Search

Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2–6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7–11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable—for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.

Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.

PURPOSE: While sampled or short-frame realizations have shown the potential power of deep learning to reduce radiation dose for PET images, evidence in true injected ultra-low-dose cases is lacking. Therefore, we evaluated deep learning enhancement using a significantly reduced injected radiotracer protocol for amyloid PET/MRI. METHODS: Eighteen participants underwent two separate (18)F-florbetaben PET/MRI studies in which an ultra-low-dose (6.64 ± 3.57 MBq, 2.2 ± 1.3% of standard) or a standard-dose (300 ± 14 MBq) was injected. The PET counts from the standard-dose list-mode data were also undersampled to approximate an ultra-low-dose session. A pre-trained convolutional neural network was fine-tuned using MR images and either the injected or sampled ultra-low-dose PET as inputs. Image quality of the enhanced images was evaluated using three metrics (peak signal-to-noise ratio, structural similarity, and root mean square error), as well as the coefficient of variation (CV) for regional standard uptake value ratios (SUVRs). Mean cerebral uptake was correlated across image types to assess the validity of the sampled realizations. To judge clinical performance, four trained readers scored image quality on a five-point scale (using 15% non-inferiority limits for proportion of studies rated 3 or better) and classified cases into amyloid-positive and negative studies. RESULTS: The deep learning–enhanced PET images showed marked improvement on all quality metrics compared with the low-dose images as well as having generally similar regional CVs as the standard-dose. All enhanced images were non-inferior to their standard-dose counterparts. Accuracy for amyloid status was high (97.2% and 91.7% for images enhanced from injected and sampled ultra-low-dose data, respectively) which was similar to intra-reader reproducibility of standard-dose images (98.6%). CONCLUSION: Deep learning methods can synthesize diagnostic-quality PET images from ultra-low injected dose simultaneous PET/MRI data, demonstrating the general validity of sampled realizations and the potential to reduce dose significantly for amyloid imaging.

To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents a unique or optimal state driven by natural selection or the contingent product of historical chance events1; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution2,3. Here we combine ancestral protein reconstruction4 with deep mutational scanning5–10 to characterize alternate histories in the sequence space around an ancient transcription factor, which evolved a novel biological function through well-characterized mechanisms11,12. We found hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history. We found that if evolution had begun from a different starting point within the network of sequences encoding the ancestral function, outcomes with different genetic and biochemical forms would likely have resulted; this contingency arises from the distribution of functional variants in sequence space and epistasis between residues. Our results illuminate the topology of the vast space of possibilities from which history sampled one path, highlighting how the outcome of evolution depends on a serial chain of compounding chance events.

Few studies have examined how people perceive psychological gender differences despite the practical importance of these perceptions for everyday life. In three studies, we examined whether there is a positive association between sexism and the tendency to exaggerate psychological gender differences. Study 1 demonstrated that the more strongly men endorsed hostile sexism and the more strongly women endorsed hostile or benevolent sexism, the larger they perceived gender differences to be across a broad range of psychological traits. Study 2 documented that the more strongly people endorsed hostile or benevolent sexism, the more likely they were to exaggerate the size of gender differences. In Studies 1 and 2, women perceived gender differences to be larger than did men, after accounting for sexism. Finally, Study 3 showed that increasing (decreasing) the perceived size of gender differences predicts corresponding increases (decreases) in sexism. These results support relevant theory, which argues that differentiation between genders underlies sexist ideologies, and they may inform future intervention studies that aim to reduce sexism by targeting exaggerated gender beliefs. Discussion highlights the proposed connection between sexism and the belief that “men are from Mars and women are from Venus”.

