induce it well above the superconducting critical temperature, T_c. Cuprates also exhibit a plethora of superstructures indicative of strong electron–lattice coupling, stripes that have been proposed to stabilize the superconductivity (13), and charge-density waves (14, 15) and the pseudogap (PG) (16) that compete with it. Another possibility is mechanisms that boost T_c from a low value expected within a conventional Bardeen-Cooper-Schrieffer (BCS) scheme. That this question remains unanswered suggests considering more unconventional approaches (4). One candidate is the dynamical structures of cuprates, S(Q, E) or experimentally S(Q, t = 0), specifically their internal quantum tunneling polarons (iqtp). An iqtp is a set of atoms oscillating between two structures that possess different geometries, energy levels, and charge distributions (17–19). A chemist would describe these endpoints as separate species, adapting this term that applies more intuitively to solutions to the atoms in crystalline solids. Neutron scattering and X-ray absorption fine structure (XAFS) measurements identified O-centered iqtps and their correlation with the superconductivity 30 y ago (17–25). We now present Cu K edge extended XAFS (EXAFS) results from “overdoped” YSr₂Cu_2.75Mo_0.25O_7.54 (YSCO-Mo) that is isostructural with YBa₂Cu₃O₇ (Fig. 1A and SI Appendix, Fig. S1), T_c = 84 K (26) and hole doping p (excess charge on the planar Cu2 site) = 0.3 to 0.5 (27) and Sr₂CuO_3.3 (SCO) that is structurally analogous to La₂CuO₄ (Fig. 1B and SI Appendix, Fig. S1), T_c = 95 K (28, 29), and p = 0.6, both synthesized via high-pressure oxygenation (HPO) (30, 31). In YSCO-Mo the Cu2-apical O (Oap) double-well potential is degenerate in the normal state but renormalizes below T_c with the energy difference between its two minima increasing with decreasing temperature by ∼6 meV. SCO is already unique among cuprates in not having intact CuO₂ planes (32, 33). Its Cu EXAFS demonstrate that it is unique among superconductors in that its Oap shift by >1 Å at its superconducting transition, challenging our conception of superconductivity as an electronic transition that is incompatible with structural transformations.Open in a separate windowFig. 1.Structures and modulus and real components of the Fourier transforms of the EXAFS spectra, χ(R), of YSCO-Mo and SCO across temperature ranges bracketing their superconducting transitions. (A) Structure representation of YSCO-Mo. The CuO₂ planes are turqoise (Cu2) and magenta (Opl), Cu-O chains are blue (Cu1) and gold (Och), Oap is red, and Sr is green. In the actual structure one-fourth of Cu1 are substituted by Mo. The orientation is shown underneath. (B) The same as A for SCO, except a significant number of Oap and half of the O sites in the a direction in the CuO₂ planes are vacant. The CuO₂ planes are blue (Cu) and gold (O). For the χ(R) spectra the blue traces denote the lowest temperatures, then green to yellow, purple, and red-orange to brown at the highest ones. (C) YSCO-Mo spectra for E of the X-ray probe beam in the aa plane, with the modulus peaks labeled with their principal sources. The first temperature above T_c is red. (D) YSCO-Mo spectra for E||c, with the Cu1- and Cu2-Oap contributions overlapping at R = 1.6 Å. The peaks at higher R are a combination of direct, two-leg path contributions from more distant neighbor atom shells and ordered multiple scattering paths. (E) SCO spectra for E||H used for the orientation that is assigned to the a direction of the orthorhombic O sublattice. T_c is red and double width. (F–I) SCO over the designated temperature ranges for E⊥H spectra that will be the contributions in the bc plane defined by the orthorhombic O sublattice. (F) The extent of the change in the spectra, and by inference in their originating structures, across the superconducting transition. The features appearing at R = 2 to 2.5 Å below T_c result from the ∼2 Å shift of the O depicted in Fig. 3 B–D. In G the first temperature above T_c is orange and double width.We have recently shown that HPO cuprates are described by their own phase diagram (34). The principal feature of the well-known one for non-HPO cuprates is the superconducting “dome” that begins at p ∼0.06, peaks at p ∼ 0.16, and ends at p ∼ 0.27. Subsequent augmentations with the microstrain in the planes (35) and hole density on the O atoms (36) explain some of the material specificity but do not modify this overall pattern. For HPO compounds the superconductivity may begin at p < 0.06 and continues to increase beyond p = 0.27 with possible flattening but no reduction in T_c. Although we have found that the excess O in YSCO-Mo is mostly taken up by domains enriched in octahedral Mo(VI) substituting in the Cu(1) chains, much of the extra charge resides in the CuO₂ planes (27) and some of the carriers constitute a normal Fermi liquid that coexists with the superconductivity (26). The inherent inhomogeneity (37) in YSCO-Mo and SCO was probed by EXAFS, which is arguably the most incisive experimental method for characterizing short-range order and is especially sensitive to its changes. Diffraction patterns originate in the long-range average structure of a material and provide precise information on the symmetry and symmetry-constrained locations of the atoms that dominate the Bragg peaks. In contrast, EXAFS—and pair distribution function (pdf) analysis—are sensitive to local order separate from the crystallographic symmetry. The element selectivity of EXAFS provides further advantages by separating the atom pairs comprising the distribution function. Especially important for this study, EXAFS measures the instantaneous structure factor, S(Q, t = 0), that incorporates the dynamic structure components, S(Q, E), observed with inelastic scattering. EXAFS therefore accesses time and energy scales corresponding to collective dynamical phenomena (25, 38, 39). Dynamical structures such as the iqtp are demonstrated when S(Q, E/t = 0) gives locations for atoms that differ from those (19, 38) obtained from diffraction and elastic scattering measurements (20–22, 40). This complementarity was the basis for the original identification of the Cu-Oap two-site distribution (41) and its assignment to the double-well potential of the iqtp (17, 19, 42).     

