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.     

Collagen IV differentially regulates planarian stem cell potency and lineage progression

The extracellular matrix (ECM) provides a precise physical and molecular environment for cell maintenance, self-renewal, and differentiation in the stem cell niche. However, the nature and organization of the ECM niche is not well understood. The adult freshwater planarian Schmidtea mediterranea maintains a large population of multipotent stem cells (neoblasts), presenting an ideal model to study the role of the ECM niche in stem cell regulation. Here we tested the function of 165 planarian homologs of ECM and ECM-related genes in neoblast regulation. We identified the collagen gene family as one with differential effects in promoting or suppressing proliferation of neoblasts. col4-1, encoding a type IV collagen α-chain, had the strongest effect. RNA interference (RNAi) of col4-1 impaired tissue maintenance and regeneration, causing tissue regression. Finally, we provide evidence for an interaction between type IV collagen, the discoidin domain receptor, and neuregulin-7 (NRG-7), which constitutes a mechanism to regulate the balance of symmetric and asymmetric division of neoblasts via the NRG-7/EGFR pathway.

Across the animal kingdom, stem cell function is regulated by the microenvironment in the surrounding niche (1), where the concentration of molecular signals for self-renewal and differentiation can be precisely regulated (2). The niche affects stem cell biology in many processes, such as aging and tissue regeneration, as well as pathological conditions such as cancer (3). Most studies have been done in tissues with large stem cell populations, such as the intestinal crypt (4) and the hair follicle (5) in mice. Elucidation of the role of the stem cell niche in tissue regeneration requires the study of animals with high regenerative potential, such as freshwater planarians (flatworms) (6). Dugesia japonica and Schmidtea mediterranea are two well-studied species that possess the ability to regenerate any missing body part (6, 7).Adult S. mediterranea maintain a high number of stem cells (neoblasts)—∼10 to 30% of all somatic cells in the adult worm—with varying potency, including pluripotent cells (8–14). Neoblasts are the only proliferating somatic cells: they are molecularly heterogeneous, but all express piwi-1 (15–18). Lineage-committed neoblasts are “progenitors” that transiently express both piwi-1 and tissue-specific genes (15, 19). Examples include early intestinal progenitors (γ neoblast, piwi-1⁺/hnf4⁺) (8, 10, 15, 19–21) and early epidermal progenitors (ζ neoblast, piwi-1⁺/zfp-1⁺) (8, 15). Other progenitor markers include collagen for muscles (22), ChAT for neurons (23), and cavII for protonephridia (24, 25). During tissue regeneration, neoblasts are recruited to the wound site, where they proliferate then differentiate to replace the missing cell types (16, 26). Some neoblasts express the pluripotency marker tgs-1, and are designated as clonogenic neoblasts (cNeoblasts) (10, 11). cNeoblasts are located in the parenchymal space adjacent to the gut (11).Neoblasts are sensitive to γ-irradiation and can be preferentially depleted in the adult planarian (27). After sublethal γ-irradiation, remaining cNeoblasts can repopulate the stem cell pool within their niche (10, 11). The close proximity of neoblasts to the gut suggests gut may be a part of neoblast niche (28, 29). When gut integrity was impaired by silencing gata4/5/6, the egfr-1/nrg-1 ligand-receptor pair, or wwp1, maintenance of non–γ-neoblasts were also disrupted (20, 30, 31), but whether that indicates the gut directly regulates neoblast remains unclear. There is evidence indicating the dorsal-ventral (D/V) transverse muscles surrounding the gut may promote neoblast proliferation and migration, with the involvement of matrix metalloproteinase mt-mmpB (32, 33). The central nervous system has also been implicated in influencing neoblast maintenance through the expression of EGF homolog neuregulin-7 (nrg-7), a ligand for EGFR-3, affecting the balance of neoblast self-renewal (symmetric or asymmetric division) (34).In other model systems, an important component of the stem-cell niche is the extracellular matrix (ECM) (35). Germline stem cells in Drosophila are anchored to niche supporting cells with ECM on one side, while the opposite side is exposed to differentiation signals, allowing asymmetric cell fate outcomes for self-renewal or differentiation following division (36–38). Few studies have addressed the ECM in planarians, largely due to the lack of genetic tools to manipulate the genome, the absence of antibodies to specific planarian ECM homologs, or the tools required to study cell fate changes. However, the genomes of D. japonica (39–41) and S. mediterranea (41–45), and single-cell RNA-sequencing (scRNA-seq) datasets for S. mediterranea are now available (11, 46–50). A recent study of the planarian matrisome demonstrated that muscle cells are the primary source of many ECM proteins (51), which, together with those produced by neoblasts and supporting parenchymal cells, may constitute components of the neoblast niche. For example, megf6 and hemicentin restrict neoblast’s localization within the parenchyma (51, 52). Functional studies also implicate ECM-modifiers, such as matrix metalloproteases (MMPs) in neoblast migration and regeneration. For example, reducing the activity of the ECM-degrading enzymes mt-mmpA (26, 33), mt-mmpB (53), or mmp-1 (33) impaired neoblast migration, proliferation, or overall tissue growth, respectively. Neoblasts are also likely to interact with ECM components of the niche via cell surface receptors, such as β1 integrin, inactivation of which impairs brain regeneration (54, 55).Here, we identified planarian ECM homologs in silico, followed by systematic functional assessment of 165 ECM and ECM-related genes by RNA interference (RNAi), to determine the effect on neoblast repopulation in planarians challenged by a sublethal dose of γ-irradiation (10). Surprisingly, multiple classes of collagens were shown to have the strongest effects. In particular, we show that the type IV collagens (COLIV) of basement membranes (BMs), were required to regulate the repopulation of neoblasts as well as lineage progression to progenitor cells. Furthermore, our data support an interaction between COLIV and the discoidin domain receptor (DDR) in neurons that activates signaling of NRG-7 in the neoblasts to regulate neoblast self-renewal versus differentiation. Together, these data demonstrate multifaceted regulation of planarian stem cells by ECM components.     

