Assessment of battery utilization and energy consumption in the large-scale development of urban electric vehicles

Electrifying transportation in the form of the large-scale development of electric vehicles (EVs) plays a pivotal role in reducing urban atmospheric pollution and alleviating fossil fuel dependence. However, the rising scale of EV deployment is exposing problems that were previously hidden in small-scale EV applications, and the lack of large-scale EV operating data deters relevant explorations. Here, we report several issues related to the battery utilization and energy consumption of urban-scale EVs by connecting three unique datasets of real-world operating states of over 3 million Chinese EVs, operational data, and vehicle feature data. Meanwhile, by incorporating climatic data and EV data outside China, we extend our models to several metropolitan areas worldwide. We find that blindly increasing the battery energy of urban EVs could be detrimental to sustainable development. The impact of changes in the energy consumption of EVs would be exacerbated in large-scale EV utilization, especially during seasonal shifts. For instance, even with a constant monthly driving demand, the average energy consumption of Beijing light-duty EVs would change by up to 21% during winter–spring shifts. Our results may also prove useful for research on battery resources, urban power supply, environmental impacts, and policymaking.

Large-scale electrification of transport is considered an effective solution to decrease the use of petroleum-derived fuels and mitigate the urban accumulation of air pollutants. The global stock of light-duty electric vehicles (LDEVs) exceeded 7.2 million in 2019 (1, 2), and China accounted for the largest share at ∼47%, followed by Europe and the United States. To further boost the electric vehicle (EV) market, numerous jurisdictions have introduced incentives or adopted action plans: China has prolonged subsidies for EVs to 2022 (3); the European Union has provided new tax schemes for electric cars (4); and several regions in the United States and Canada, such as California and Quebec, respectively, have enacted incentives for zero-emission vehicle programs (5, 6). The International Energy Agency indicated that the global EV stock would need to increase to 140 million by 2030 (2) to achieve the goals of existing government policies [the Stated Policies Scenario (7)]. In this context, from 2019 to 2030, the global battery capacity production and electricity demand from EVs would soar ninefold to 1.5 TWh ⋅ y⁻¹ and sixfold to 550 TWh ⋅ y⁻¹, respectively (2, 8). Accordingly, the global demand for the critical metals used in EV batteries, including cobalt, lithium, manganese, and nickel, would increase by 8 to 14 times from 2019 to 2030 (2, 9).The surging demand for battery resources and energy from EVs signifies a need to reassess the real-world battery utilization and energy consumption of urban-scale EVs. Research topics on this front have focused on analyzing the supply risks of battery resources (10–12), battery recycling (13–15), sustainability (16–18), charging planning (19–21), and the impact on urban power grids (22–24). A common and indispensable input of these studies is accurate battery utilization or energy consumption of urban EVs. Meanwhile, since the environmental gains of EVs can only be measured from electricity production processes, the energy consumption of urban EVs is also an important basis for research on emissions (25–28), air pollution (29, 30), and health benefits (31, 32). However, owing to the absence of urban-scale EV operating data, most existing assessments are conducted by relying on macroscopic evaluations or the simulations that are calibrated with aggregate-level parameters (33–35). When applied to large-scale EV applications, these simplifications can lead to nonnegligible biases in the results (36) as they cannot reflect the complexity of driving trajectories and varying battery performance in EV operation. On the other hand, in small-scale EV samples, the overall levels of battery utilization and energy consumption tend to be altered by the special use behavior of individual users. This phenomenon conceals some trends that would otherwise have been evident, such as low battery utilization and seasonal changes in the energy consumption of EVs.In 2016, the National Monitoring and Management Center for New Energy Vehicles was established in China, which serves as the national big data platform for EVs. The center has the only datasets in the world that contain real-time operating data of nationwide EVs (the number of EVs in the datasets exceeded 3 million in 2020). For the EVs in some metropolitan areas in China, such as Beijing and Shanghai, the coverage of the platform can reach up to 80%. The data content primarily includes two parts: dynamic vehicular data (general vehicle status, subsystem operating data, and location data) and static information (metadata and attributes). The temporal and spatial resolutions of the dynamic vehicular data are 1 to 30 s and 1 to 10 m, respectively. This large-scale and high-precision data source of Chinese EVs, coupled with EV datasets outside China, provides unique data support for achieving the large-scale assessments in this work (see Materials and Methods).Here, we present a fact-based assessment of battery utilization and energy consumption in urban-scale EV applications to expose several issues affecting battery resources and the urban power supply. To this end, we combine four types of data: 1) EV operating data, 2) EV operational data describing the fleet types and license plate regions, 3) vehicle feature data providing the specifications of EVs, and 4) climate data providing ambient temperatures in different urban areas (see Materials and Methods). To understand the impact of regional variability, nine metropolitan areas worldwide with large EV markets (37) are selected in this work. Accordingly, we first analyze the changes in battery utilization that are affected by user behavior or limited by current battery technology. We investigate how different fleet types and climatic conditions can affect the battery utilization of urban EVs. We also display the developing trends of battery utilization in urban-scale EV groups under different directions of battery technology improvement. Then, we assess the energy consumption of urban EVs from different perspectives. We observe that in some continental climate regions, the energy consumption of EVs fluctuates greatly in different months because of temperature shifts. These fluctuations and step changes are unfavorable as they can greatly amplify the original daily energy demand of EVs, especially in urban-scale EVs. We show the extent to which this problem can be addressed as EV technology improves. The results demonstrate how often-ignored changes in the battery utilization and energy consumption of urban EVs could affect the resource efficiency of EV batteries and urban power supply.     

First-in-class humanized FSH blocking antibody targets bone and fat

Blocking the action of FSH genetically or pharmacologically in mice reduces body fat, lowers serum cholesterol, and increases bone mass, making an anti-FSH agent a potential therapeutic for three global epidemics: obesity, osteoporosis, and hypercholesterolemia. Here, we report the generation, structure, and function of a first-in-class, fully humanized, epitope-specific FSH blocking antibody with a K_D of 7 nM. Protein thermal shift, molecular dynamics, and fine mapping of the FSH–FSH receptor interface confirm stable binding of the Fab domain to two of five receptor-interacting residues of the FSHβ subunit, which is sufficient to block its interaction with the FSH receptor. In doing so, the humanized antibody profoundly inhibited FSH action in cell-based assays, a prelude to further preclinical and clinical testing.

Obesity and osteoporosis affect nearly 650 million and 200 million people worldwide, respectively (1, 2). Yet the armamentarium for preventing and treating these disorders remains limited, particularly when compared with public health epidemics of a similar magnitude. It has also become increasingly clear that obesity and osteoporosis track together clinically. First, body mass does not protect against bone loss; instead, obesity can be permissive to osteoporosis and a high fracture risk (3, 4). Furthermore, the menopausal transition marks the onset not only of rapid bone loss, but also of visceral obesity and dysregulated energy balance (5–9). These physiologic aberrations have been attributed traditionally to a decline in serum estrogen, although, during the perimenopause—2 to 3 y prior to the last menstrual period—serum estrogen is within the normal range, while FSH levels rise to compensate for reduced ovarian reserve (10–12). In our view, therefore, the early skeletal and metabolic derangements cannot conceivably be explained solely by declining estrogen (13, 14).The past decade has shown that pituitary hormones can act directly on the skeleton and other tissues, a paradigm shift that is in stark contrast to previously held views on their sole regulation of endocrine targets (15–25). We and others have shown that FSH can bypass the ovary to act on G_i-coupled FSH receptors (FSHRs) on osteoclasts to stimulate bone resorption and inhibit bone formation (26, 27). This mechanism, which could underscore the bone loss during early menopause, is testified by the strong correlations between serum FSH, bone turnover, and bone mineral density (7–9, 14, 16, 26). Likewise, activating polymorphisms in the FSHR in postmenopausal women are linked to a high bone turnover and reduced bone mass (27). It therefore made biological and clinical sense to inhibit FSH action during this period to prevent bone loss.Toward this goal, we generated murine polyclonal and monoclonal antibodies to a 13-amino-acid–long binding epitope of FSHβ (28–31). The mouse and human FSHβ epitopes differ by just two amino acids; hence, blocking antibodies to the human epitope showed efficacy in mice (28). The antibodies displayed two sets of actions: they attenuated the loss of bone after ovariectomy by inhibiting bone resorption and stimulating bone formation and displayed profound effects on body composition and energy metabolism (28, 29, 31). Most notably, in a series of contemporaneously reproduced experiments, we (M.Z. and C.J.R.) found that FSH blockade reduced body fat, triggered adipocyte beiging, and increased thermogenesis in models of obesity, notably post ovariectomy and after high-fat diet (29). Our findings have been further confirmed independently by two groups who used a FSHβ–GST fusion protein or tandem repeats of the 13-amino-acid–long FSHβ epitope for studies on bone and fat, respectively (32, 33). Consistent with the mouse data, inhibiting FSH secretion using a GnRH agonist in prostate cancer patients resulted in low body fat compared with orchiectomy, wherein FSH levels are high (34). This interventional clinical trial provides evidence for a therapeutic benefit of reducing FSH levels on body fat in people. There is also new evidence that FSH blockade lowers serum cholesterol (35, 36).Thus, both emerging and validated datasets on the antiobesity, osteoprotective, and lipid-lowering actions of FSH blockade in mice and in humans prompted our current attempt to develop and characterize an array of fully humanized FSH-blocking antibodies for future testing in people. Here, we report that our lead first-in-class humanized antibody, Hu6, and two related molecules, Hu26 and Hu28, bind human FSH with a high affinity (K_Ds <10 nM), block the binding of FSH on the human FSHR, and inhibit FSH action in functional cell-based assays.     