From the Cover: Transgenic cotton and sterile insect releases synergize eradication of pink bollworm a century after it invaded the United States

Invasive organisms pose a global threat and are exceptionally difficult to eradicate after they become abundant in their new habitats. We report a successful multitactic strategy for combating the pink bollworm (Pectinophora gossypiella), one of the world’s most invasive pests. A coordinated program in the southwestern United States and northern Mexico included releases of billions of sterile pink bollworm moths from airplanes and planting of cotton engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt). An analysis of computer simulations and 21 y of field data from Arizona demonstrate that the transgenic Bt cotton and sterile insect releases interacted synergistically to reduce the pest’s population size. In Arizona, the program started in 2006 and decreased the pest’s estimated statewide population size from over 2 billion in 2005 to zero in 2013. Complementary regional efforts eradicated this pest throughout the cotton-growing areas of the continental United States and northern Mexico a century after it had invaded both countries. The removal of this pest saved farmers in the United States $192 million from 2014 to 2019. It also eliminated the environmental and safety hazards associated with insecticide sprays that had previously targeted the pink bollworm and facilitated an 82% reduction in insecticides used against all cotton pests in Arizona. The economic and social benefits achieved demonstrate the advantages of using agricultural biotechnology in concert with classical pest control tactics.

Invasive life forms pose a major global threat and are especially difficult to eradicate after they become widespread and abundant in their new habitats (1–4). The pink bollworm (Pectinophora gossypiella), one of the world’s most invasive insects, is a voracious lepidopteran pest of cotton that was first detected in the United States in 1917 (5–8). For most of the past century, it was particularly destructive in the southwestern United States, including Arizona, where its larvae fed almost exclusively on cotton, consuming the seeds inside bolls and disrupting lint production (6, 8). In 1969, its peak seasonal density at an Arizona study site was 1.8 million larvae per hectare (ha), which translates to over 200 billion larvae in the 126,000 ha of cotton planted statewide that year (9, 10). In 1990, this pest cost Arizona cotton growers $48 million, including $32 million damage to cotton despite $16 million spent for insecticides sprayed to control it (11). In several field trials, mass releases of sterile pink bollworm moths to mate with wild moths reduced progeny production somewhat, yet did not suppress established populations because the sterile moths did not sufficiently outnumber the wild moths (6, 12–14).Pink bollworm control was revolutionized in 1996 by the introduction of cotton genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt). Bt proteins kill some major insect pests yet are not toxic to most nontarget organisms, including people and many beneficial insects (15–17). Transgenic Bt cotton helped to reduce the total annual cost of pink bollworm damage and insecticide treatments to $32 million in the United States (18). Although Bt cotton kills essentially 100% of susceptible pink bollworm larvae (19–21), this pest rapidly evolved resistance to Bt proteins in laboratory selection experiments in Arizona and in Bt cotton fields in India (20–24). To delay the evolution of resistance to Bt cotton, farmers in Arizona planted “refuges” of non-Bt cotton that yielded abundant susceptible moths to mate with the rare resistant moths emerging from Bt cotton (Fig. 1A). The refuge strategy, which has been mandated in the United States and many other countries, but was not adopted widely by farmers in India, helped preserve pink bollworm susceptibility to Bt cotton in Arizona from 1996 to 2005 (24).Open in a separate windowFig. 1.Management strategies. (A) The refuge strategy is the primary approach adopted worldwide to delay the evolution of pest resistance to Bt crops and was used in Arizona from 1996 to 2005. Refuges of non-Bt cotton planted near Bt cotton produce abundant susceptible moths (blue) to mate with the rare resistant moths (red) emerging from Bt cotton. If the inheritance of resistance to Bt cotton is recessive, as in pink bollworm, the heterozygous offspring from matings between resistant and susceptible moths die when they feed on Bt cotton bolls as larvae (24). (B) Bt cotton and sterile moth releases were used together in Arizona from 2006 to 2014 as part of a multitactic program to eradicate the pink bollworm. Susceptible sterile moths (brown) were released from airplanes to mate with the rare resistant moths emerging from Bt cotton. The few progeny produced by such matings (48) are expected to be heterozygous for resistance and to die when they feed on Bt cotton bolls as larvae.As part of a coordinated, multitactic effort to eradicate the pink bollworm from the southwestern United States and northern Mexico, a new strategy largely replacing refuges with mass releases of sterile pink bollworm moths was initiated in Arizona during 2006 (Fig. 1B; 24–27). To enable this novel strategy, the US Environmental Protection Agency granted a special exemption from the refuge requirement, which allowed Arizona cotton growers to plant up to 100% of their cotton with Bt cotton (28). We previously reported data from 1998 to 2009 showing that this innovative strategy sustained susceptibility of pink bollworm to Bt cotton while reducing the pest’s population density (25). Here, to test the idea of eradicating pink bollworm with the combination of Bt cotton and sterile releases, we conducted computer simulations and analyzed field data collected in Arizona from 1998 to 2018.     

De novo determination of near-surface electrostatic potentials by NMR

Electrostatic potentials computed from three-dimensional structures of biomolecules by solving the Poisson–Boltzmann equation are widely used in molecular biophysics, structural biology, and medicinal chemistry. Despite the approximate nature of the Poisson–Boltzmann theory, validation of the computed electrostatic potentials around biological macromolecules is rare and methodologically limited. Here, we present a unique and powerful NMR method that allows for straightforward and extensive comparison with electrostatic models for biomolecules and their complexes. This method utilizes paramagnetic relaxation enhancement arising from analogous cationic and anionic cosolutes whose spatial distributions around biological macromolecules reflect electrostatic potentials. We demonstrate that this NMR method enables de novo determination of near-surface electrostatic potentials for individual protein residues without using any structural information. We applied the method to ubiquitin and the Antp homeodomain–DNA complex. The experimental data agreed well with predictions from the Poisson–Boltzmann theory. Thus, our experimental results clearly support the validity of the theory for these systems. However, our experimental study also illuminates certain weaknesses of the Poisson–Boltzmann theory. For example, we found that the theory predicts stronger dependence of near-surface electrostatic potentials on ionic strength than observed in the experiments. Our data also suggest that conformational flexibility or structural uncertainties may cause large errors in theoretical predictions of electrostatic potentials, particularly for highly charged systems. This NMR-based method permits extensive assessment of near-surface electrostatic potentials for various regions around biological macromolecules and thereby may facilitate improvement of the computational approaches for electrostatic potentials.