Hierarchical supramolecular assembly of a single peptoid polymer into a planar nanobrush with two distinct molecular packing motifs

Hierarchical nanomaterials have received increasing interest for many applications. Here, we report a facile programmable strategy based on an embedded segmental crystallinity design to prepare unprecedented supramolecular planar nanobrush-like structures composed of two distinct molecular packing motifs, by the self-assembly of one particular diblock copolymer poly(ethylene glycol)-block-poly(N-octylglycine) in a one-pot preparation. We demonstrate that the superstructures result from the temperature-controlled hierarchical self-assembly of preformed spherical micelles by optimizing the crystallization−solvophobicity balance. Particularly remarkable is that these micelles first assemble into linear arrays at elevated temperatures, which, upon cooling, subsequently template further lateral, crystallization-driven assembly in a living manner. Addition of the diblock copolymer chains to the growing nanostructure occurs via a loosely organized micellar intermediate state, which undergoes an unfolding transition to the final crystalline state in the nanobrush. This assembly mechanism is distinct from previous crystallization-driven approaches which occur via unimer addition, and is more akin to protein crystallization. Interestingly, nanobrush formation is conserved over a variety of preparation pathways. The precise control ability over the superstructure, combined with the excellent biocompatibility of polypeptoids, offers great potential for nanomaterials inaccessible previously for a broad range of advanced applications.

Biomacromolecules fold and assemble into complex, well-organized hierarchical structures by a network of noncovalent interactions, which enable tremendous architectural diversity in nature (1, 2). For example, polypeptide chains encoded with assembly information in their monomer sequence can fold into highly ordered conformations, which give rise to their biological functionality (3). Inspired by these intricate natural designs, numerous efforts have been devoted to fabricating hierarchical nanostructures using synthetic polymeric materials (4–11). However, the precision control over the assembly process and structure across many length scales, as commonly seen in biomacromolecules, remains a challenging task (12). This is because the assembly information content encoded within synthetic macromolecules is considerably lower.Synthetic chemists have looked to develop polymer systems that retain many of the structural features found in natural biopolymers. Bioinspired synthetic polymers have attracted growing attention, because of their inherent structural advantages, facile synthetic approaches, and improved stability, to serve as promising materials for the de novo design and assembly of hierarchical nanostructures. In particular, polypeptoids are a class of peptidomimetic polymers based on a polar amide backbone (13–15). This differs substantially from carbon-chain polymers such as polyethylene and polypropylene. The amide groups impart higher water solubility, excellent biocompatibility, the opportunity for multiple backbone−backbone interactions, and enable a wide range of bioactivities. Polypeptoids are devoid of hydrogen bond donating sites and chirality on the backbone due to the N substitution. This simplifies the complex molecular interactions inherent in peptidomimetic materials, resulting in efficient engineering and controllable architecture construction. For example, polypeptoids with alkyl side chain groups are semicrystalline with inherent characteristic packing domains, which is in sharp contrast to polypeptides (16–19).Macromolecular crystallization is an essential process in both nature and materials manufacturing. The self-assembly of block copolymers containing crystalline blocks generally enables the formation of multiscale architectures with a high level of control over morphology and dimension (20, 21). Recently, living crystallization-driven self-assembly has been demonstrated to be an effective strategy to precisely control the nanoscale morphology (22–30). Inspired by the natural encoded information-guided self-assembly, we based our design on a hydrophobic poly(N-alkylglycine) peptoid block that is known to form a rectangular crystalline lattice with controllable dimension and two melting transitions (31). It is also known that solvophobic interaction is the predominant driving force for assembly of systems with solvophobic segments (5). The delicate interplay between crystallization and solvophobicity is essential for biomolecule self-assembly (32), which potentially serves as a powerful strategy for self-assembly of block copolymers. Thus, we embarked on a study of block copolymers, where the relative strength of these two factors could be systematically adjusted. By optimizing the balance between these two factors, we discovered that poly(ethylene glycol)-block-poly(N-octylglycine) (PEG-b-PNOG) formed unique supramolecular planar nanobrush architectures in high yield. We developed a simple temperature-controlled assembly strategy to create superbrushes consisting of two distinct packing domains: a long core fiber, or “spine,” with lengths up to ∼2.0 µm, and laterally splayed shorter fibers of ∼400 nm in length on apposed side surfaces of the spine. We further demonstrated that this lateral growth of the brush exhibits living growth manner via a micelle intermediate, fairly distinct from known living crystallization-driven self-assembly approaches (16, 23, 33), where assemblies grow via the direct attachment of block unimers. Our results coincide with the reported “particle attachment” strategy observed in a range of biomacromolecules and small molecules, where intermediate higher-ordered species form in solution prior to their attachment to the crystal lattice, in contrast to monomer-by-monomer crystal growth (1, 32, 34, 35). Such pathways allow for the optimization of interactions to facilitate thermodynamic favored transition from the initial species to hierarchical assemblies.     

Global citation inequality is on the rise

Citations are important building blocks for status and success in science. We used a linked dataset of more than 4 million authors and 26 million scientific papers to quantify trends in cumulative citation inequality and concentration at the author level. Our analysis, which spans 15 y and 118 scientific disciplines, suggests that a small stratum of elite scientists accrues increasing citation shares and that citation inequality is on the rise across the natural sciences, medical sciences, and agricultural sciences. The rise in citation concentration has coincided with a general inclination toward more collaboration. While increasing collaboration and full-count publication rates go hand in hand for the top 1% most cited, ordinary scientists are engaging in more and larger collaborations over time, but publishing slightly less. Moreover, fractionalized publication rates are generally on the decline, but the top 1% most cited have seen larger increases in coauthored papers and smaller relative decreases in fractional-count publication rates than scientists in the lower percentiles of the citation distribution. Taken together, these trends have enabled the top 1% to extend its share of fractional- and full-count publications and citations. Further analysis shows that top-cited scientists increasingly reside in high-ranking universities in western Europe and Australasia, while the United States has seen a slight decline in elite concentration. Our findings align with recent evidence suggesting intensified international competition and widening author-level disparities in science.