Chemokine CCL5 promotes robust optic nerve regeneration and mediates many of the effects of CNTF gene therapy

Ciliary neurotrophic factor (CNTF) is a leading therapeutic candidate for several ocular diseases and induces optic nerve regeneration in animal models. Paradoxically, however, although CNTF gene therapy promotes extensive regeneration, recombinant CNTF (rCNTF) has little effect. Because intraocular viral vectors induce inflammation, and because CNTF is an immune modulator, we investigated whether CNTF gene therapy acts indirectly through other immune mediators. The beneficial effects of CNTF gene therapy remained unchanged after deleting CNTF receptor alpha (CNTFRα) in retinal ganglion cells (RGCs), the projection neurons of the retina, but were diminished by depleting neutrophils or by genetically suppressing monocyte infiltration. CNTF gene therapy increased expression of C-C motif chemokine ligand 5 (CCL5) in immune cells and retinal glia, and recombinant CCL5 induced extensive axon regeneration. Conversely, CRISPR-mediated knockdown of the cognate receptor (CCR5) in RGCs or treating wild-type mice with a CCR5 antagonist repressed the effects of CNTF gene therapy. Thus, CCL5 is a previously unrecognized, potent activator of optic nerve regeneration and mediates many of the effects of CNTF gene therapy.

Like most pathways in the mature central nervous system (CNS), the optic nerve cannot regenerate once damaged due in part to cell-extrinsic suppressors of axon growth (1, 2) and the low intrinsic growth capacity of adult retinal ganglion cells (RGCs), the projection neurons of the eye (3–5). Consequently, traumatic or ischemic optic nerve injury or degenerative diseases such as glaucoma lead to irreversible visual losses. Experimentally, some degree of regeneration can be induced by intraocular inflammation or growth factors expressed by inflammatory cells (6–10), altering the cell-intrinsic growth potential of RGCs (3–5), enhancing physiological activity (11, 12), chelating free zinc (13, 14), and other manipulations (15–19). However, the extent of regeneration achieved to date remains modest, underlining the need for more effective therapies.Ciliary neurotrophic factor (CNTF) is a leading therapeutic candidate for glaucoma and other ocular diseases (20–23). Activation of the downstream signal transduction cascade requires CNTF to bind to CNTF receptor-α (CNTFRα) (24), which leads to recruitment of glycoprotein 130 (gp130) and leukemia inhibitory factor receptor-β (LIFRβ) to form a tripartite receptor complex (25). CNTFRα anchors to the plasma membrane through a glycosylphosphatidylinositol linkage (26) and can be released and become soluble through phospholipase C-mediated cleavage (27). CNTF has been reported to activate STAT3 phosphorylation in retinal neurons, including RGCs, and to promote survival, but it is unknown whether these effects are mediated by direct action of CNTF on RGCs via CNTFRα (28). Our previous studies showed that CNTF promotes axon outgrowth from neonate RGCs in culture (29) but fails to do so in cultured mature RGCs (8) or in vivo (6). Although some studies report that recombinant CNTF (rCNTF) can promote optic nerve regeneration (20, 30, 31), others find little or no effect unless SOCS3 (suppressor of cytokine signaling-3), an inhibitor of the Jak-STAT pathway, is deleted in RGCs (5, 6, 32). In contrast, multiple studies show that adeno-associated virus (AAV)-mediated expression of CNTF in RGCs induces strong regeneration (33–40). The basis for the discrepant effects of rCNTF and CNTF gene therapy is unknown but is of considerable interest in view of the many promising clinical and preclinical outcomes obtained with CNTF to date.Because intravitreal virus injections induce inflammation (41), we investigated the possibility that CNTF, a known immune modulator (42–44), might act by elevating expression of other immune-derived factors. We report here that the beneficial effects of CNTF gene therapy in fact require immune system activation and elevation of C-C motif chemokine ligand 5 (CCL5). Depletion of neutrophils, global knockout (KO) or RGC-selective deletion of the CCL5 receptor CCR5, or a CCR5 antagonist all suppress the effects of CNTF gene therapy, whereas recombinant CCL5 (rCCL5) promotes axon regeneration and increases RGC survival. These studies point to CCL5 as a potent monotherapy for optic nerve regeneration and to the possibility that other applications of CNTF and other forms of gene therapy might similarly act indirectly through other factors.     

Improved bounds on entropy production in living systems

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Thermodynamic laws place fundamental limits on the efficiency and fitness of living systems (1, 2). To maintain cellular order and perform essential biological functions such as sensing (3–6), signaling (7), replication (8, 9) or locomotion (10), organisms consume energy and dissipate heat. In doing so, they increase the entropy of their environment (2), in agreement with the second law of thermodynamics (11). Obtaining reliable estimates for the energy consumption and entropy production in living matter holds the key to understanding the physical boundaries (12–14) that constrain the range of theoretically and practically possible biological processes (3). Recent experimental (6, 15, 16) and theoretical (17–20) advances in the imaging and modeling of cellular and subcellular dynamics have provided groundbreaking insights into the thermodynamic efficiency of molecular motors (14, 21), biochemical signaling (16, 22, 23) and reaction (24) networks, and replication (9) and adaption (25) phenomena. Despite such major progress, however, it is also known that the currently available entropy production estimators (26, 27) can fail under experimentally relevant conditions, especially when only a small set of observables is experimentally accessible or nonequilibrium transport currents (28–30) vanish.To help overcome these limitations, we introduce here a generic optimization framework that can produce significantly improved bounds on the entropy production in living systems. We will prove that these bounds are optimal given certain measurable statistics. From a practical perspective, our method requires observations of only a few coarse-grained state variables of an otherwise hidden Markovian network. We demonstrate the practical usefulness by determining improved entropy production bounds for bacterial flagella motors (10, 31), growing microtubules (32, 33), and calcium oscillations (7, 34) in human embryonic kidney cells.Generally, entropy production rates can be estimated from the time series of stochastic observables (35). Thermal equilibrium systems obey the principle of detailed balance, which means that every forward trajectory is as likely to be observed as its time reversed counterpart, neutralizing the arrow of time (36). By contrast, living organisms operate far from equilibrium, which means that the balance between forward and reversed trajectories is broken and net fluxes may arise (1, 37–39). When all microscopic details of a nonequilibrium system are known, one can measure the rate of entropy production by comparing the likelihoods of forward and reversed trajectories in sufficiently large data samples (35, 36). However, in most if not all biophysical experiments, many degrees of freedom remain hidden to the observer, demanding methods (28, 40, 41) that do not require complete knowledge of the system. A powerful alternative is provided by thermodynamic uncertainty relations (TURs), which use the mean and variance of steady-state currents to bound entropy production rates (18, 19, 26, 42–48). Although highly useful when currents can be measured (44–47), or when the system can be externally manipulated (40, 49), these methods give, by construction, trivial zero bounds for current-free nonequilibrium systems, such as driven one-dimensional (1D) nonperiodic oscillators. In the absence of currents, potential asymmetries in the forward and reverse trajectories can still be exploited to bound the entropy production rate (29, 30, 50), but to our knowledge no existing method is capable of producing nonzero bounds when forward and reverse trajectories are statistically identical. Moreover, even though previous bounds can become tight in some cases (51), optimal entropy production estimators for nonequilibrium systems are in general unknown.To obtain bounds that are provably optimal under reasonable conditions on the available data, we reformulate the problem here within an optimization framework. Formally, we consider any steady-state Markovian dynamics for which only coarse-grained variables are observable, where these observables may appear non-Markovian. We then search over all possible underlying Markovian systems to identify the one which minimizes the entropy production rate while obeying the observed statistics. More specifically, our algorithmic implementation leverages information about successive transitions, allowing us to discover nonzero bounds on entropy production even when the coarse-grained statistics appear time symmetric. We demonstrate this for both synthetic test data and experimental data (52) for flagella motors. Subsequently, we consider the entropy production of microtubules (33), which slowly grow before rapidly shrinking in steady state, to show how refined coarse graining in space and time leads to improved bounds. The final application to calcium oscillations in human embryonic kidney cells (34) illustrates how external stimulation with drugs can increase entropy production.     