Due to the fundamental importance of electrostatic interactions in chemistry and biology, electrostatic potentials are invaluable information for the understanding of molecular recognition, enzymatic catalysis, and other functions of proteins and nucleic acids (1–4). Quantification of electrostatics is also important for successful protein engineering (5) and structure-based drug design (6). Computational approaches based on the Poisson–Boltzmann theory are commonly used to calculate electrostatic potentials from three-dimensional (3D) molecular structures (1, 7). Owing to available software such as Adaptive Poisson-Boltzmann Solver (APBS) (8, 9) and DelPhi (10, 11), computation of the electrostatic potentials around biomolecules has gained widespread popularity in the fields of molecular biophysics, structural biology, and medicinal chemistry.However, the computed electrostatic potentials may not necessarily be accurate even if the 3D structures are precisely and accurately determined. Importantly, the Poisson–Boltzmann theory is approximate with known limitations. The electrostatic models based on this theory are valid under assumptions, which simplify the calculations (12). The lack of consideration of correlations between ions can diminish accuracy in calculations of electrostatic potentials for systems at high ionic strength (13). Due to the assumption of a dielectric continuum, the electrostatic potentials predicted with the Poisson–Boltzmann theory may be inaccurate for zones near the first hydration layer. Electrostatic potentials predicted for regions near highly charged molecular surfaces may also be inaccurate due to the assumption of linear dielectric response. Nonetheless, the Poisson–Boltzmann theory can accurately predict electrostatic interactions at longer range (7). The extent of validity for such electrostatic potentials near molecular surfaces remains to be addressed more rigorously through experiments.Despite the need, experimental validation of computed electrostatic potentials is rather rare and methodologically limited for biological macromolecules. The validity of electrostatic models has been examined using pK_a data on titratable side-chain moieties (14–16), redox potentials of redox-active groups (17, 18), and electron–electron double resonance (19). Among them, pK_a data have been most commonly used for the validation, but even fundamentally incorrect electrostatic models can reproduce pK_a data (20). Electrostatic fields can be experimentally determined by vibrational spectroscopy, for example, for nitrile groups that are conjugated to cysteine thiol moieties of proteins (21, 22). However, the approaches utilizing vibrational spectroscopy or electron–electron double resonance provide only limited information about the extrinsically introduced probes, which may perturb native systems.In this paper, we present a unique and powerful method for de novo determination of near-surface electrostatic potentials for many protein residues, regardless of their side-chain types, and without using any chemical modifications. In this method, data of NMR paramagnetic relaxation enhancement (PRE) arising from analogous charged paramagnetic cosolutes are analyzed for ¹H nuclear magnetizations of proteins (Fig. 1). The PRE data reflect the electrostatic biases in spatial distributions of charged paramagnetic cosolutes and permit the determination of near-surface electrostatic potentials around proteins without using any structural information. The de novo determination of near-surface electrostatic potentials can greatly facilitate the examination of theoretical models for electrostatics of biological macromolecules.Open in a separate windowFig. 1.NMR PRE arising from cationic amino-methyl-PROXYL or anionic carboxy-PROXYL reflects their spatial distribution bias due to near-surface electrostatic potentials around a biological macromolecule.     

Hyperspectral interference tomography of nacre

Structural characterization of biologically formed materials is essential for understanding biological phenomena and their enviro-nment, and for generating new bio-inspired engineering concepts. For example, nacre—the inner lining of some mollusk shells—encodes local environmental conditions throughout its formation and has exceptional strength due to its nanoscale brick-and-mortar structure. This layered structure, comprising alternating transparent aragonite (CaCO₃) tablets and thinner organic polymer layers, also results in stunning interference colors. Existing methods of structural characterization of nacre rely on some form of cross-sectional analysis, such as scanning or transmission electron microscopy or polarization-dependent imaging contrast (PIC) mapping. However, these techniques are destructive and too time- and resource-intensive to analyze large sample areas. Here, we present an all-optical, rapid, and nondestructive imaging technique—hyperspectral interference tomography (HIT)—to spatially map the structural parameters of nacre and other disordered layered materials. We combined hyperspectral imaging with optical-interference modeling to infer the mean tablet thickness and its disorder in nacre across entire mollusk shells from red and rainbow abalone (Haliotis rufescens and Haliotis iris) at various stages of development. We observed that in red abalone, unexpectedly, nacre tablet thickness decreases with age of the mollusk, despite roughly similar appearance of nacre at all ages and positions in the shell. Our rapid, inexpensive, and nondestructive method can be readily applied to in-field studies.