Science is a highly stratified social system. The distribution of scientific rewards is remarkably uneven, and a relatively small stratum of elite scientists enjoys exceptional privileges in terms of funding, research facilities, professional reputation, and influence (1–5). The so-called Matthew effect, well-documented in science (6–15), implies that accomplished scientists receive more rewards than their research alone merits, and recent evidence indicates a widening gap between the “haves” and the “have nots” of science in terms of salary levels (5), research funding (16), and accumulation of scientific awards (17).Inequality may foster creative competition in the science system (18, 19). However, it can also lead to a dense concentration of resources with diminishing returns on investment (intellectual and fiscal) (16, 20), and to monopolies in the marketplace of ideas (21, 22).The social processes that sort scientists into more or less prestigious strata are complex and multifaceted (1, 10, 23) and may be changing in response to external pressures such as globalization, the advent of new information technologies, and shifts in university governance models (3). However, a few common characteristics have always separated elite scientists from the rest of us, most notably their scientific output and visibility. Publications and citations are critical building blocks for status and success in science (23, 24), and the scientific elite accounts for a large share of what is published and cited.In 1926, Lotka observed that the publication frequencies of chemists followed an inverse-square distribution, where the number of authors publishing N papers would be ∼1/N² of the number of authors publishing one paper (25). Building on Lotka’s work, de Solla Price later went on to suggest that 50% of all publications were produced by a mere 6% of all scientists (26). More recent research demonstrates even larger disparities in citation distributions at the author level (2, 6, 11, 27, 28), but variations in citation concentration across disciplinary, institutional, and national boundaries remain uncertain. Further, it is unclear whether the observed inequalities in citation shares have intensified over time.Advances in author-disambiguation methods (29) allow us to investigate these questions on a global scale. We used a linked dataset of 4,042,612 authors and 25,986,133 articles to examine temporal trends in the concentration of citations at the author level, and differences in the degree of concentration across fields, countries, and institutions.Publication and citation data were retrieved from Clarivate’s Web of Science (WoS). We limited our focus to disciplines within the medical and health sciences, natural sciences, and agricultural sciences, where journal publication is the primary form of scholarly communication (Materials and Methods). We used a disambiguation algorithm to create publication profiles for all authors with five or more publication entries in WoS. The disambiguated dataset allowed us to measure developments in citation concentration from 2000 onward.Per-author citation impact was measured using field-normalized citation scores (ncs). ncs is calculated by dividing the raw per-paper citation scores with the average citation counts of comparable papers published in the same year and subfield. ncs was rescaled to account for citation inflation, represented here as nics. We report per-author cumulative citation impact based on a full and fractional counting. The full counting gives the sum of nics for all papers published by a scientist. The fractional counting also gives the sum of citations accrued by a scientist in all her papers, but divides the per-article citation scores with the number of contributors per paper. We use citation density plots and Gini coefficients to gauge trends in citation imbalance and concentration.     

Modulation of immune cell reactivity with cis-binding Siglec agonists

Inflammatory pathologies caused by phagocytes lead to numerous debilitating conditions, including chronic pain and blindness due to age-related macular degeneration. Many members of the sialic acid-binding immunoglobulin-like lectin (Siglec) family are immunoinhibitory receptors whose agonism is an attractive approach for antiinflammatory therapy. Here, we show that synthetic lipid-conjugated glycopolypeptides can insert into cell membranes and engage Siglec receptors in cis, leading to inhibitory signaling. Specifically, we construct a cis-binding agonist of Siglec-9 and show that it modulates mitogen-activated protein kinase (MAPK) signaling in reporter cell lines, immortalized macrophage and microglial cell lines, and primary human macrophages. Thus, these cis-binding agonists of Siglecs present a method for therapeutic suppression of immune cell reactivity.