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

In the open ocean, elevated carbon flux (ECF) events increase the delivery of particulate carbon from surface waters to the seafloor by severalfold compared to other times of year. Since microbes play central roles in primary production and sinking particle formation, they contribute greatly to carbon export to the deep sea. Few studies, however, have quantitatively linked ECF events with the specific microbial assemblages that drive them. Here, we identify key microbial taxa and functional traits on deep-sea sinking particles that correlate positively with ECF events. Microbes enriched on sinking particles in summer ECF events included symbiotic and free-living diazotrophic cyanobacteria, rhizosolenid diatoms, phototrophic and heterotrophic protists, and photoheterotrophic and copiotrophic bacteria. Particle-attached bacteria reaching the abyss during summer ECF events encoded metabolic pathways reflecting their surface water origins, including oxygenic and aerobic anoxygenic photosynthesis, nitrogen fixation, and proteorhodopsin-based photoheterotrophy. The abundances of some deep-sea bacteria also correlated positively with summer ECF events, suggesting rapid bathypelagic responses to elevated organic matter inputs. Biota enriched on sinking particles during a spring ECF event were distinct from those found in summer, and included rhizaria, copepods, fungi, and different bacterial taxa. At other times over our 3-y study, mid- and deep-water particle colonization, predation, degradation, and repackaging (by deep-sea bacteria, protists, and animals) appeared to shape the biotic composition of particles reaching the abyss. Our analyses reveal key microbial players and biological processes involved in particle formation, rapid export, and consumption, that may influence the ocean’s biological pump and help sustain deep-sea ecosystems.

As a central component of the ocean’s biological carbon pump (1–5), sinking particles mediate the export of photosynthetically derived organic matter, and the transport of carbon and energy to abyssal depths. At the open ocean time-series study site Station ALOHA (6, 7) in the North Pacific Subtropical Gyre (NPSG), prominent summertime elevated carbon flux (ECF) events called the “summer export pulse” (SEP) (8) typically occur from July through August. These summer ECF events, referred to henceforth as the SEP, are defined as those periods when summertime particulate carbon flux at 4,000 m exceeds the mean annual flux by 150% or more (8). Time-series measurements of particulate carbon, nitrogen, phosphorus, and silica flux have provided a long-term record of the amounts of carbon and nutrients reaching cold, well-oxygenated abyssal waters (8). These data also provide estimates of the amount of carbon sequestered in the deep ocean in the form of sinking particulate material that has escaped remineralization in the upper water column. Despite these critical datasets, the biological origins and composition of sinking particles, especially during periods of elevated flux, are less well known.Historically, sinking particle-associated biota have been characterized and quantified in sediment trap collected samples via light microscopy (9, 10), or analyses of organic biomarkers like carotenoids or other photosynthetic pigments (11). Shell-bearing organisms like coccolithophorids, diatoms, tintinnids, foraminifera, radiolarians, or pelagic mollusk shells are the most readily identified by microscopic techniques (12). This approach cannot identify most microorganisms (including smaller protists, fungi, archaea, and bacteria), or soft-bodied pelagic metazoans like siphonophores or other hydrozoans. Additionally, the mineral-containing shells of some common pelagic organisms (like the aragonite shells of pteropods, or the strontium sulfate tests of Acantharea) dissolve at depths exceeding 1,000 m and so are difficult to quantify in deeper sediment traps (13, 14). New in situ optical techniques for identifying and quantifying sinking organisms have also been recently developed (15, 16), but these too suffer from the same difficulties encountered using traditional light microscopy. As a consequence, few comprehensive inventories of sinking particle-associated biota currently exist.Recent studies are now beginning to apply nucleic acid-based taxonomic and genomic analyses to characterize particle-associated microorganisms. A few of these studies have used serial filtration of seawater to identify microbial taxa found in different particle size fractions (17–21). However, these approaches cannot identify or differentiate sinking from suspended particles (22). One approach to address this challenge employs large volume settling chambers, which can separate and differentiate suspended from sinking particles in seawater (22). Other oceanographic tools, like sediment traps that capture sinking particles in situ (23), are also being coupled with gene-based taxonomic analyses to determine the composition and variability of sinking particle-associated microbiota (22, 24–31). Different methods to preserve cells and nucleic acids in situ have been developed, including the use of non–cross-linking, precipitative fixatives (27, 29, 32) or poisons like mercuric chloride (31). These approaches have been leveraged to characterize microbial assemblages found on sinking particles and those responsible for particle degradation, using paired sediment traps deployed with or without preservatives (25, 27, 28, 33).Despite great progress, few quantitative studies have linked elevated carbon flux events with their corresponding sinking particle-associated organisms reaching the deep ocean. In a recent sediment trap study off the California coast, Preston et al. (30) found that a single diatom species was associated with a bloom that led to elevated carbon flux to the abyss. A recent global ocean biogeographic survey of microbial metagenomes (from seawater sampled on filters) used optically estimated carbon flux at 150 m to infer associations of microorganisms with carbon flux (15). Another previous report, documenting the SEP events in the NPSG over several decades, postulated the involvement of diatom–diazotroph associations based on 1 y of biological data (8). Although a subsequent 1-y metagenomic study of sinking particle-associated microbes was conducted in 2014 in the NPSG (29), no elevated carbon flux events occurred that year, so no conclusions about SEP events could be inferred (29).To better characterize the organisms and biological processes associated with ECF events in the NPSG, we conducted a 3-y metagenomic time-series study (21 time points per year) of particles sinking to abyssal depths (4,000 m) in the open ocean. We identified specific microbial populations whose abundances positively correlated with elevated carbon flux to the abyss. The temporal variability of carbon flux correlating microorganisms was analyzed, and distinguishing genomic features and inferred traits of sinking particle associated microbes were characterized. Our analyses provide perspective on microbial components and dynamics associated with the open ocean biological pump and inferred biological processes and variability associated with carbon transport to the deep ocean.     

Circular swimming motility and disordered hyperuniform state in an algae system

Active matter comprises individually driven units that convert locally stored energy into mechanical motion. Interactions between driven units lead to a variety of nonequilibrium collective phenomena in active matter. One of such phenomena is anomalously large density fluctuations, which have been observed in both experiments and theories. Here we show that, on the contrary, density fluctuations in active matter can also be greatly suppressed. Our experiments are carried out with marine algae (Effrenium voratum), which swim in circles at the air–liquid interfaces with two different eukaryotic flagella. Cell swimming generates fluid flow that leads to effective repulsions between cells in the far field. The long-range nature of such repulsive interactions suppresses density fluctuations and generates disordered hyperuniform states under a wide range of density conditions. Emergence of hyperuniformity and associated scaling exponent are quantitatively reproduced in a numerical model whose main ingredients are effective hydrodynamic interactions and uncorrelated random cell motion. Our results demonstrate the existence of disordered hyperuniform states in active matter and suggest the possibility of using hydrodynamic flow for self-assembly in active matter.