In this work, the nano- and macroscale tribological properties of maghemite (γ-Fe2O3) nanoparticles in aqueous solution are compared and contrasted for alumina contacts as a function of nanoparticle concentration. A quartz crystal microbalance (QCM) technique was used for nanotribology measurements and a ball-on-disk method was used to measure macroscale friction coefficients. Statistical methods were employed to identify significant associations between the QCM and ball-on-disk measurements, employing selected candidate performance factors for each system. In particular, the macroscale response was parameterized by % reduction in the friction coefficient while candidate QCM “bulk” and “surface” performance factors were selected from functions of the frequency f and resistance Rm shifts upon addition of nanoparticles to the water surrounding the QCM. Incremental increases in concentration were performed and reductions in friction and drag forces were observed for concentrations up to 0.6 wt%, after which further reductions were not observed. The factor δRfilm/δffilm exhibited a linear correlation with the reduction in macroscale friction coefficient, defined as the ratio of the shift in resistance to the shift in frequency attributable to interfacial effects and changes in the glide plane location. Atomic force microscopy was also utilized to both qualitatively and quantitatively determine surface roughness before and after particle uptake, leading to the observations that particles are easily removed from the surface and do not significantly alter surface morphology.

Mangroves provide numerous ecosystem services, including biodiversity values such as nesting sites for piscivorous waterbirds. High concentrations of waterbirds at nest sites are hypothesized to affect ecosystem dynamics, yet few studies have examined their effects as a nutrient source in mangroves. We examined the effects of nutrient enrichment by colonial waterbirds at a mangrove rookery in the Gulf of Fonseca, Honduras. We compared nutrient inputs via bird guano deposition and macronutrient levels in the vegetation and soils between a small island that hosted large numbers of roosting waterbirds and an adjacent island with little evidence of waterbird activity. Nest density at the rookery was 1721 ± 469 nests ha−1. Rookery birds deposited 7.2 ± 3.4 g m−2 day−1 guano dry weight, delivering an estimated 1.12 Mg ha−1 nitrogen and 0.16 Mg ha−1 phosphorus to the island over a 120 day breeding season. This large nutrient influx contributed to substantially higher concentrations of biologically important nutrients in the rookery soils (seven times more plant available phosphorus, eight times more nitrate, and two times more ammonium). Rookery mangrove leaves contained significantly higher concentrations of nitrogen and phosphorus compared to the control site. These results suggest that colonial waterbirds significantly influence nutrient dynamics of mangroves at local scales. Further research is needed to understand the effects of avian derived nutrients on mangrove growth rates, nutrient export to adjacent waters, invertebrate communities, and mangrove associated fisheries.

Among the many ecosystem services provided by mangrove ecosystems, their role in carbon (C) sequestration and storage is quite high compared to other tropical forests. Mangrove forests occupy less than 1 % of tropical forested areas but account for approximately 3 % of global carbon sequestration by tropical forests. Yet there remain many areas where little data on the size and variation of mangrove C stocks exist. To address this gap and examine the range of C stocks in mangroves at landscape scales, we quantified C stocks of Honduran mangroves along the Pacific and Caribbean coasts and the Bay Islands. We also examined differences in ecosystem C stocks due to size and structure of mangrove vegetation found in Honduras. Ecosystem C stocks ranged from 570 Mg C ha−1 in the Pacific coast to ~1000 Mg C ha−1 in Caribbean coast and the Bay Islands. Ecosystem C stocks on the basis of mangrove structure were 1200, 800 and 900 Mg C ha−1, in low, medium and tall mangroves, respectively. We did not find significant differences in ecosystem C stocks on the basis of location (Pacific coast, Caribbean coast and Bay Islands) or mangrove type (low, medium and tall). Mangrove soils represented the single largest pool of total C in these ecosystems, with 87, 81 and 94 % at the Pacific coast, Caribbean coast and the Bay Islands, respectively. While there were no significant differences in total ecosystem stocks among mangrove types, there were differences in where carbon is stored. Mangrove soils among low, medium and tall mangroves contained 99, 93 and 80 % of the total ecosystem C stocks. In addition, we found a small yet significant negative correlation between vegetation C pools and pore water salinity and pH at the sampled sites. Conversion of mangroves into other land use types such as aquaculture or agriculture could result in loses of these soil C reserves due to mineralization and oxidation. Coupled with their other ecosystem services, an understanding of the size of mangrove ecosystem C stocks underscores their values in the formulation of conservation and climate change mitigation strategies in Central America.