Sialic acid-binding immunoglobulin (IgG)-like lectins (Siglecs) are a family of immune checkpoint receptors that are on all classes of immune cells (1–5). Siglecs bind various sialoglycan ligands and deliver signals to the immune cells that report on whether the target is healthy or damaged, “self” or “nonself.” Of the 14 human Siglecs, 9 contain cytosolic inhibitory signaling domains. Accordingly, engagement of these inhibitory Siglecs by sialoglycans suppresses the activity of the immune cell, leading to an antiinflammatory effect. In this regard, inhibitory Siglecs have functional parallels with the T cell checkpoint receptors CTLA-4 and PD-1 (6–9). As with these clinically established targets for cancer immune therapy, there has been a recent surge of interest in antagonizing Siglecs to potentiate immune cell reactivity toward cancer (10). Conversely, engagement of Siglecs with agonist antibodies can suppress immune cell reactivity in the context of antiinflammatory therapy. This approach has been explored to achieve B cell suppression in lupus patients by agonism of CD22 (Siglec-2) (11, 12), and to deplete eosinophils for treatment of eosinophilic gastroenteritis by agonism of Siglec-8 (13). Similarly, a CD24 fusion protein has been investigated clinically as a Siglec-10 agonist for both graft-versus-host disease and viral infection (14, 15).Traditionally, Siglec ligands have been studied as functioning in trans, that is, on an adjacent cell (16–18), or as soluble clustering agents (9, 19). In contrast to these mechanisms of action, a growing body of work suggests that cis ligands for Siglecs (i.e., sialoglycans that reside on the same cell membrane) cluster these receptors and maintain a basal level of inhibitory signaling that increases the threshold for immune cell activation. Both Bassik and coworkers (20) and Wyss-Coray and coworkers (21) have linked the depletion of cis Siglec ligands with increased activity of macrophages and microglia, and other studies have shown that a metabolic blockade of sialic acid renders phagocytes more prone to activation (22).Synthetic ligands are a promising class of Siglec agonists (17, 23, 24). Many examples rely on clustering architectures (e.g., sialopolymers, nanoparticles, liposomes) to induce their effect (19, 23–26). Indeed, we have previously used glycopolymers to study the effects of Siglec engagement in trans on natural killer (NK) cell activity (16). We and other researchers have employed glycopolymers (16, 23), glycan-remodeling enzymes (27, 28), chemical inhibitors of glycan biosynthesis (22), and mucin overexpression constructs (29, 30) to modulate the cell-surface levels of Siglec ligands. However, current approaches lack specificity for a given Siglec.We hypothesized that Siglec-specific cis-binding sialoglycans displayed on immune cell surfaces could dampen immune cell activity with potential therapeutic applications. Here we test this notion with the synthesis of membrane-tethered cis-binding agonists of Siglec-9 (Fig. 1). Macrophages and microglia widely express Siglec-9 and are responsible for numerous pathologies including age-related inflammation (31), macular degeneration (32), neural inflammation (33), and chronic obstructive pulmonary disease (34). We designed and developed a lipid-linked glycopolypeptide scaffold bearing glycans that are selective Siglec-9 ligands (pS9L-lipid). We show that pS9L-lipid inserts into macrophage membranes, binds Siglec-9 specifically and in cis, and induces Siglec-9 signaling to suppress macrophage activity. By contrast, a lipid-free soluble analog (pS9L-sol) binds Siglec-9 but does not agonize Siglec-9 or modulate macrophage activity. Membrane-tethered glycopolypeptides are thus a potential therapeutic modality for inhibiting phagocyte activity.Open in a separate windowFig. 1.Lipid-tethered glycopolypeptides cluster and agonize Siglecs in cis on effector cells. (A) Immune cells express activating receptors that stimulate inflammatory signaling. (B) Clustering of Siglec-9 by cis-binding agonists stimulates inhibitory signaling that quenches activation.     

Defining principles that influence antimicrobial peptide activity against capsulated Klebsiella pneumoniae

The extracellular polysaccharide capsule of Klebsiella pneumoniae resists penetration by antimicrobials and protects the bacteria from the innate immune system. Host antimicrobial peptides are inactivated by the capsule as it impedes their penetration to the bacterial membrane. While the capsule sequesters most peptides, a few antimicrobial peptides have been identified that retain activity against encapsulated K. pneumoniae, suggesting that this bacterial defense can be overcome. However, it is unclear what factors allow peptides to avoid capsule inhibition. To address this, we created a peptide analog with strong antimicrobial activity toward several K. pneumoniae strains from a previously inactive peptide. We characterized the effects of these two peptides on K. pneumoniae, along with their physical interactions with K. pneumoniae capsule. Both peptides disrupted bacterial cell membranes, but only the active peptide displayed this activity against capsulated K. pneumoniae. Unexpectedly, the active peptide showed no decrease in capsule binding, but did lose secondary structure in a capsule-dependent fashion compared with the inactive parent peptide. We found that these characteristics are associated with capsule-peptide aggregation, leading to disruption of the K. pneumoniae capsule. Our findings reveal a potential mechanism for disrupting the protective barrier that K. pneumoniae uses to avoid the immune system and last-resort antibiotics.

Multidrug-resistant (MDR) bacterial infections have become a major threat to human health (1–3). Mortality rates from infections caused by gram-negative bacteria, specifically Klebsiella pneumoniae, are on the rise owing to the lack of effective antibiotics to treat the emergent MDR strains (4–7). The capsule of K. pneumoniae is composed of extracellular polysaccharides that promote infection by masking the bacteria from immune recognition and provide an especially potent barrier against peptide-based antimicrobials, including innate host defense peptides and last-resort polymyxin antibiotics (8–14).Antimicrobial peptides are commonly amphipathic, with both a charged and a hydrophobic character (15). The anionic nature of the bacterial capsule promotes an electrostatic attraction to cationic antimicrobial peptides, and peptide hydrophobicity has been proposed to enhance capsule binding through nonionic interactions (9, 12, 16). Interaction with the bacterial capsule is thought to induce structural changes that cause sequestration of antimicrobial peptides to prevent them from reaching their bacterial membrane target (16, 17). While the bacterial capsule inhibits host defense peptides and polymyxins, a few amphipathic antimicrobial peptides have been identified that can retain activity against capsulated K. pneumoniae (18–21). However, it is not known what enables some peptides to avoid sequestration by the capsule of K. pneumoniae while the capsule effectively neutralizes our innate host defense peptides with similar physicochemical properties. This lack of knowledge prevents us from understanding how to bypass the capsule barrier that K. pneumoniae uses to avoid our innate immune response and last-resort treatment options.Here we characterize the synthetic evolution of a peptide inhibited by capsule to a peptide with potent activity against capsulated K. pneumoniae. Remarkably, our results indicate that rather than reduced interactions, our active peptide retains binding to capsule and undergoes conformational changes associated with capsule aggregation. We present a model in which peptide-driven sequestration of capsule disrupts this barrier and reduces its ability to protect K. pneumoniae against antimicrobial attack. These findings provide insight into improving antimicrobial peptide activity against K. pneumoniae and may help strengthen our understanding of the inability of innate host defense peptides to act on capsulated bacteria.     