Active matter exists over a wide range of spatial and temporal scales (1–6) from animal groups (7, 8) to robot swarms (9–11), to cell colonies and tissues (12–16), to cytoskeletal extracts (17–20), to man-made microswimmers (21–25). Constituent particles in active matter systems are driven out of thermal equilibrium at the individual level; they interact to develop a wealth of intriguing collective phenomena, including clustering (13, 22, 24), flocking (11, 26), swarming (12, 13), spontaneous flow (14, 20), and giant density fluctuations (10, 11). Many of these observed phenomena have been successfully described by particle-based or continuum models (1–6), which highlight the important roles of both individual motility and interparticle interactions in determining system dynamics.Current active matter research focuses primarily on linearly swimming particles which have a symmetric body and self-propel along one of the symmetry axes. However, a perfect alignment between the propulsion direction and body axis is rarely found in reality. Deviation from such a perfect alignment leads to a persistent curvature in the microswimmer trajectories; examples of such circle microswimmers include anisotropic artificial micromotors (27, 28), self-propelled nematic droplets (29, 30), magnetotactic bacteria and Janus particles in rotating external fields (31, 32), Janus particle in viscoelastic medium (33), and sperm and bacteria near interfaces (34, 35). Chiral motility of circle microswimmers, as predicted by theoretical and numerical investigations, can lead to a range of interesting collective phenomena in circular microswimmers, including vortex structures (36, 37), localization in traps (38), enhanced flocking (39), and hyperuniform states (40). However, experimental verifications of these predictions are limited (32, 35), a situation mainly due to the scarcity of suitable experimental systems.Here we address this challenge by investigating marine algae Effrenium voratum (41, 42). At air–liquid interfaces, E. voratum cells swim in circles via two eukaryotic flagella: a transverse flagellum encircling the cellular anteroposterior axis and a longitudinal one running posteriorly. Over a wide range of densities, circling E. voratum cells self-organize into disordered hyperuniform states with suppressed density fluctuations at large length scales. Hyperuniformity (43, 44) has been considered as a new form of material order which leads to novel functionalities (45–49); it has been observed in many systems, including avian photoreceptor patterns (50), amorphous ices (51), amorphous silica (52), ultracold atoms (53), soft matter systems (54–61), and stochastic models (62–64). Our work demonstrates the existence of hyperuniformity in active matter and shows that hydrodynamic interactions can be used to construct hyperuniform states.     

Identifying hydrophobic protein patches to inform protein interaction interfaces

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Protein–protein interactions play a crucial role in numerous biological processes, ranging from signal transduction and immune response to protein aggregation and phase behavior (1–3). Consequently, being able to understand, predict, and modulate protein interactions has important implications for understanding cellular processes and mitigating the progression of disease (4, 5). A necessary first step toward this ambitious goal is uncovering the interfaces through which proteins interact (6–8). In principle, identifying hydrophobic protein regions, which interact weakly with water, should be a promising strategy for uncovering protein interaction interfaces (9, 10). Indeed, the release of weakly interacting hydration waters from hydrophobic regions can drive protein interactions, as well as other aqueous assemblies (11–13). However, even when the structure of a protein is available at atomistic resolution, it is challenging to identify its hydrophobic patches because they are not uniformly nonpolar, but display variations in polarity and charge at the nanoscale. Moreover, the emergent hydrophobicity of a protein patch stems from the collective response of protein hydration waters to the nanoscale chemical and topographical patterns displayed by the patch (14–20) and cannot be captured by simply counting the number of nonpolar groups in the patch, or even through more involved additive approaches, such as hydropathy scales or surface-area models (21–28).To address this challenge, we build upon seminal theoretical advances and molecular simulation studies, which have shown that near a hydrophobic surface, it is easier to disrupt surface–water interactions and form interfacial cavities (29–34). To uncover protein regions that have the weakest interactions with water, here, we employ specialized molecular simulations, wherein protein–water interactions are disrupted by systematically displacing water molecules from the protein hydration shell (35–37). By identifying the protein patches that nucleate cavities most readily in our simulations, we are then able to uncover the most hydrophobic protein regions. Interestingly, we find that both hydrophobic and hydrophilic protein patches are highly heterogeneous and contain comparable numbers of nonpolar and polar atoms. Our results thus highlight the nontrivial relationship between the chemical composition of protein patches and their emergent hydrophobicity (24–26), and further emphasize the importance of accounting for the collective solvent response in characterizing protein hydrophobicity (16). We then interrogate whether the most hydrophobic protein patches, which nucleate cavities readily, are also likely to mediate protein interactions. Across five proteins that participate in either homodimer or heterodimer formation, we find that roughly 60 to 70% of interfacial contacts and only about 10 to 20% of noncontacts nucleate cavities. Our work thus provides a versatile computational framework for characterizing hydrophobicity and uncovering interaction interfaces of not just proteins, but also of other complex amphiphilic solutes, such as cavitands, dendrimers, and patchy nanoparticles (38–41).     

From the Cover: Evidence from South Africa for a protracted end-Permian extinction on land

Earth’s largest biotic crisis occurred during the Permo–Triassic Transition (PTT). On land, this event witnessed a turnover from synapsid- to archosauromorph-dominated assemblages and a restructuring of terrestrial ecosystems. However, understanding extinction patterns has been limited by a lack of high-precision fossil occurrence data to resolve events on submillion-year timescales. We analyzed a unique database of 588 fossil tetrapod specimens from South Africa’s Karoo Basin, spanning ∼4 My, and 13 stratigraphic bin intervals averaging 300,000 y each. Using sample-standardized methods, we characterized faunal assemblage dynamics during the PTT. High regional extinction rates occurred through a protracted interval of ∼1 Ma, initially co-occurring with low origination rates. This resulted in declining diversity up to the acme of extinction near the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary. Regional origination rates increased abruptly above this boundary, co-occurring with high extinction rates to drive rapid turnover and an assemblage of short-lived species symptomatic of ecosystem instability. The “disaster taxon” Lystrosaurus shows a long-term trend of increasing abundance initiated in the latest Permian. Lystrosaurus comprised 54% of all specimens by the onset of mass extinction and 70% in the extinction aftermath. This early Lystrosaurus abundance suggests its expansion was facilitated by environmental changes rather than by ecological opportunity following the extinctions of other species as commonly assumed for disaster taxa. Our findings conservatively place the Karoo extinction interval closer in time, but not coeval with, the more rapid marine event and reveal key differences between the PTT extinctions on land and in the oceans.