Complex optical phenomena can emerge from a variety of biological or bio-inspired processes, from arrays of colors in peacocks (1) and other birds (2), butterflies (3), and opals (4), to the metal-like sheen of herring (5) and unique polarization-dependent properties of jewel beetles (6) and Pollia fruit (7). Nacre, or mother-of-pearl, is a prominent biologically formed mineral structure found throughout our oceans. It lines the inside of the shells formed by many mollusks, including bivalves, cephalopods, and gastropods. It features brilliant iridescent colors (Fig. 1) and is studied and emulated in part because of its outstanding mechanical performance (8, 9). The striking, colorful appearance of nacre has been a source of scientific curiosity since the days of Brewster (10), Rayleigh (11), and Raman (12, 13), and is the product of optical interference resulting from multiple interface reflections as light propagates through its stratified structure comprising stacks of transparent polygonal aragonite tablets (CaCO₃) interspersed with organic polymer (chitin and proteins) layers (14–16) (Fig. 1A). Nacre is one of seven mollusk shell structures (17). In the nacre structure, the aragonite tablets are typically 5 to 10 μm in diameter and hundreds of nanometers thick [200 to 1,100 nm across all shells, and 250 to 500 nm in red abalone (18)], while the organic sheets are an order of magnitude thinner (14, 16, 19). In columnar nacre formed by gastropods like abalone and snails (Fig. 1), co-oriented tablets are stacked on top of one another, while in sheet nacre formed by bivalves like pearl oysters and pen shells, co-oriented tablets are staggered diagonally (18) (see Movie S1 for an animation showing how co-oriented tablets are stacked in columnar nacre). Despite the significant structural and formation–mechanism differences, the thicknesses of tablets and organic layers are similar in columnar and sheet nacre, and so are the optical and mechanical behavior (20). The resulting palette of colors is primarily dependent on the nacre tablet thickness and the viewing angle, and the optical response that yields these colors can be understood as that of a Bragg reflector (21) with disorder in the layer thicknesses, where the optical band gaps are determined by the thicknesses of the transparent layers (5, 22, 23). Thus, the spectrum of light reflected from a nacre surface encodes information about its physical structure (Fig. 1 B–D).Open in a separate windowFig. 1.(A) Nacre, the colorful iridescent inner lining of some mollusk shells. Here, the red abalone, or H. rufescens, shell features columnar nacre, which comprises thousands of layers of polygonal aragonite tablets interspersed with organic sheets. (B) A close-up photograph of the nacre surface shows a variety of colors and nonuniformities. (C and D) Given a broadband white light source illuminating nacre at a fixed angle of incidence, variations in color are observed due to the difference in average thickness of aragonite tablets comprising nacre. (E) Hyperspectral interference tomography (HIT) setup: A hyperspectral camera collects predominantly specular reflectance data across a sample illuminated by a collimated source at a fixed angle of incidence from the normal to the sample (θ). The reflected light is polarized using a wire-grid polarizer. (F) A color photograph of a region of nacre that was analyzed. (G) Map of the mean tablet thickness (MTT) obtained using HIT, overlaid on a grayscale rendering of the photograph in F. Highlighted in red is a 5 × 5-mm region used to analyze the ontogeny of nacre in Fig. 4. The region around this area was masked off using opaque tape, which is highlighted with the dashed white box.Understanding and characterizing the structure of nacre and other biomaterials have deep and surprising implications. For example, the average thickness of the tablets comprising ancient nacre can be used as a proxy for local ocean temperatures at the time of nacre formation, enabling paleoclimatology spanning hundreds of millions of years (18, 24, 25). The structure of nacre is also an inspiration for engineered materials thousands of times stronger than the constituent materials (15, 26, 27). To that end, new techniques have been developed to probe and understand the structure of nacre, such as polarization-dependent imaging contrast (PIC) mapping using X-ray absorption near-edge structure spectroscopy combined with photoemission electron spectromicroscopy (18, 28, 29), or X-ray nanotomography (30). However, these characterization techniques such as cross-sectional electron microscopy result in the destruction of the sample and are time-consuming and costly.Here, we present a method for rapid, nondestructive, and large-scale structural characterization of disordered and nonuniform stratified thin-film materials and apply it to the analysis of nacre. Our all-optical method employs hyperspectral imaging combined with thin-film modeling to extract nacre mean tablet thicknesses (MTTs) and tablet degree of disorder (σ)—defined as the standard deviation of the thicknesses—across large areas (Fig. 1 E–G). This characterization method is designated as hyperspectral interference tomography (HIT). We used HIT to map the structure of mollusk shell nacre across many stages of development and identified a previously unexplored relationship between the age of the organism and the structure of the nacre layer. We investigated two particular species of nacre-forming mollusks, Haliotis rufescens (red abalone) and Haliotis iris (paua, or rainbow abalone; data only in SI Appendix), for which the aragonite tablet thicknesses lie within a range of 250 to 500 nm (18, 31); however, the method is applicable to any other transparent layered structure of animal, plant, geologic, or synthetic origin.     

Increasing the rate of the hydrogen evolution reaction in neutral water with protic buffer electrolytes

Electrocatalytic generation of H₂ is challenging in neutral pH water, where high catalytic currents for the hydrogen evolution reaction (HER) are particularly sensitive to the proton source and solution characteristics. A tris(hydroxymethyl)aminomethane (TRIS) solution at pH 7 with a [2Fe-2S]-metallopolymer electrocatalyst gave catalytic current densities around two orders of magnitude greater than either a more conventional sodium phosphate solution or a potassium chloride (KCl) electrolyte solution. For a planar polycrystalline Pt disk electrode, a TRIS solution at pH 7 increased the catalytic current densities for H₂ generation by 50 mA/cm² at current densities over 100 mA/cm² compared to a sodium phosphate solution. As a special feature of this study, TRIS is acting not only as the primary source of protons and the buffer of the pH, but the protonated TRIS ([TRIS-H]⁺) is also the sole cation of the electrolyte. A species that is simultaneously the proton source, buffer, and sole electrolyte is termed a protic buffer electrolyte (PBE). The structure–activity relationships of the TRIS PBE that increase the HER rate of the metallopolymer and platinum catalysts are discussed. These results suggest that appropriately designed PBEs can improve HER rates of any homogeneous or heterogeneous electrocatalyst system. General guidelines for selecting a PBE to improve the catalytic current density of HER systems are offered.