A key requirement for synaptic Reelin signaling in ketamine-mediated behavioral and synaptic action

Ketamine is a noncompetitive N-methyl-D-aspartate (NMDA) receptor antagonist that produces rapid antidepressant action in some patients with treatment-resistant depression. However, recent data suggest that ∼50% of patients with treatment-resistant depression do not respond to ketamine. The factors that contribute to the nonresponsiveness to ketamine’s antidepressant action remain unclear. Recent studies have reported a role for secreted glycoprotein Reelin in regulating pre- and postsynaptic function, which suggests that Reelin may be involved in ketamine’s antidepressant action, although the premise has not been tested. Here, we investigated whether the disruption of Reelin-mediated synaptic signaling alters ketamine-triggered synaptic plasticity and behavioral effects. To this end, we used mouse models with genetic deletion of Reelin or apolipoprotein E receptor 2 (Apoer2), as well as pharmacological inhibition of their downstream effectors, Src family kinases (SFKs) or phosphoinositide 3-kinase. We found that disruption of Reelin, Apoer2, or SFKs blocks ketamine-driven behavioral changes and synaptic plasticity in the hippocampal CA1 region. Although ketamine administration did not affect tyrosine phosphorylation of DAB1, an adaptor protein linked to downstream signaling of Reelin, disruption of Apoer2 or SFKs impaired baseline NMDA receptor–mediated neurotransmission. These results suggest that maintenance of baseline NMDA receptor function by Reelin signaling may be a key permissive factor required for ketamine’s antidepressant effects. Taken together, our results suggest that impairments in Reelin-Apoer2-SFK pathway components may in part underlie nonresponsiveness to ketamine’s antidepressant action.

Major depressive disorder (MDD) is a serious disorder that affects ∼20.6% of the US population and is a leading cause of suicide (1). One crucial problem in treating patients with MDD is an incomplete response rate to medications, where a large fraction of patients do not show a response to primary antidepressant medications (2, 3). Recent clinical findings demonstrate that a subanesthetic dose of ketamine, a noncompetitive N-methyl-d-aspartate receptor (NMDAR) antagonist, produces rapid antidepressant effects within hours in some patients with treatment-resistant depression or MDD (4–6). However, ∼50% of patients with treatment-resistant depression do not respond to ketamine (7), and factors involved in the nonresponsiveness to ketamine remain unclear.The hippocampus is a brain region that has been linked to the pathophysiological changes in MDD. Patients with MDD show a decrease in hippocampal volume and function (8–12). In contrast, MDD patients treated with classic antidepressants have a reversal in hippocampal volume changes along with an improvement in hippocampus-dependent cognitive function (13–15). Previous preclinical studies have shown animal models of depression also exhibit a decrease in hippocampal volume and function (13), and hippocampal synaptic functional enhancement is required to mediate antidepressant responses (16–18). This enhancement of hippocampal function has been suggested to be a key requirement to exert an antidepressant response.Ketamine induces rapid molecular changes that elicit synaptic plasticity in the hippocampus (16, 19–22). Specifically, ketamine rapidly generates synaptic potentiation of field excitatory postsynaptic potentials (fEPSPs) in CA3–CA1 synapses in the hippocampus (ketamine potentiation) by inducing the rapid translation of brain-derived neurotrophic factor (BDNF) and trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) onto the postsynaptic surface (16, 19, 23, 24). Recent studies have shown that if key factors for the antidepressant effects of ketamine, such as BDNF (16, 25, 26) or AMPA receptors (16, 27), are deleted or blocked, the synaptic potentiation in the hippocampus concurrently disappears, suggesting that the synaptic potentiation underlies ketamine’s antidepressant effects (16, 19).Ketamine-mediated potentiation of fEPSPs in CA3–CA1 synapses has been shown to require a block of NMDAR activation by spontaneous glutamate release. Ketamine produces synaptic potentiation in the presence of tetrodotoxin, which blocks sodium channels, and thereby the generation of action potentials, suggesting that blocking NMDARs activated by the spontaneous presynaptic release is key to producing the synaptic potentiation (19, 21, 28, 29). In agreement with this premise, deletion of Vps10p-tail-interactor-1a (Vti1a) and vesicle-associated membrane protein 7 (VAMP7), which are soluble N-ethylmaleimide–sensitive factor attachment protein receptor proteins selectively involved in spontaneous neurotransmitter release (30, 31) in the CA3 hippocampal region, occluded the ketamine potentiation (32). Collectively, these lines of evidence suggest spontaneous glutamate release, and NMDARs are important factors for ketamine potentiation. Thus, it is possible that if these pre- or postsynaptic components are impaired, ketamine may not produce the synaptic potentiation and antidepressant effects.Reelin is a secreted glycoprotein and acts as a neuromodulator in the adult brain by regulating pre- and postsynaptic machinery. Reelin binds to its receptors, apolipoprotein E receptor 2 (Apoer2) and very-low-density lipoprotein receptor (VLDLR) and increases tyrosine phosphorylation in Disabled-1 (DAB1) (33–35). The Reelin pathway regulates pre- or postsynaptic function through its downstream signaling pathways in the adult brain. In presynaptic terminals, the Reelin-Apoer2 pathway activates phosphoinositide 3-kinase (PI3K) and increases Ca²⁺ release from intracellular stores, which in turn mobilizes VAMP7-containing synaptic vesicles and augments spontaneous release (31). At the postsynaptic sites, Reelin’s binding to Apoer2 reciprocally activates DAB1 and Src family kinases (SFKs). Subsequently, the activated SFKs increase tyrosine phosphorylation in NMDAR subunits, GluN2A and GluN2B (34–37), and increase NMDAR open probability (37–39). Since pre- and postsynaptic components regulated by Reelin have been suggested to be important for ketamine potentiation (16, 19–21, 32), it is conceivable that disrupted Reelin signaling may abrogate the antidepressant action and synaptic plasticity of ketamine.To examine this premise, we used genetically modified mice with a deletion of either Reelin or Apoer2 and investigated changes in antidepressant-like behaviors and synaptic potentiation in the CA1 hippocampal region following ketamine treatment. We also used pharmacological inhibitors to examine the effects of signaling molecules downstream of Reelin-Apoer2, specifically SFKs and PI3K, on ketamine-induced behavioral changes and synaptic plasticity. Lastly, we investigated whether the disruption of ketamine’s effects is due to a requirement for the activation of Reelin-dependent signaling or the impairment of NMDAR function by the disruption of Reelin-dependent signaling. Our results suggest that disruption of the Reelin-Apoer2-SFKs pathway depresses NMDAR function and diminishes ketamine’s use-dependent NMDAR antagonism, thereby rendering synapses nonresponsive to ketamine’s action as well as subsequent antidepressant responses. Taken together, these results provide insight into understanding the cellular and molecular mechanisms underlying ketamine’s antidepressant effects.     