Mass extinctions are major perturbations of the biosphere resulting from a wide range of different causes including glaciations and sea level fall (1), large igneous provinces (2), and bolide impacts (3, 4). These events caused permanent changes to Earth’s ecosystems, altering the evolutionary trajectory of life (5). However, links between the broad causal factors of mass extinctions and the biological and ecological disturbances that lead to species extinctions have been difficult to characterize. This is because ecological disturbances unfold on timescales much shorter than the typical resolution of paleontological studies (6), particularly in the terrestrial record (6–8). Coarse-resolution studies have demonstrated key mass extinction phenomena including high extinction rates and lineage turnover (7, 9), changes in species richness (10), ecosystem instability (11), and the occurrence of disaster taxa (12). However, finer time resolutions are central to determining the association and relative timings of these effects, their potential causal factors, and their interrelationships. Achieving these goals represents a key advance in understanding the ecological mechanisms of mass extinctions.The end-Permian mass extinction (ca. 251.9 Ma) was Earth’s largest biotic crisis as measured by taxon last occurrences (13–15). Large outpourings from Siberian Trap volcanism (2) are the likely trigger of calamitous climatic changes, including a runaway greenhouse effect and ocean acidification, which had profound consequences for life on land and in the oceans (16–18). An estimated 81% of marine species (19) and 89% of tetrapod genera became extinct as established Permian ecosystems gave way to those of the Triassic. In the ocean, this included the complete extinction of reef-forming tabulate and rugose corals (20, 21) and significant losses in previously diverse ammonoid, brachiopod, and crinoid families (22). On land, many nonmammalian synapsids became extinct (16), and the glossopterid-dominated floras of Gondwana also disappeared (23). Stratigraphic sequences document a global “coral gap” and “coal gap” (24, 25), suggesting reef and forest ecosystems were rare or absent for up to 5 My after the event (26). Continuous fossil-bearing deposits documenting patterns of turnover across the Permian–Triassic transition (PTT) on land (27) and in the oceans (28) are geographically widespread (29, 30), including marine and continental successions that are known from China (31, 32) and India (33). Continental successions are known from Russia (34), Australia (35), Antarctica (36), and South Africa’s Karoo Basin (Fig. 1 and 37–40), the latter providing arguably the most densely sampled and taxonomically scrutinized (41–43) continental record of the PTT. The main extinction has been proposed to occur at the boundary between two biostratigraphic zones with distinctive faunal assemblages, the Daptocephalus and Lystrosaurus declivis assemblage zones (Fig. 1), which marks the traditional placement of the Permian–Triassic geologic boundary [(37) but see ref. 44]. Considerable research has attempted to understand the anatomy of the PTT in South Africa (38, 39, 45–52) and to place it in the context of biodiversity changes across southern Gondwana (53, 54) and globally (29, 31, 32, 44, 47, 55).Open in a separate windowFig. 1.Map of South Africa depicting the distribution of the four tetrapod fossil assemblage zones (Cistecephalus, Daptocephalus, Lystrosaurus declivis, Cynognathus) and our two study sites where fossils were collected in this study (sites A and B). Regional lithostratigraphy and biostratigraphy within the study interval are shown alongside isotope dilution–thermal ionization mass spectrometry dates retrieved by Rubidge et al., Botha et al., and Gastaldo et al. (37, 44, 80). The traditional (dashed red line) and associated PTB hypotheses for the Karoo Basin (37, 44) are also shown. Although traditionally associated with the PTB, the Daptocephalus–Lystrosaurus declivis Assemblage Zone boundary is defined by first appearances of co-occurring tetrapod assemblages, so its position relative to the three PTB hypotheses is unchanged. The Ripplemead member (*) has yet to be formalized by the South African Committee for Stratigraphy.Decades of research have demonstrated the richness of South Africa’s Karoo Basin fossil record, resulting in hundreds of stratigraphically well-documented tetrapod fossils across the PTT (37, 39, 56). This wealth of data has been used qualitatively to identify three extinction phases and an apparent early postextinction recovery phase (39, 45, 51). Furthermore, studies of Karoo community structure and function have elucidated the potential role of the extinction and subsequent recovery in breaking the incumbency of previously dominant clades, including synapsids (11, 57). Nevertheless, understanding patterns of faunal turnover and recovery during the PTT has been limited by the scarcity of quantitative investigations. Previous quantitative studies used coarsely sampled data (i.e., assemblage zone scale, 2 to 3 Ma time intervals) to identify low species richness immediately after the main extinction, potentially associated with multiple “boom and bust” cycles of primary productivity based on δ¹³C variation during the first 5 My of the Triassic (41, 58). However, many details of faunal dynamics in this interval remain unknown. Here, we investigate the dynamics of this major tetrapod extinction at an unprecedented time resolution (on the order of hundreds of thousands of years), using sample-standardized methods to quantify multiple aspects of regional change across the Cistecephalus, Daptocephalus, and Lystrosaurus declivis assemblage zones.     

Cholinergic suppression of hippocampal sharp-wave ripples impairs working memory

Learning and memory are assumed to be supported by mechanisms that involve cholinergic transmission and hippocampal theta. Using G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) with a fiber-photometric fluorescence readout in mice, we found that cholinergic signaling in the hippocampus increased in parallel with theta/gamma power during walking and REM sleep, while ACh3.0 signal reached a minimum during hippocampal sharp-wave ripples (SPW-R). Unexpectedly, memory performance was impaired in a hippocampus-dependent spontaneous alternation task by selective optogenetic stimulation of medial septal cholinergic neurons when the stimulation was applied in the delay area but not in the central (choice) arm of the maze. Parallel with the decreased performance, optogenetic stimulation decreased the incidence of SPW-Rs. These findings suggest that septo–hippocampal interactions play a task-phase–dependent dual role in the maintenance of memory performance, including not only theta mechanisms but also SPW-Rs.

The neurotransmitter acetylcholine is thought to be critical for hippocampus-dependent declarative memories (1, 2). Reduction in cholinergic neurotransmission, either in Alzheimer’s disease or in experiments with cholinergic antagonists, such as scopolamine, impairs memory function (3–8). Acetylcholine may bring about its beneficial effects on memory encoding by enhancing theta rhythm oscillations, decreasing recurrent excitation, and increasing synaptic plasticity (9–11). Conversely, drugs which activate cholinergic receptors enhance learning and, therefore, are a neuropharmacological target for the treatment of memory deficits in Alzheimer’s disease (5, 12, 13).The contribution of cholinergic mechanisms in the acquisition of long-term memories and the role of the hippocampal–entorhinal–cortical interactions are well supported by experimental data (5, 12, 13). In addition, working memory or “short-term” memory is also supported by the hippocampal–entorhinal–prefrontal cortex (14–16). Working memory in humans is postulated to be a conscious process to “keep things in mind” transiently (16). In rodents, matching to sample task, spontaneous alternation between reward locations, and the radial maze task have been suggested to function as a homolog of working memory [“working memory like” (17)].Cholinergic activity is a critical requirement for working memory (18, 19) and for sustaining theta oscillations (10, 20–22). In support of this contention, theta–gamma coupling and gamma power are significantly higher in the choice arm of the maze, compared with those in the side arms where working memory is no longer needed for correct performance (23–26). It has long been hypothesized that working memory is maintained by persistent firing of neurons, which keep the presented items in a transient store in the prefrontal cortex and hippocampal–entorhinal system (27–31), although the exact mechanisms are debated (32–37). An alternative hypothesis holds that items of working memory are stored in theta-nested gamma cycles (38). Common in these models of working memory is the need for an active, cholinergic system–dependent mechanism (39–41). However, in spontaneous alternation tasks, the animals are not moving continuously during the delay, and theta oscillations are not sustained either. During the immobility epochs, theta is replaced by intermittent sharp-wave ripples (SPW-R), yet memory performance does not deteriorate. On the contrary, artificial blockade of SPW-Rs can impair memory performance (42, 43), and prolongation of SPW-Rs improves performance (44). Under the cholinergic hypothesis of working memory, such a result is unexpected.To address the relationship between cholinergic/theta versus SPW-R mechanism in spontaneous alternation, we used a G protein–coupled receptor-activation–based acetylcholine sensor (GRAB_ACh3.0) (45) to monitor acetylcholine (ACh) activity during memory performance in mice. In addition, we optogenetically enhanced cholinergic tone, which suppresses SPW-Rs by a different mechanism than electrically or optogenetically induced silencing of neurons in the hippocampus (43, 44). We show that cholinergic signaling in the hippocampus increases in parallel with theta power/score during walking and rapid eye movement (REM) sleep and reaches a transient minimum during SPW-Rs. Selective optogenetic stimulation of medial septal cholinergic neurons decreased the incidence of SPW-Rs during non-REM sleep (46–48), as well as during the delay epoch of a working memory task and impaired memory performance. These findings demonstrate that memory performance is supported by complementary theta and SPW-R mechanisms.     