Molecular hydrogen (H₂), a clean-burning and energy-dense fuel source, has been widely discussed as an attractive way to store intermittent energy from solar and wind through water electrolysis (1, 2). Current commercial electrolyzers can be separated into two categories based on their operating pH. The first are acidic polymer electrolyte membrane electrolyzers that work best with rare and expensive platinum-based electrocatalysts for the hydrogen evolution reaction (HER) (3). The second are strongly alkaline electrolyzers that suffer from caustic basic reaction conditions (4). Neutral pH conditions with inexpensive catalysts composed of Earth-abundant elements are a target for practical solar-to-hydrogen fuel devices due to lower cost and fewer safety concerns (5), but achieving fast rates with mild overpotentials under neutral conditions remains a challenge (6–12). In the pH range from 5 to 9, the electrocatalytic activity of platinum (Pt) itself does not conform to the expected thermodynamic potential shift with pH dependence of −59 mV/pH (13). This is due to the low concentration of the hydronium ion in this pH range and a transition to water as the primary reactant, which has a higher thermodynamic requirement for hydrogen evolution (13). Studies of electrocatalysts using buffers to maintain the pH in this range and ionic salts such as potassium chloride (KCl) to provide ionic strength to ensure high solution conductivity have shown that the buffer can aid the HER activity, presumably by acting as a proton donor (6, 14–18). To extend the scope of water-soluble electrocatalysts, biopolymers and bioinspired metallopolymer catalysts have also been studied (7, 12, 17–26). Bren and coworkers recently reported particularly enlightening studies of the effects of buffer pK_a and structure on the mechanism of the hydrogen evolution reaction for cobalt minienzymes (17, 18).We recently reported a new metallopolymer catalyst system built around a customized [2Fe-2S] catalyst site with a bridging aryldithiolato ligand which exhibits remarkable catalytic activity, air stability, and chemical stability (21). The electrocatalytic mechanism of the [2Fe-2S] catalysts with aryldithiolato ligands is known from previous studies and these catalysts operate at rates of 10⁵ s⁻¹ and faster (27–30). The readily synthesized and water-soluble metallopolymer composed of tertiary amine side-chain groups, PDMAEMA-g-[2Fe-2S] (Fig. 1), approached the current density of Pt operating in neutral water under the same conditions and matched the Faradaic yield (97 ± 3%) (21). Although the detailed structural and mechanistic causality of these profound improvements for these metallopolymer electrocatalysts remain subjects of study, the nature of this molecular system is ideal for studying solution effects on the HER reaction at neutral pH for complexes that are normally insoluble in water. In the course of characterizing these electrocatalysts, solutions containing tris(hydroxymethyl)aminomethane (TRIS) at pH 7 were discovered to be exceptionally advantageous to the catalytic rate. In contrast to the few previous studies of TRIS buffer with electrocatalysts (14, 15, 18), we utilized TRIS at a high concentration. At pH 7, TRIS is sufficiently in the cationic protonated form that additional electrolyte such as KCl is not needed for conductance. This important distinction from conventional studies allows TRIS to simultaneously play the roles of pH buffer, proton source, and sole electrolyte. There is precedence in employing buffers in a manner in which they are the sole electrolyte (7, 31–34). Referring to such species simply as a “buffer” or as an “electrolyte” is inadequate in representing the three functions including proton source. For the purposes of this paper we term a species that serves all three functions a protic buffer electrolyte (PBE). In the following discussion, a TRIS PBE solution is one in which [TRIS-H]⁺Cl⁻ is the sole electrolyte and the cation is a proton source, and a sodium phosphate PBE solution is one in which Na⁺[H₂PO₄]⁻ is the sole electrolyte and the anion is a proton source.Open in a separate windowFig. 1.(A) Depiction of the 2e⁻ electrocatalytic HER with POEGMA-g-[2Fe-2S] and/or PDMAEMA-g-[2Fe-2S] metallopolymers using TRIS or sodium phosphate protic buffer electrolytes at pH 7. (B) Image of POEGMA-g-[2Fe-2S] with MW = 14,216 grown in silico. The [2Fe-2S] active site is in the center of the polymer, blue represents the polymer backbone, and the rest are the oligo(ethylene glycol) side chains. See SI Appendix for the details of modeling and a larger image.One of the key unanswered questions for these new catalyst systems is whether the metallopolymer composition (i.e., amine side-chain groups) or the PBEs are more important to afford this outstanding catalytic activity. Herein we study the effects of PBEs by comparing the HER performances of a standard platinum catalyst and a [2Fe-2S] metallopolymer catalyst in TRIS PBE solutions, sodium phosphate PBE solutions, and a KCl electrolyte solution without a PBE. For this study, nonionic water-soluble metallopolymers were used, which were made using oligo(ethylene glycol) side-chain groups on the polymer to avoid the possibility of contributing effects of the protonated amino groups of PDMAEMA-g-[2Fe-2S] referred to earlier. The metallopolymer catalyst used in this work is designated as POEGMA-g-[2Fe-2S] (Fig. 1). We previously reported that this water-soluble metallopolymer was largely inactive for H₂ electrocatalysis at neutral pH in phosphate buffer (22). The current findings suggest that the use of electrolytes composed of inexpensive cationic organic proton donors can be readily applied to any homogeneous or heterogeneous electrocatalyst system as a facile means to enhance HER activity.     

Dimensions of invasiveness: Links between local abundance,geographic range size,and habitat breadth in Europe’s alien and native floras

Understanding drivers of success for alien species can inform on potential future invasions. Recent conceptual advances highlight that species may achieve invasiveness via performance along at least three distinct dimensions: 1) local abundance, 2) geographic range size, and 3) habitat breadth in naturalized distributions. Associations among these dimensions and the factors that determine success in each have yet to be assessed at large geographic scales. Here, we combine data from over one million vegetation plots covering the extent of Europe and its habitat diversity with databases on species’ distributions, traits, and historical origins to provide a comprehensive assessment of invasiveness dimensions for the European alien seed plant flora. Invasiveness dimensions are linked in alien distributions, leading to a continuum from overall poor invaders to super invaders—abundant, widespread aliens that invade diverse habitats. This pattern echoes relationships among analogous dimensions measured for native European species. Success along invasiveness dimensions was associated with details of alien species’ introduction histories: earlier introduction dates were positively associated with all three dimensions, and consistent with theory-based expectations, species originating from other continents, particularly acquisitive growth strategists, were among the most successful invaders in Europe. Despite general correlations among invasiveness dimensions, we identified habitats and traits associated with atypical patterns of success in only one or two dimensions—for example, the role of disturbed habitats in facilitating widespread specialists. We conclude that considering invasiveness within a multidimensional framework can provide insights into invasion processes while also informing general understanding of the dynamics of species distributions.