Genetically edited CD34+ cells derived from human iPS cells in vivo but not in vitro engraft and differentiate into HIV-resistant cells

Genetic editing of induced pluripotent stem (iPS) cells represents a promising avenue for an HIV cure. However, certain challenges remain before bringing this approach to the clinic. Among them, in vivo engraftment of cells genetically edited in vitro needs to be achieved. In this study, CD34⁺ cells derived in vitro from iPS cells genetically modified to carry the CCR5Δ32 mutant alleles did not engraft in humanized immunodeficient mice. However, the CD34⁺ cells isolated from teratomas generated in vivo from these genetically edited iPS cells engrafted in all experiments. These CD34⁺ cells also gave rise to peripheral blood mononuclear cells in the mice that, when inoculated with HIV in cell culture, were resistant to HIV R5-tropic isolates. This study indicates that teratomas can provide an environment that can help evaluate the engraftment potential of CD34⁺ cells derived from the genetically modified iPS cells in vitro. The results further confirm the possibility of using genetically engineered iPS cells to derive engraftable hematopoietic stem cells resistant to HIV as an approach toward an HIV cure.

A major objective of recent HIV research is to develop a “cure” for this virus infection that avoids lifelong adherence to antiretroviral therapy (ART). One of the approaches toward reaching this objective has been to genetically delete or mutate genes encoding for proteins that promote HIV infection and spread. An attractive candidate for this strategy is the Ccr5 gene, for which a genetic mutation causing a 32-bp deletion has been shown to be associated with natural protection from HIV infection and disease (1, 2). The Ccr5 gene encodes CCR5, a human cell-surface chemokine receptor that is a coreceptor for HIV attachment and infection of cells (3, 4). The Ccr5 allele with its 32-bp deletion results in a truncated isoform of the CCR5 receptor, CCR5Δ32, which is not expressed at the cell surface. Thus, entry of the virus into the cell is blocked (5).Induced pluripotent stem (iPS) cells (6), because of their capacity to differentiate into CD34⁺ hematopoietic stem cells (HSCs) (7), can reconstitute a full immune system (8, 9). These iPS cells are therefore a target of choice for genetic engineering. Our group and others have demonstrated that iPS cells generated from the peripheral blood mononuclear cells (PBMC) of both healthy individuals (10) and HIV-infected patients under ART (11) can have their wild-type allele of the Ccr5 gene genetically edited to carry the Ccr5 Δ32 mutation (12, 13). Notably, using CRISPR/Cas9 technology, the Ccr5 gene can be modified to have the naturally occurring Δ32 variant allele that has been associated with resistance to R5-tropic viruses. Moreover, while it is not present at the cell surface, the truncated CCR5Δ32 protein is still expressed and, as such, could have other important physiological roles (14–17).We have confirmed that the genetically modified Ccr5 Δ32 iPS cells can be differentiated into CD34⁺ HSCs in vitro (10, 18). Under appropriate cell culture conditions, they can give rise to various myeloid and lymphoid cell lineages (10, 11, 18). This result can also be observed with the formation of teratomas following the injection of large quantities of iPS cells into mice. Teratomas are multicellular tumors composed of many different cell types including HSCs. Notably, immune cells with the CCR5Δ32 mutation differentiated in vitro from the genetically modified iPS cell-derived HSCs and inoculated with HIV are resistant to R5-tropic virus infection (10, 18).These results have suggested that editing Ccr5 in iPS cells from HIV-infected subjects can be a promising strategy toward an HIV cure. The pluripotent stem cells can be induced from a small number of PBMC from the patients and genetically modified to become resistant to HIV infection (10, 11, 18). In this case, leukapheresis to obtain large amounts of these cells (19) is not required. The edited HSCs could then be transplanted back to the original patient without concern for immune cell rejection. Therefore, because these experiments were performed in cell culture, an important remaining question is whether in vitro-edited iPS cells can differentiate into HSCs that can be transplanted back into a recipient in vivo (20).To address this question, transplantation of the in vitro-derived CD34⁺ cells was attempted under various conditions in animal models of humanized or immunodeficient mice (21). In approaches to obtain sufficient numbers of CD34⁺ cells for transplantation, our ability to grow them in vitro offered an opportunity. However, although we could expand CD34⁺ cells substantially in culture (18), we observed that engraftment of these cell culture-derived CD34⁺ cells in humanized NSG-BLT mice did not occur. Thus, alternatively, to study the genetically edited cells in vivo, we explored the use of differentiated CD34⁺ cells in vivo via the generation of teratomas from iPS cells. We found that not only did these teratomas successfully yield human CD34⁺ cells, but importantly, these CD34⁺ cells could engraft in recipient immunodeficient NSG mice. This observation has been made by Nakauchi and colleagues (22) with different mouse strains. Finally, we confirmed that the PBMC formed in mice from these teratoma-derived genetically edited CD34⁺ cells are resistant to ex vivo R5-tropic HIV infection when they carry the mutant Δ32 Ccr5 allele.     