Evolution and global charge conservation for polarization singularities emerging from non-Hermitian degeneracies

Core concepts in singular optics, especially the polarization singularities, have rapidly penetrated the surging fields of topological and non-Hermitian photonics. For open photonic structures with non-Hermitian degeneracies in particular, polarization singularities would inevitably encounter another sweeping concept of Berry phase. Several investigations have discussed, in an inexplicit way, connections between both concepts, hinting at that nonzero topological charges for far-field polarizations on a loop are inextricably linked to its nontrivial Berry phase when degeneracies are enclosed. In this work, we reexamine the seminal photonic crystal slab that supports the fundamental two-level non-Hermitian degeneracies. Regardless of the invariance of nontrivial Berry phase (concerning near-field Bloch modes defined on the momentum torus) for different loops enclosing both degeneracies, we demonstrate that the associated far polarization fields (defined on the momentum sphere) exhibit topologically inequivalent patterns that are characterized by variant topological charges, including even the trivial scenario of zero charge. Moreover, the charge carried by the Fermi arc actually is not well defined, which could be different on opposite bands. It is further revealed that for both bands, the seemingly complex evolutions of polarizations are bounded by the global charge conservation, with extra points of circular polarizations playing indispensable roles. This indicates that although not directly associated with any local charges, the invariant Berry phase is directly linked to the globally conserved charge, physical principles underlying which have all been further clarified by a two-level Hamiltonian with an extra chirality term. Our work can potentially trigger extra explorations beyond photonics connecting Berry phase and singularities.

Pioneered by Pancharatnam, Berry, Nye, and others (1–10), Berry phase and singularities have become embedded languages all across different branches of photonics. Optical Berry phase is largely manifested through either polarization evolving Pancharatnam–Berry phase or the spin-redirection Bortolotti–Rytov–Vladimirskii–Berry phase (2, 4, 5, 11–15); while optical singularities are widely observed as singularities of intensity (caustics) (6), phase (vortices) (7), or polarization (8–10). As singularities for complex vectorial waves, polarization singularities are skeletons of electromagnetic waves and are vitally important for understanding various interference effects underlying many applications (16–20).There is a superficial similarity between the aforementioned two concepts: Both the topological charge of polarization field [Hopf index of line field (21, 22)] and Berry phase are defined on a closed circuit. Despite this, it is quite unfortunate that almost no definite connections have been established between them in optics. This is fully understandable: Berry phase is defined on the Pancharatnam connection (parallel transport) that decides the phase contrast between neighboring states on the loop (3, 4); while the polarization charge reflects accumulated orientation rotations of polarization ellipses, which has no direct relevance to the overall phase of each state. This explains why in pioneering works where both concepts were present (23–27), their interplay was rarely elaborated on.Spurred by studies into bound states in the continuum, polarization singularities have gained enormous renewed interest in open periodic photonic structures, manifested in different morphologies with both fundamental and higher-order half-integer charges (28–50). Simultaneously, the significance of Berry phase has been further reinforced in surging fields of topological and non-Hermitian photonics (1, 23, 26, 51–56). In open periodic structures involving band degeneracies, Berry phase and polarization singularity would inevitably meet, which sparks the influential work on non-Hermitian degeneracy (36) and several other following studies (40, 43, 45) discussing both concepts simultaneously. Although not claimed explicitly, those works hint that nontrivial Berry phase produces nonzero polarization charges.Aiming to bridge Berry phase and polarization singularity, we reexamine the seminal photonic crystal slab (PCS) that supports elementary two-level non-Hermitian degeneracies. It is revealed that with an invariant nontrivial π Berry phase, the corresponding polarization fields on different isofrequency contours enclosing both non-Hermitian degenerate points (or equivalently exceptional points [EPs]) (26) exhibit diverse patterns characterized by different polarization charges, even including the trivial zero charge. It is further revealed that the charge carried by the Fermi arc is actually not well defined, which could be different on opposite bands. We also discover that such complexity of field evolutions is constrained by global charge conservation for both bands, with extra points of circular polarizations (C points) playing pivotal roles. This reveals the explicit connection between globally conserved charge and the invariant Berry phase, underlying which the physical mechanisms have been further clarified by a two-level Hamiltonian with an extra chirality term (25). We show that such an unexpected connection is generically manifest in various structures, despite the fact that Berry phase and polarization charge actually characterize different entities of near-field Bloch modes and their projected far polarization fields, respectively: Bloch modes are defined on the momentum torus and can be folded into the irreducible Brillouin zone; while polarization fields are defined on the momentum sphere, due to the involvement of out-of-plane wave vectors along which there is no periodicity. Our study can spur further investigations in other subjects beyond photonics to explore conceptual interconnectedness, where both the concepts of Berry phase and singularities are present.     

Conditions and extent of volatile loss from the Moon during formation of the Procellarum basin

Rocks from the lunar interior are depleted in moderately volatile elements (MVEs) compared to terrestrial rocks. Most MVEs are also enriched in their heavier isotopes compared to those in terrestrial rocks. Such elemental depletion and heavy isotope enrichments have been attributed to liquid–vapor exchange and vapor loss from the protolunar disk, incomplete accretion of MVEs during condensation of the Moon, and degassing of MVEs during lunar magma ocean crystallization. New Monte Carlo simulation results suggest that the lunar MVE depletion is consistent with evaporative loss at 1,670 ± 129 K and an oxygen fugacity +2.3 ± 2.1 log units above the fayalite-magnetite-quartz buffer. Here, we propose that these chemical and isotopic features could have resulted from the formation of the putative Procellarum basin early in the Moon’s history, during which nearside magma ocean melts would have been exposed at the surface, allowing equilibration with any primitive atmosphere together with MVE loss and isotopic fractionation.

Returned samples of basaltic rocks from the Moon provided evidence decades ago that the Moon is depleted in volatile elements compared to the Earth (1), with lunar basalt abundances of moderately volatile elements (MVEs) being ∼1/5 that of terrestrial basalt abundances for alkali elements and ∼1/40 for other MVE, such as Zn, Ag, In, and Cd (2). The theme of lunar volatiles thus seemed settled. Yet, the unambiguous detection in 2008 of lunar indigenous hydrogen and other volatile elements, such as F, Cl, and S in pyroclastic glasses (3), heralded a new era of research into lunar volatiles, overturning the decades-old paradigm of a bone-dry Moon (e.g., refs. 4 and 5). Here, we define volatile elements as those with 50% condensation temperatures below these of the major rock-forming elements Fe, Mg, and Si (6). This paradigm shift was accompanied by new measurements of volatile stable isotope compositions (e.g., H, C, N, Cl, K, Cr, Cu, Zn, Ga, Rb, and Sn) in a wealth of bulk lunar samples (7–18) and in the mineral phases and melt inclusions they host (19–28). These studies have shown that the stable isotope compositions of most MVEs (e.g., K, Zn, Ga, and Rb) are enriched in their heavier isotopes with respect to the bulk silicate Earth (BSE) (9, 11, 13–15, 17). Such heavy isotope enrichment is associated with elemental depletion, which has been variously attributed to liquid–vapor exchange and vapor loss from the protolunar disk (17, 18), incomplete accretion of MVEs during condensation of the Moon (13, 29, 30), and degassing of these elements during lunar magma ocean crystallization (9, 11, 14, 15, 25, 31). Almost all these hypotheses have typically assumed that the MVE depletions and associated MVE isotope fractionations are relevant to the whole Moon. However, our lunar sample collections are biased, as all Apollo and Luna returned samples come from the lunar nearside from within or around the anomalous Procellarum KREEP Terrane (PKT) region (e.g., ref. 32), where KREEP stands for enriched in K, REEs, and P. Barnes et al. (26) proposed that the heavy Cl isotope signature measured in KREEP-rich Apollo samples resulted from metal-chloride degassing from late-stage lunar magma ocean melts in response to a large crust-breaching impact event, spatially associated with the PKT region, which facilitated exposure of these late-stage melts to the lunar surface. Here, we further investigate whether a localized impact event could have been responsible for the general MVE depletion and heavy MVE isotope enrichment measured in lunar samples.     

Cognitive aging is associated with redistribution of synaptic weights in the hippocampus

Behaviors that rely on the hippocampus are particularly susceptible to chronological aging, with many aged animals (including humans) maintaining cognition at a young adult-like level, but many others the same age showing marked impairments. It is unclear whether the ability to maintain cognition over time is attributable to brain maintenance, sufficient cognitive reserve, compensatory changes in network function, or some combination thereof. While network dysfunction within the hippocampal circuit of aged, learning-impaired animals is well-documented, its neurobiological substrates remain elusive. Here we show that the synaptic architecture of hippocampal regions CA1 and CA3 is maintained in a young adult-like state in aged rats that performed comparably to their young adult counterparts in both trace eyeblink conditioning and Morris water maze learning. In contrast, among learning-impaired, but equally aged rats, we found that a redistribution of synaptic weights amplifies the influence of autoassociational connections among CA3 pyramidal neurons, yet reduces the synaptic input onto these same neurons from the dentate gyrus. Notably, synapses within hippocampal region CA1 showed no group differences regardless of cognitive ability. Taking the data together, we find the imbalanced synaptic weights within hippocampal CA3 provide a substrate that can explain the abnormal firing characteristics of both CA3 and CA1 pyramidal neurons in aged, learning-impaired rats. Furthermore, our work provides some clarity with regard to how some animals cognitively age successfully, while others’ lifespans outlast their “mindspans.”