Human socioeconomic activities are altering species’ global distributions, bridging natural dispersal barriers through the accidental and intentional relocation of organisms, and opening opportunities for them to expand into new regions beyond their historic native ranges (1). The outcome of any given introduction event, however, is dependent on ecological and stochastic processes, and many introduced alien species fail to establish and persist (2, 3). Even species that do achieve persistent, self-sustaining populations (i.e., become naturalized sensu ref. 4) show varying degrees of success (i.e., invasiveness) in newly occupied regions. This has been true for natural colonization events throughout Earth’s history [e.g., on islands (5, 6) and during continental biotic interchanges (7–9)] and is certainly the case for the ongoing surge of human-mediated introductions (10–12). Disentangling the factors that lead to invasion success provides an opportunity not only for anticipating and mediating future anthropogenic invasions but also for better understanding the dynamics underlying natural range expansions (13).Quantifying a species’ success in invading the alien range is complex, a fact reflected in the diverse criteria applied by different authorities when deciding whether or not to classify naturalized species as invasive (14). Recent efforts have therefore recognized that invasiveness cannot be captured by a single metric but rather encompasses multiple aspects of ecological success and impact (15, 16). Some proposed metrics, such as spread rate and socioeconomic impacts, are difficult to quantify for large numbers of species (4, 17). However, Rabinowitz’s three-dimensional scheme for characterizing the rarity or commonness of species in their native distributions (18, 19) has been successfully co-opted as a valuable perspective for better understanding the success of alien species (16, 20, 21). Applied in the context of introduced species, this framework recognizes the potential for established aliens to vary along at least three demographic dimensions of invasiveness: 1) in local abundance within the naturalized range, 2) in geographic range size or extent of the naturalized range, and 3) in habitat breadth in the naturalized range (16). We subsequently distinguish these metrics as dimensions of invasiveness when measured in the naturalized distributions of alien species and dimensions of commonness when measured in species native distributions.Considering invasiveness within a multidimensional framework is particularly important if species vary independently among different dimensions (16, 21). Such a scenario opens the possibility for aliens to achieve invasion success in many different ways (Fig. 1). In other words, there could exist different forms of invasiveness, similar to the different forms of rarity or commonness originally proposed by Rabinowitz (19). On the other hand, theoretical concepts and empirical examples suggest correlations between Rabinowitz’s dimensions of commonness among species in their native distributions (6, 22, 23). For example, a positive relationship between local abundance and extent of geographic occurrence or range size has been documented at various scales for numerous taxa (24–26), including plants (24, 27–31), with niche breadth proposed as a linking mechanism (24, 26, 32). If the processes that generate these patterns in native distributions act similarly in species alien distributions, some of the forms of invasiveness outlined in Fig. 1 should be less likely to occur than others. More specifically, if the invasiveness dimensions are correlated, species should vary from excelling (abundant, widespread, generalists; form AWG in Fig. 1) to performing poorly (scarce, restricted, specialists; form 0 in Fig. 1) in all three invasiveness dimensions (33). On the other hand, these macroecological patterns are not without exception, and a recent assessment found little support for correlations among commonness dimensions in Europe’s native flora (34). Alien distributions may further differ because aliens vary in their residence time, and particularly recently introduced species may be in disequilibrium and still increasing along one or more of the invasiveness dimensions (21, 35–37). In line with these alternatives, a continuum from overall poor invaders to species succeeding in all three dimensions has been documented for the regional alien flora of French grassland communities (20), while associations among dimensions were found to be low for the herbaceous alien flora of Southeast Australia (16). The correspondence among different invasiveness dimensions at broader geographic scales has yet to be assessed.Open in a separate windowFig. 1.Conceptual diagram outlining the eight different forms of invasiveness depending on success in zero, one, two, or three dimensions of invasiveness (based on refs. 16, 18, and 20). Forms of invasiveness within the cyan polygon are associated with high naturalized abundance, within the magenta polygon with widespread naturalized geographic extent, and within the yellow polygon with high naturalized habitat breadth. The overlap between magenta and cyan is blue, between cyan and yellow is green, between magenta and yellow is red, and between all three is black. The forms of invasiveness are comparable to analogous forms of commonness used to describe species in their native distributions, and we refer to the same abbreviations in both cases.Functional traits play a role in mediating invasion processes, but efforts to identify characteristics of successful invaders have generally resulted in few or inconsistent associations (38, 39). However, distinguishing between different components of invasiveness may provide additional clarity if each is influenced by different traits or if the same trait has contrasting effects on different dimensions (15, 16, 21, 40, 41). For example, many plant traits are associated with general trade-offs between rapid growth (i.e., acquisitive growth strategies) versus stress tolerance and survival (i.e., conservative growth strategies) (42–44), and one can hypothesize scenarios where these divergent strategies are associated with success in different dimensions of invasiveness (40, 41). Another example are specialized adaptations for long-distance dispersal that may promote rapid range expansion, both in extent and into new habitats, but likely do not provide any advantages that would influence local abundances (45, 46). For habitat specialists, their specific habitat associations may additionally be important for determining whether or not they become widespread (31).A number of hypotheses for invasion success additionally emphasizes the importance of unique ecological dynamics that emerge when species are decoupled from constraints experienced in their native environments (47). For example, because species are able to occupy unfilled niches where introduced [i.e., Darwin’s naturalization hypothesis (48, 49)] or because they leave behind important herbivores, competitors, or pathogens that limit populations in the native distribution [i.e., enemy release (50, 51)]. These mechanisms may be less likely when species expand into areas near the native range, for example, during natural range expansions or intracontinental introductions, as the alien individuals are more likely to encounter conditions similar to those that limited their native distribution compared to species introduced from further abroad (e.g., those with extracontinental origins) (52–54).Here, we combine vegetation plot data covering Europe (55) with databases of alien and native distributions (56, 57), plant traits (58, 59), and historical dates of introduction (60) to provide a comprehensive assessment of multidimensional invasion success for the European alien seed plant flora. First, we test for correlations among local abundance, geographic extent, and habitat breadth of alien species in their naturalized distributions and classify species into one of the eight forms of invasiveness (Fig. 1). We ask whether some forms of invasiveness rarely occur and specifically whether species tend to fit along a continuum ranging from generally poor invaders to super invaders—species excelling in all three dimensions. In addition, we compare relationships among dimensions of invasiveness to those among dimensions of commonness measured for Europe’s native flora, assessing similarities and differences in patterns of distribution between contexts. Next, we explore likely drivers of each invasiveness dimension, testing whether the year of first alien occurrence in Europe, functional traits related to ecological strategies, specialized adaptations for long-distance dispersal, habitat associations, and region of origin explain different forms of invasion success.     