Parasite-mediated sexual selection theory suggests that females may choose male partners who possess a relatively low pathogen load in order to maximize their reproductive investment (e.g. by avoiding pathogens or producing pathogen-resistant offspring). However, males might also maximize their reproductive investment by preferring unparasitized females; even in non-sex-role-reversed systems where female choice predominates. We address this hypothesis in the fruit fly Drosophila melanogaster where female choice plays a major selective role. Females in this system exhibit reduced fecundity when parasitized, creating the opportunity for simultaneous parasite-mediated male choice. To address our hypothesis, virgin females were either prick-injected with a sub-lethal dose of the gram-negative bacteria Pseudomonas aeuginosa (pricked-parasitized group, PP), prick-injected with sterile media (pricked-unparasitized group, PU) or unpricked and unparasitized (UU group). Twenty-four hours post-infection, females were decapitated to minimize the confounding effects of female behavior on male preference (decapitated females will stand upright, but lack reproductive behavior). Males were then assigned to one of two different two-choice trials (experiment A: PU versus UU females or experiment B: PP versus UU females) and their courtship behavior monitored. In experiment A, males exhibited no courtship preference for either female. However, experiment B males preferentially courted UU females more often than PP females. These results suggest that males prefer unparasitized mates, which could play a significant role in shaping disease resistance in this system. These data also provide some of the first evidence that males prefer unparasitized females in systems that do not exhibit sex-role reversal.

Bioactivity-directed fractionation of the organic extracts of two filamentous fungi of the Bionectriaceae, strains MSX 64546 and MSX 59553 from the Mycosynthetix library, led to the isolation of a new dimeric epipolythiodioxopiperazine alkaloid, verticillin H (1), along with six related analogs, Sch 52900 (2), verticillin A (3), gliocladicillin C (4), Sch 52901 (5), 11'-deoxyverticillin A (6) and gliocladicillin A (7). The structures of compounds 1-7 were determined by extensive NMR and HRMS analyses, as well as by comparisons to the literature. All compounds (1-7) were evaluated for cytotoxicity against a panel of human cancer cell lines, displaying IC(50) values ranging from 1.2 μM to 10 nM. Compounds 1-5 were examined for activity in the NF-κB assay, where compounds 2 and 3 revealed activity in the sub-micromolar range. Additionally, compounds 1, 3 and 4 were tested for EGFR inhibition using an enzymatic assay, while compound 3 was examined against an overexpressing EGFR(+ve) cancer cell line.

The effects of sequence variation on function are elucidated by a study of protein evolution.

Crystal and molecular structures for aryl- and benzyl-substituted 3-hydroxy-3,4-dihydroisobenzopyran-1-one are described. For the 4,4-dimethyl derivative, two monoclinic modifications are produced on sublimation: (1) P21/c, a = 23.668(6) A b = 11.749(4) A c = 7.215(2) A β = 96.70(2)○; V = 1992.6(10) A3; (2) P21/c, a = 11.509(4) A, b = 12.429(4) A, c = 6.933(2) A, β = 91.12(3)○, V = 991.6(6) A. In both, hydroxy groups are pseudoaxial, and molecules form dimeric complementary but noncooperative hydrogen bonds. In the 6-methoxy derivative (3), P21/c; a = 14.185(7) A b = 4.105(4) A c = 15.598(13) A β = 98.59(6)○; V = 898.1(10) A3, the hydroxy group is pseudoequatorial, and the intermolecular hydrogen bonding forms infinite chains. In the 4,4-dimethyl-7-nitro derivative (4), C2/c, a = 19.365(4), b = 8.425(2), c = 13.464(4), β = 92.62(2), V = 2194.2(7) A3, the hydroxy group is pseudoaxial, and the intermolecular hydrogen bonding forms chains. Compared to the unmethylated compounds, the interbond angles within the ring at the dimethylated carbon are contracted.