Aging is the biggest risk factor for Alzheimer’s disease, but many aged individuals nevertheless retain the ability to perform cognitive tasks with young adult (YA)-like competency, and are thus resilient to age-related cognitive decline and dementias (1, 2). The mechanisms of such resilience are unknown, but are thought to involve neural or cognitive reserve, brain network adaptations, or simply the ability to maintain cognitive brain circuits in a YA-like state (3–5). Much of the cellular and functional insight into the concept or risk of/resilience against age-related cognitive impairments has come from animal models of normal/nonpathological aging (6–10). Many of these studies have shown that circuit function abnormalities are associated with behavioral impairments. The cellular and structural bases for such functional aberrations, however, remain largely unknown.Two of the most well-studied cognitive domains that show susceptibility to chronological aging in both rodents and nonhuman primates are working memory and spatial/temporal memory (6–10). Importantly, these cognitive domains engage anatomically distinct neurocognitive systems, with the former relying on prefrontal/orbitofrontal cortical circuits and the latter relying on hippocampal circuitry. Interestingly, although behavioral deficits in these two domains (in the case of rat models of cognitive aging) begin to emerge, worsen, and become increasingly prevalent between 12 and 18 mo of age in most strains (reviewed in refs. 9 and 11), cognitive aging within hippocampus-dependent forms of learning and memory are relatively independent of those that engage the prefrontal/orbitofrontal cortical neural systems (6–9, 12–15).Neither the mechanisms underlying the conservation of memory function across chronological aging nor those contributing to the age-related emergence and exacerbation of memory impairments are clearly understood for either neurocognitive system. It is clear, however, that neither frank neuronal loss (16, 17) nor overall synapse loss (18) contributes to cognitive aging within the medial temporal lobe/hippocampal memory system. Rather, the intriguing idea that has emerged from work in both the hippocampal and the prefrontal/orbitofrontal cortical memory systems is that there are functional alterations in the synaptic connections in individual microcircuits embedded within these larger neuroanatomical systems (6–10, 19–31).Axospinous synapses (including those in hippocampal and cortical circuits) are characterized on the basis of the three-dimensional morphology of their postsynaptic densities (PSDs) (20, 32–34). The most-abundant axospinous synaptic subtype has a continuous, macular, disk-shaped PSD, as compared to the less-abundant perforated synaptic subtype, which has at least one discontinuity in its PSD (34). In addition to differing substantially with regard to relative frequency, perforated and nonperforated synapses also harbor major differences in size and synaptic AMPA-type and NMDA-type receptor expression levels (AMPAR and NMDAR, respectively) (34–38). There is also evidence that perforated and nonperforated synapses are differentially involved in synaptic plasticity (39–44) and in preservation of—or reductions in—memory function during chronological aging (6, 20, 45). Layered onto these general distinctions between perforated and nonperforated synapses are more specific differences in their characteristics when considered within neural circuits. For example, perforated synapses have a stronger and more consistent influence on neuronal computation within hippocampal region CA1 than their nonperforated counterparts, which nevertheless outnumber the former by a roughly 9-to-1 ratio (34, 46, 47).These and other circuit-specific differences necessitate a circuit-based approach to understanding the synaptic bases underlying the retention or loss of YA-like memory function in the aging brain. In many ways, the hippocampal system is particularly convenient for such circuit-based approaches (48, 49). Information about the internal and external world is funneled to the parahippocampal system and then relayed via the entorhinal cortex to the dentate gyrus, the first component of the so-called trisynaptic circuit in the hippocampus proper. Granule cells in the dentate gyrus then transmit their computations to hippocampal region CA3 via the mossy fibers, which form very large and anatomically distinct synapses called mossy fiber bouton–thorny excrescence synaptic complexes in the stratum lucidum (SL). CA3 pyramidal neurons then integrate information from their autoassociational connections in the stratum radiatum (SR) and stratum oriens (SO), with both direct entorhinal inputs in stratum lacunosum-moleculare (SLM) and the dentate gyrus inputs in the SL, and convey this information to hippocampal CA1 pyramidal neurons. Neurons in hippocampal CA1 then integrate this information in their basal and apical SR dendrites with direct entorhinal cortical inputs in their most distal, tufted dendrites in the SLM, and represent the first and largest extrahippocampal output from the hippocampus proper. Thus, the computations performed both within individual hippocampal subregions and between them as an interconnected neurocognitive system are complex, and involve a combination of intrinsic (i.e., membrane-bound ion channels that regulate membrane excitability) and synaptic (i.e., ligand-gated ion channels expressed at both excitatory and inhibitory synapses) influences. Additionally, age-related changes at any level of these complex circuits will have downstream consequences on the accuracy/reliability of the information being relayed to extrahippocampal regions via CA1 pyramidal neurons.Given the amount of evidence supporting a possible synaptic explanation for age-related learning and memory impairments in hippocampus-dependent forms of cognition (6–10), we combined patch-clamp physiology, serial section conventional and immunogold electron microscopy (EM), quantitative Western blot analyses, and behavioral characterization using two hippocampus-dependent forms of learning in YA (6- to 8-mo old) and aged rats (28- to 29-mo old) to examine two interconnected hippocampal regions implicated in cognitive aging: Regions CA1 and CA3. We focused on CA1 and CA3 because of their central location in the hippocampal circuit (48–50), their similar laminar dendritic structure (48–50), and their well-documented age-related changes in place field specificity and reliability (51–56).We find that the synaptic architecture and balance of synaptic weights in YA and aged, learning-unimpaired (AU) rats is remarkably similar, but that both are different in aged, learning-impaired (AI) rats. Moreover, this restructuring among “unsuccessful” cognitive agers has an intriguing specificity: It involves only AMPARs, only perforated axospinous synapses, and only hippocampal region CA3, which together shift the balance of synaptic weights that drive action potential output in CA3 pyramidal neurons maladaptively toward an overemphasis of the autoassociational synapses that interconnect CA3 pyramidal neurons.     

ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating

Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14–ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA–VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid–RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.