Replisome bypass of a protein-based R-loop block by Pif1

Efficient and faithful replication of the genome is essential to maintain genome stability. Replication is carried out by a multiprotein complex called the replisome, which encounters numerous obstacles to its progression. Failure to bypass these obstacles results in genome instability and may facilitate errors leading to disease. Cells use accessory helicases that help the replisome bypass difficult barriers. All eukaryotes contain the accessory helicase Pif1, which tracks in a 5′–3′ direction on single-stranded DNA and plays a role in genome maintenance processes. Here, we reveal a previously unknown role for Pif1 in replication barrier bypass. We use an in vitro reconstituted Saccharomyces cerevisiae replisome to demonstrate that Pif1 enables the replisome to bypass an inactive (i.e., dead) Cas9 (dCas9) R-loop barrier. Interestingly, dCas9 R-loops targeted to either strand are bypassed with similar efficiency. Furthermore, we employed a single-molecule fluorescence visualization technique to show that Pif1 facilitates this bypass by enabling the simultaneous removal of the dCas9 protein and the R-loop. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.

Efficient and faithful replication of the genome is essential to maintain genome stability and is carried out by a multiprotein complex called the replisome (1–4). There are numerous obstacles to progression of the replisome during the process of chromosome duplication. These obstacles include RNA-DNA hybrids (R-loops), DNA secondary structures, transcribing RNA polymerases, and other tightly bound proteins (5–9). Failure to bypass these barriers may result in genome instability, which can lead to cellular abnormalities and genetic disease. Cells contain various accessory helicases that help the replisome bypass these difficult barriers (10–20). A subset of these helicases act on the opposite strand of the replicative helicase (1, 2, 14, 19).All eukaryotes contain an accessory helicase, Pif1, which tracks in a 5′–3′ direction on single-stranded DNA (ssDNA) (11–16). Pif1 is important in pathways such as Okazaki-fragment processing and break-induced repair that require the removal of DNA-binding proteins as well as potential displacement of R-loops (11–13, 21, 15–18, 22–25). Genetic studies and immunoprecipitation pull-down assays indicate that Pif1 interacts with PCNA (the DNA sliding clamp), Pol ε (the leading-strand polymerase), the MCMs (the motor subunits of the replicative helicase CMG), and RPA (the single-stranded DNA-binding protein) (15, 26, 27). Pif1 activity in break-induced repair strongly depends on its interaction with PCNA (26). These interactions with replisomal components suggest that Pif1 could interact with the replisome during replication. In Escherichia coli, the replicative helicase is the DnaB homohexamer that encircles the lagging strand and moves in a 5′–3′ direction (20). E. coli accessory helicases include the monomeric UvrD (helicase II) and Rep, which move in the 3′–5′ direction and operate on the opposite strand from the DnaB hexamer. It is known that these monomeric helicases promote the bypass of barriers during replication such as stalled RNA polymerases (5). The eukaryotic replicative helicase is the 11-subunit CMG (Cdc45, Mcm2–7, GINS) and tracks in the 3′–5′ direction, opposite to the direction of Pif1 (25, 28). Once activated by Mcm10, the MCM motor domains of CMG encircle the leading strand (29–32). We hypothesized that, similar to UvrD and Rep in E. coli, Pif1 interacts with the replisome tracking in the opposite direction to enable bypass of replication obstacles.In this report, we use an in vitro reconstituted Saccharomyces cerevisiae replisome to study the role of Pif1 in bypass of a “dead” Cas9 (dCas9), which is a Cas9 protein that is deactivated in DNA cleavage but otherwise fully functional in DNA binding. As with Cas9, dCas9 is a single-turnover enzyme that can be programmed with a guide RNA (gRNA) to target either strand. The dCas9–gRNA complex forms a roadblock consisting of an R-loop and a tightly bound protein (dCas9), a construct that is similar to a stalled RNA polymerase. This roadblock (hereafter dCas9 R-loop) arrests replisomes independent of whether the dCas9 R-loop is targeted to the leading or lagging strand (30). Besides its utility due to its programmable nature (33), the use of the dCas9 R-loop allows us to answer several mechanistic questions. For example, the ability to program the dCas9 R-loop block to any specific sequence enables us to observe whether block removal is different depending on whether the block is on the leading or lagging strand. Furthermore, the inner diameter of CMG can accommodate double-stranded DNA (dsDNA) and possibly an R-loop, but not a dCas9 protein. Using the dCas9 R-loop block allows us to determine the fate of each of its components.Here, we report that Pif1 enables the bypass of the dCas9 R-loop by the replisome. Interestingly, dCas9 R-loops targeted to either the leading or lagging strand are bypassed with similar efficiency. In addition, the PCNA clamp is not required for bypass of the block, indicating that Pif1 does not need to interact with PCNA during bypass of the block. We used a single-molecule fluorescence imaging to show that both the dCas9 and the R-loop are displaced as an intact nucleoprotein complex. We propose that Pif1 is a general displacement helicase for replication bypass of both R-loops and protein blocks.     

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.     

Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road

Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.