From the Cover: Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China

The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U–Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS ¹⁴C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS ¹⁴C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.

The fossil record suggests that Homo sapiens had evolved in Africa by 315,000 y ago (315 ka) (1), spread into West Asia before 177 ka (2), but disappeared and were seemingly replaced by Homo neanderthalensis until ca. 75 to 55 ka (3, 4). A second and final excursion from Africa by so-called anatomically modern humans (AMHs) occurred soon after and broadly coincides with the extinction of the last archaic hominins, ca. 40 to 30 ka (5, 6). This dispersal involved the ancestors of all present-day non-Africans and according to molecular data occurred ca. 65 to 45 ka (7, 8). Additional support for this “late dispersal” theory is provided by the geographical structure of contemporary DNA lineages with all non-Africans closely related to present-day and ancient eastern African populations (9, 10), as well as a clinal pattern of decreasing diversity from Africa to Eurasia, the signature of serial founder effect (10–12). Corroboration has also been provided by the estimated split time between western and eastern Eurasians of ca. 47 to 42 ka as determined by ancient DNA (aDNA) from the 46,880 to 43,210 cal y B.P. (calendar year before present, i.e., before AD1950) Ust’-Ishim femur (western Siberia, Russian Federation) and the 42,000 to 39,000 cal B.P. Tianyuan skeleton (Northeast China) (13–15). Finally, the upper age boundary for this dispersal is set by interbreeding between early AMHs and the Neanderthals estimated to have occurred ca. 65 to 47 ka and the ancestors of New Guineans with the Denisovans ca. 46 ka and again ca. 30 ka (13, 16–19).In contrast, some paleoanthropologists have suggested that AMHs settled mainland East Asia much earlier, within the period of ca. 120 to 70 ka, in accordance with the “early dispersal” theory. This model is based largely upon the dating of isolated human teeth recovered at Huanglong, Luna, and Fuyan caves and a partial mandible from Zhirendong in southern China (20–24). Yet several researchers have raised questions about these and other sites on the basis of uncertainties surrounding the identification of some of them as AMHs, relationships between human remains and dated materials, or limited information available about their depositional context and dating (25–27).Here, we describe the results of an investigation of the arrival time of AMHs in southern China at five apparent early AMH cave localities involving aDNA analyses of human teeth and the dating of flowstones, sediments, fossil remains, and charcoal. The five localities we studied are the following:

• 1)Huanglong cave, located about 25 km from the town of Yunxi, northern Hubei Province (Fig. 1). Excavations by the Hubei Provincial Institute of Cultural Relics and Archaeology during three field seasons from 2004 to 2006 provided a rich mammal record, comprising 91 taxa and representing a Middle to Late Pleistocene Ailuropoda-Stegodon fauna, stone artifacts, and seven AMH teeth dated indirectly with U–Th dating on thin flowstone formations ca. 101 to 81 ka (20).Open in a separate windowFig. 1.(A) Geographical location of Huanglong Cave (1), Luna Cave (2), Fuyan Cave (3), Yangjiapo Cave (4), and Sanyou Cave (5). (B) Human remains from three localities: Yangjiapo Cave (i), Sanyou Cave (ii), and Fuyan Cave (iii). b = buccal, d = distal, l = lingual, m = mesial, and o = occlusal).
• 2)Luna cave, situated in the karst mountains of the southeastern part of the Bubing basin, Guangxi Zhuang Autonomous Region (Fig. 1). A small sample of mammal fossils (Ailuropoda-Stegodon assemblage), stone artifacts, and two AMH teeth were recovered during excavations by the Natural History Museum of Guangxi Autonomous Region in 2004 and 2008. They have since been dated indirectly through U–Th dating of flowstone in the range ca. 127 to 70 ka (21).
• 3)Fuyan cave, located in Daoxian County, Hunan Province (Fig. 1). Excavations from 2011 to 2013 resulted in a large sample of mammal fossils (Ailuropoda-Stegodon faunal group) and 47 AMH teeth but no associated artifacts (22). They have been dated indirectly using U–Th dating of flowstone within the range ca. 120 to 80 ka (22). Two additional (in situ) AMH teeth, stratigraphically associated with the original finds, were recovered by us during field investigations at the site during early 2019.
• 4)Yangjiapo Cave is a large karstic chamber located in Jianshi County (Fig. 1). It was excavated during 2004 by the Hubei Provincial Institute of Cultural Relics and Archeology and yielded 11 AMH teeth found in association with the fragmentary bones of 80 species belonging to an Ailuropoda-Stegodon fauna, implying it should be of similar age to Huanglong, Luna, and Fuyan caves. No stone artifacts or other cultural remains were found.
• 5)Sanyou Cave is a small chamber within a limestone hill at the confluence of the Yangtze River and Xiling Gorge, close to Yichang city, Hubei Province (Fig. 1). A small excavation was undertaken in 1986 by the Yichang Museum and led to the recovery of a possible Late Pleistocene age partial AMH cranial vault (Fig. 1).