Human rhinoviruses are the cause of more than half of common colds (1). Medical visits and missed days of school and work cost tens of billions of US dollars annually (2, 3). There is currently no cure for rhinovirus infections, and the available treatments are only symptomatic. Rhinoviruses belong to the family Picornaviridae, genus Enterovirus, and are classified into species A, B, and C (4). Rhinoviruses A and B can belong to either “major” or “minor” groups, based on their utilization of intercellular adhesion molecule-1 (ICAM-1) or low-density lipoprotein receptor for cell entry (5–7). Type C rhinoviruses use CDHR3 as a receptor (8). Rhinovirus 14 belongs to the species rhinovirus B and uses ICAM-1 as a receptor. Receptors recognized by rhinoviruses and other enteroviruses can be divided into two groups based on their function in the infection process (9). Attachment receptors such as DAF, PSGL1, KREMEN1, CDHR3, and sialic acid enable the binding and endocytosis of virus particles into cells (10–13). In contrast, uncoating receptors including ICAM-1, CD155, CAR, and SCARB2 enable virus cell entry but also promote genome release from virus particles (5, 14–16).Virions of rhinoviruses are nonenveloped and have icosahedral capsids (17). Genomes of rhinoviruses are 7,000 to 9,000 nucleotide-long single-stranded positive-sense RNA molecules (1, 17). The rhinovirus genome encodes a single polyprotein that is co- and posttranslationally cleaved into functional protein subunits. Capsid proteins VP1, VP3, and VP0, originating from one polyprotein, form a protomer, 60 of which assemble into a pseudo-T = 3 icosahedral capsid. To render the virions mature and infectious, VP0 subunits are cleaved into VP2 and VP4 (18, 19). VP1 subunits form pentamers around fivefold symmetry axes, whereas subunits VP2 and VP3 form heterohexamers centered on threefold symmetry axes. The major capsid proteins VP1 through 3 have a jelly roll β-sandwich fold formed by two β-sheets, each containing four antiparallel β-strands, which are conventionally named B to I (20–22). The two β-sheets contain the strands BIDG and CHEF, respectively. The C termini of the capsid proteins are located at the virion surface, whereas the N termini mediate interactions between the capsid proteins and the RNA genome on the inner surface of the capsid. VP4 subunits are attached to the inner face of the capsid formed by the major capsid proteins. The surfaces of rhinovirus virions are characterized by circular depressions called canyons, which are centered around fivefold symmetry axes of the capsids (21).The VP1 subunits of most rhinoviruses, but not those of rhinovirus 14, contain hydrophobic pockets, which are filled by molecules called pocket factors (17, 21, 23, 24). It has been speculated that pocket factors are fatty acids or lipids (25). The pockets are positioned immediately below the canyons. The exposure of rhinoviruses to acidic pH induces expulsion of the pocket factors, which leads to the formation of activated particles and genome release (17, 26–32). The activated particles are characterized by capsid expansion, a reduction in interpentamer contacts, the release of VP4 subunits, externalization of N termini of VP1 subunits, and changes in the distribution of RNA genomes (17, 26–29, 33, 34). Artificial hydrophobic compounds that bind to VP1 pockets with high affinity inhibit infection by rhinoviruses (35, 36).ICAM-1 is an endothelial- and leukocyte-associated protein that stabilizes cell–cell interactions and facilitates the movement of leukocytes through endothelia (37). ICAM-1 can be divided into an extracellular amino-terminal part composed of five immunoglobulin domains, a single transmembrane helix, and a 29-residue–long carboxyl-terminal cytoplasmic domain. The immunoglobulin domains are characterized by a specific fold that consists of seven to eight β-strands, which form two antiparallel β-sheets in a sandwich arrangement (38–40). The immunoglobulin domains of ICAM-1 are stabilized by disulfide bonds and glycosylation (38–41). The connections between the immunoglobulin domains are formed by flexible linkers that enable bending of the extracellular part of ICAM-1. For example, the angle between domains 1 and 2 differs by 8° between molecules in distinct crystal forms (38, 42). As a virus receptor, ICAM-1 enables the virus particles to sequester at the cell surface and mediates their endocytosis (5). The structures of complexes of rhinoviruses 3, 14, and 16, and CVA21 with ICAM-1 have been determined to resolutions of 9 to 28 Å (42–46). It was shown that ICAM-1 molecules bind into the canyons at the rhinovirus surface, approximately between fivefold and twofold symmetry axes (42–46). ICAM-1 interacts with residues from all three major capsid proteins. It has been speculated that the binding of ICAM-1 triggers the transition of virions of rhinovirus 14 to activated particles and initiates genome release (45, 47). However, the limited resolution of the previous studies prevented characterization of the corresponding molecular mechanism.Here, we present the cryo-electron microscopy (cryo-EM) reconstruction of the rhinovirus 14 virion, which contains resolved density of octanucleotide segments of the RNA genome that interact with VP2 subunits. Furthermore, we show that the binding of ICAM-1 to rhinovirus 14 induces changes in its capsid and genome, which are required for subsequent virus activation and genome release at acidic pH.     

Attention recruits frontal cortex in human infants

Young infants learn about the world by overtly shifting their attention to perceptually salient events. In adults, attention recruits several brain regions spanning the frontal and parietal lobes. However, it is unclear whether these regions are sufficiently mature in infancy to support attention and, more generally, how infant attention is supported by the brain. We used event-related functional magnetic resonance imaging (fMRI) in 24 sessions from 20 awake behaving infants 3 mo to 12 mo old while they performed a child-friendly attentional cuing task. A target was presented to either the left or right of the infant’s fixation, and offline gaze coding was used to measure the latency with which they saccaded to the target. To manipulate attention, a brief cue was presented before the target in three conditions: on the same side as the upcoming target (valid), on the other side (invalid), or on both sides (neutral). All infants were faster to look at the target on valid versus invalid trials, with valid faster than neutral and invalid slower than neutral, indicating that the cues effectively captured attention. We then compared the fMRI activity evoked by these trial types. Regions of adult attention networks activated more strongly for invalid than valid trials, particularly frontal regions. Neither behavioral nor neural effects varied by infant age within the first year, suggesting that these regions may function early in development to support the orienting of attention. Together, this furthers our mechanistic understanding of how the infant brain controls the allocation of attention.

Having an attention system that is capable of swiftly orienting to salient events (i.e., stimulus-driven attention) is essential for many behaviors. This is perhaps most true in infancy, during which exploration is thought to be critical (1) and attention allows infants to fully experience learning moments (2). The value of attention in early development might explain why infants are equipped with the capacity to flexibly allocate attention: They can saccade to onsets soon after birth (3), use cues to facilitate orienting (4, 5), and make predictions about upcoming events (6). Yet, how the infant brain supports attention remains a mystery.An extensive literature in adults could inform our understanding of the neural basis of stimulus-driven attention in infants. Regions collectively referred to as the frontoparietal network, including right temporal parietal junction (TPJ), superior parietal lobe (SPL), lateral occipital cortex (LOC), frontal eye fields (FEF), middle/inferior frontal gyrus (MFG/IFG), and pulvinar, have been implicated in the orienting of stimulus-driven and goal-directed attention (7–10). Other regions including the anterior cingulate cortex (ACC), insula, and basal ganglia, referred to as the cingulo-opercular or salience network (11), have been implicated in the maintenance and updating of task goals. However, the cingulo-opercular network is activated for stimulus-driven attention when the orienting is unexpected (12). Together, this suggests several functionally distinct regions that may be recruited for stimulus-driven attention across the age span.Yet, the regions that support stimulus-driven attention in adults are anatomically immature in infants (13–16), and functional connectivity between these regions, critical for supporting attention in adults (17, 18), undergoes rapid development in the first year of life (19–24). Indeed, these regions undergo functional changes late into adolescence (17, 18). Furthermore, the regions that support stimulus-driven attention in adults are also recruited for maintaining goals and volitionally directing attention based on them (i.e., goal-directed attention) (25–27). However, goal-directed attention is less developed than stimulus-driven attention in infants (28–31), suggesting immaturity in some parts of infant attention networks. These threads of evidence led to the proposal that some regions, like the MFG/IFG and ACC, are not sufficiently mature in infancy to support attention, and instead, the TPJ, SPL, and FEF are recruited (32). An alternative account suggests that the frontoparietal and cingulo-opercular networks are capable of functioning in early infancy (20, 33, 34), even if there is anatomical immaturity (35).Existing studies of the infant attention system have been inconclusive about the extent to which the infant brain recruits adult attention networks. Electroencephalography (EEG) with infants suggested that some neural signatures of attention (36, 37) and error processing (33, 38) are adult-like. However, EEG has insufficient spatial resolution to resolve which regions are supporting attention. Functional near-infrared spectroscopy (fNIRS) offers potentially greater resolution (6, 39), but is unable to localize activity beyond regions close to the scalp surface, including deeper, ventral, medial, and subcortical structures such as the ACC and basal ganglia. Moreover, many aspects of attention behavior develop throughout infancy (40), such as disengagement (41), inhibition (42), and goal-directed attention (28–31), raising the expectation that the underlying brain systems would also show age-dependent changes. Hence, it remains unclear how stimulus-driven attention is supported in the infant brain.We used functional magnetic resonance imaging (fMRI) and offline gaze coding to investigate the behavioral and neural basis of stimulus-driven attention in awake behaving infants under a year old. Among noninvasive techniques, fMRI is uniquely capable of resolving brain-wide, fine-grained attention processes. Recent innovations have made it possible to collect data from awake behaving infants (43–46). Using a developmental variant (4, 47) of the Posner cuing task (48), we simultaneously recorded gaze behavior and whole-brain fMRI activity to uncover the neural basis of attention in infants.