Eurasia is the largest landmass on Earth and has a rich demographic, cultural, and economic history. It was one of the birthplaces of agriculture and hosts the richest variety of crops, including vegetable crops (1–3). Eurasia is also the likely area of origin of many plant pathogens (4–6), but there have been few detailed studies of exactly when and where these pathogens emerged. Possibly owing to a lack of genetic sequence data, there also remains a poor understanding of the migration pathways of plant viruses and other plant pathogens in Eurasia.Turnip mosaic potyvirus (TuMV) is probably the most widespread and important plant virus and occurs throughout subtropical and temperate regions (7). It mainly damages dicotyledonous domestic brassica crops, which are important food vegetables and were probably developed from wild Brassica plants by plant breeders during the expansion of agriculture. First described from brassica crops in 1921 in the United States (8, 9), TuMV has been ranked behind only cucumber mosaic cucumovirus as the most important virus infecting field-grown vegetables (10, 11).Brassica vegetables, the main host plants of TuMV in modern agriculture (7, 10), mostly originated in the Mediterranean and Western Eurasia (12, 13). These economically important plants are commonly known as cabbages or mustard plants and include turnip, cauliflower, and broccoli. A possible wild ancestor of cabbage was originally found in Western and Southern Europe (14). Brassica vegetables then spread to East Asia, including Japan and Korea, while the first record of the cultivation of Chinese cabbage dates from the 15th century CE. The edible radish (Raphanus sativus) possibly originated from ancestral wild radish (Raphanus raphanistrum) in the Mediterranean region and was domesticated in Asia prior to Roman times (15).Within the genus Potyvirus (family Potyviridae), TuMV is closely related to viruses from monocotyledonous narcissus, scallion, wild onion, and yam to form the TuMV phylogenetic group (16–19). Potyviruses infect a wide range of flowering plants (16, 19, 20) and are spread by aphids in a nonpersistent manner and sometimes in seeds and infected living plant materials. They have a genome that is a single-stranded, positive-sense RNA of ∼10,000 nucleotides (nt). The genome has one major open reading frame (ORF), which is translated into one large polyprotein, and a small overlapping ORF, a “pretty interesting Potyviridae ORF” (21). The polyprotein is autocatalytically hydrolyzed into at least 10 mature proteins (19, 22).In terms of its evolution and epidemiology, the potyvirus TuMV is among the best studied of the plant-infecting RNA viruses. We have shown that it probably originated from a virus of wild orchids in Europe (7, 23). While adapting to wild and domestic Brassicaceae plants, TuMV spread from its center of emergence in Southern Europe, Asia Minor, and the Middle East to other parts of the world, including East Asia (24–27), Oceania (28), and the Americas (7, 29). However, the evolution and epidemiology of this virus in Eurasia remain poorly studied, leaving considerable uncertainty about its past migration pathways and its evolutionary dynamics and timescale.In this study, we collected TuMV isolates from locations throughout Eurasia, including countries neighboring the center of emergence. We examined the biological characteristics of viral isolates that had been sampled from these countries across half a century of growing seasons. By analyzing 579 whole genome sequences, we estimated the evolutionary rate and timescale of TuMV and inferred its phylodynamic and phylogeographic history. Our study presents one of the largest and most detailed evolutionary and epidemiological analyses of a plant pathogen, providing a comprehensive picture of the temporal and spatial spread of a major plant pathogen across Eurasia.     

Skills-adjusted human capital shows rising global gap

Human capital, broadly defined as the skills acquired through formal education, is acknowledged as one of the key drivers of economic growth and social development. However, its measurement for the working-age populations, on a global scale and over time, is still unsatisfactory. Most indicators either only consider the quantity dimension of education and disregard the actual skills or are demographically inconsistent by applying the skills of the young cohorts in school to represent the skills of the working-age population at the same time. In the case of rapidly expanding or changing school systems, this assumption is untenable. However, an increasing number of countries have started to assess the literacy skills of their adult populations by age and sex directly. Drawing on this literacy data, and by using demographic backprojection and statistical estimation techniques, we here present a demographically consistent indicator for adult literacy skills, the skills in literacy adjusted mean years of schooling (SLAMYS). The measure is given for the population aged 20 to 64 in 185 countries and for the period 1970 to 2015. Compared to the conventional mean years of schooling (MYS)—which has strongly increased for most countries over the past decades, and in particular among poor countries—the trends in SLAMYS exhibit a widening global skills gap between low- and high-performing countries.

Since antiquity, education has been considered one of the most important investments into young people aside from health. From Confucius and Socrates to modern enlightenment and up to the recent Sustainable Development Goals, the enhancement of the skills of the young generations has been an almost universal aspiration of human civilization. However, access to learning opportunities was limited to small elites, and only from the 19th century onward has it been gradually spreading to all men and subsequently women, first in Northern Europe and over the 20th century in most countries (1).To describe the relevance of education for the individual life and for national prosperity, researchers have developed the concept of human capital. In a narrow economic sense, the term refers to the level of skills embodied in an individual that could be used to generate earnings in the labor market (2–4). A broader definition includes health and general cognitive empowerment (5, 6), and looks at benefits far beyond monetary returns, ranging from demographic trends (7, 8), to criminality (9), quality of institutions, and social cohesion (10).To comprehensively assess the multiple benefits of investments in education, large globally comparable sets of data are required (11–13). So far, global indicators of adult human capital estimated at the country level and over time include mean years of schooling (MYS) (14–16) and full educational attainment distributions disaggregated by age and sex (17–21). Attempts to address the quality of education in addition to or instead of the quantity mostly use international school assessment data (22–25). While human capital theory clearly focuses on the benefits of adult skills, so far global harmonized datasets on education quality have focused on the school-age population (26, 27), despite the fact that the skills assessed in schools were found to be a poor measure of the concurrent level of adult skills in a population (28).To fill this important gap in global human capital data, we present an indicator, the skills in literacy adjusted mean years of schooling (SLAMYS). This indicator improves on currently available human capital indicators in four dimensions: 1) reliance on adult skills surveys; 2) demographic consistency; 3) global availability; and 4) temporal evolution since 1970. By introducing SLAMYS, we not only provide insights in the evolution of inequality in adult skills between countries and over time, but also present researchers with a consistent global dataset for further studies on the relationship between human capital and development outcomes.Our empirical exercise relies on data harmonization, demographic modeling, and statistical estimation for 185 countries. Empirical adult literacy skills assessment scores came from four different survey types: International Adult Literacy Survey (IALS) (29), Program for the International Assessment of Adult Competencies (PIAAC) (30), Skills toward Employment and Productivity Survey (STEP) (31), and Demographic and Health Survey (DHS) (32). Existing estimates of educational attainment distributions and resulting MYS by age and sex for all countries for 1970 to 2015 were collected from the Wittgenstein Centre (WIC) Human Capital Data Explorer (20). For countries without direct empirical evidence on adult literacy skills, the statistical estimation model included among others, adult literacy, school enrolment rates, educational expenditure, and pupil–teacher ratios from the United Nations Educational, Scientific and Cultural Organization (UNESCO) Institute of Statistics (33), and harmonized learning scores from the Global Dataset on Education Quality (34). The specific data and methods applied are described in detail in SI Appendix.