     

Drivers of fatal bird collisions in an urban center

Millions of nocturnally migrating birds die each year from collisions with built structures, especially brightly illuminated buildings and communication towers. Reducing this source of mortality requires knowledge of important behavioral, meteorological, and anthropogenic factors, yet we lack an understanding of the interacting roles of migration, artificial lighting, and weather conditions in causing fatal bird collisions. Using two decades of collision surveys and concurrent weather and migration measures, we model numbers of collisions occurring at a large urban building in Chicago. We find that the magnitude of nocturnal bird migration, building light output, and wind conditions are the most important predictors of fatal collisions. The greatest mortality occurred when the building was brightly lit during large nocturnal migration events and when winds concentrated birds along the Chicago lakeshore. We estimate that halving lighted window area decreases collision counts by 11× in spring and 6× in fall. Bird mortality could be reduced by ∼60% at this site by decreasing lighted window area to minimum levels historically recorded. Our study provides strong support for a relationship between nocturnal migration magnitude and urban bird mortality, mediated by light pollution and local atmospheric conditions. Although our research focuses on a single site, our findings have global implications for reducing or eliminating a critically important cause of bird mortality.

North America has lost nearly one-third of its birdlife in the last half-century, with migratory species experiencing particularly acute declines (1). Fatal collisions with built structures represent a major source of direct, human-caused bird mortality across North America, second only to predation by domestic cats (2). Estimates indicate that between 365 million and 988 million birds die annually in collisions with buildings in the United States, with another 16 million to 42 million annual deaths in Canada (2, 3). Birds may collide with glass windows because they reflect the surrounding environment or allow birds to perceive a seemingly open pathway to the interior of the building (4). For the billions of birds that migrate at night, outdoor lighting (e.g., streetlights and floodlights) and interior lighting from buildings may be disorienting and draw birds into built-up areas, at high risk to collide with infrastructure (5–8). Light pollution not only alters nocturnal migratory behavior on a large scale (5, 7), but is also an acute conservation concern. Nocturnal collisions with well-lit communication towers alone are estimated to kill appreciable percentages of the populations of sensitive species (9).Avian collisions with lighted structures have been documented in the scientific literature as early as the 19th century (10–12). In recent decades, this link between collisions and light pollution has been the subject of detailed investigation (8, 13–16). Observers of bird–building collisions and tower kills have long remarked on the apparent influence of meteorological factors such as cloud ceiling, fog, frontal passage, and abrupt changes in conditions, all of which have been associated with large mortality events (10, 13, 17–24). Steady-burning lights may be particularly hazardous (25). Due to high building density and intensity of artificial lighting, cities are of particular concern. Reports of mass collisions at lighted buildings in urban areas are frequent in both the popular and scientific press (13, 19–21, 26).Understanding, predicting, and preventing collision mortality are areas of active scientific inquiry and priorities for policymakers (1, 13). Collisions occur more frequently during migration seasons and impact numerous species of migratory birds (29), and recent work suggests that nocturnal migratory movements can be useful for predicting bird–window collisions (30). Lights-out programs, which encourage the public to extinguish outdoor lighting to protect migratory birds, are receiving increasing attention (13). The act of extinguishing lighting allows birds to immediately return to normal, safe behavior (7) and reduces mortality at lighted buildings (13). Presently, advisories are generally issued for a given time period (e.g., peak migration periods) or on specific nights when weather conditions are favorable for large migratory movements [e.g., using migration forecasting, (31, 32)].Here, we integrate meteorological, migration-intensity, and window-radiance data to understand how these factors interact to cause bird collisions. We use a 21-y dataset of fatal collisions recorded at a single large building (McCormick Place Lakeside Center) in Chicago, IL (Fig. 1), to understand the behavioral, environmental, and anthropogenic drivers of these mortality events. Chicago poses the greatest potential risk from light pollution to migrating birds of all cities in the United States (33), and over 40,000 dead birds have been recovered from McCormick Place alone since 1978 (Figs. 2 and ​and3).3). Since 2000, we have recorded the number of birds and the lighting status of each window bay during dawn collision monitoring. Nocturnal lighting at McCormick Place correlates positively with bird collisions in many songbird species (34), but this association has not been quantified in the context of other important factors, including migration intensity and weather conditions. We estimate the effect of window lighting on collision counts and assess how the intensity of nocturnal bird migration mediates this relationship. We also test whether wind and weather conditions may magnify these associations. Finally, we investigate the spatiotemporal scales at which weather and migration data best explain collision mortality, identifying the times of night and areas of airspace associated with these events.Open in a separate windowFig. 1.Location of McCormick Place along the Chicago lakefront. The Lakeside Center building monitored in this study is highlighted in red in a three-dimensional rendering.Open in a separate windowFig. 2.Summary of collisions recorded at McCormick Place and regional bird migration between 2000 and 2020. (Upper) Individual years are drawn in different colors. Dates are given for mortality events totaling more than 50 birds. Pie charts show the family (fam.) composition of collected birds, with families representing less than 5% of total collisions merged into a single “other” category. (Lower) Summed annual migration passage at the KLOT radar in estimated number of individual birds (years colored). (Lower, Inset) Summed seasonal passage totals in estimated number of birds crossing a 75-km transect, with each point representing a year. Estimates are based on methods from ref. 35.Open in a separate windowFig. 3.Recorded collisions by year and window lighting. (A) Collisions recorded at McCormick Place between 1982 and 2020 for spring (light gray) and fall (dark gray) seasons. Horizontal lines with numeric labels show average seasonal collision totals before and after the window-lighting regime changed from fully lighted to partially lighted in 1999. The year 1997 is not shown because construction limited access to the site during that year. (B) Mean recorded daily collisions by window-lighting status from 2000 to 2020.