Neanderthals hunted and butchered straight- tusked elephants, the largest terrestrial mammals of the Pleistocene, in a lake landscape on the North European plain, 125,000 years ago, as... Show moreNeanderthals hunted and butchered straight- tusked elephants, the largest terrestrial mammals of the Pleistocene, in a lake landscape on the North European plain, 125,000 years ago, as recently shown by a study of the Last Interglacial elephant assemblage from Neumark- Nord (Germany). With evidence for a remarkable focus on adult males and on their extended utilization, the data from this location are thus far without parallel in the archaeological record. Given their relevance for our knowledge of the Neanderthal niche, we investigated whether the Neumark- Nord subsistence practices were more than a local phenomenon, possibly determined by local characteristics. Analyzing elephant remains from two other Last Interglacial archaeological sites on the North European plain, Gröbern and Taubach, we identified in both assemblages similar butchering patterns as at Neumark-Nord, demonstrating that extended elephant exploitation was a widespread Neanderthal practice during the (early part of the) Last Interglacial. The substantial efforts needed to process these animals, weighing up to 13 metric tons, and the large amounts of food generated suggest that Neanderthals either had ways of storing vast amounts of meat and fat and/or temporarily aggregated in larger groups than com-monly acknowledged. The data do not allow us to rule out one of the two explanations, and furthermore both factors, short- term larger group sizes as well as some form of food preservation, may have played a role. What the data do show is that exploitation of large straight-tusked elephants was a widespread and recurring phenomenon amongst Last Interglacial Neanderthals on the North European plain. Show less
Hoang Nguyen, T.; Taherzadeh, O.A.; Ohashi, H.; Yonekura, Y.; Nishijima, S.; Yamabe, M.; ... ; Kanemoto, K. 2023
Long-lived parasites evade host immunity through highly evolved molecular strategies. The murine intestinal helminth, Heligmosomoides polygyrus, down-modulates the host immune system through... Show moreLong-lived parasites evade host immunity through highly evolved molecular strategies. The murine intestinal helminth, Heligmosomoides polygyrus, down-modulates the host immune system through release of an immunosuppressive TGF-β mimic, TGM1, which is a divergent member of the CCP (Sushi) protein family. TGM1 comprises 5 domains, of which domains 1-3 (D1/2/3) bind mammalian TGF-β receptors, acting on T cells to induce Foxp3+ regulatory T cells; however, the roles of domains 4 and 5 (D4/5) remain unknown. We noted that truncated TGM1, lacking D4/5, showed reduced potency. Combination of D1/2/3 and D4/5 as separate proteins did not alter potency, suggesting that a physical linkage is required and that these domains do not deliver an independent signal. Coprecipitation from cells treated with biotinylated D4/5, followed by mass spectrometry, identified the cell surface protein CD44 as a coreceptor for TGM1. Both full-length and D4/5 bound strongly to a range of primary cells and cell lines, to a greater degree than D1/2/3 alone, although some cell lines did not respond to TGM1. Ectopic expression of CD44 in nonresponding cells conferred responsiveness, while genetic depletion of CD44 abolished enhancement by D4/5 and ablated the ability of full-length TGM1 to bind to cell surfaces. Moreover, CD44-deficient T cells showed attenuated induction of Foxp3 by full-length TGM1, to levels similar to those induced by D1/2/3. Hence, a parasite protein known to bind two host cytokine receptor subunits has evolved a third receptor specificity, which serves to raise the avidity and cell type–specific potency of TGF-β signaling in mammalian cells. Show less
The foundations of today’s societies are provided by manufactured capital accumulation driven by investment decisions through time. Reconceiving how the manufactured assets are harnessed in the... Show moreThe foundations of today’s societies are provided by manufactured capital accumulation driven by investment decisions through time. Reconceiving how the manufactured assets are harnessed in the production–consumption system is at the heart of the paradigm shifts necessary for long-term sustainability. Our research integrates 50 years of economic and environmental data to provide the global legacy environmental footprint (LEF) and unveil the historical material extractions, greenhouse gas emissions, and health impacts accrued in today’s manufactured capital. We show that between 1995 and 2019, global LEF growth outpaced GDP and population growth, and the current high level of national capital stocks has been heavily relying on global supply chains in metals. The LEF shows a larger or growing gap between developed economies (DEs) and less-developed economies (LDEs) while economic returns from global asset supply chains disproportionately flow to DEs, resulting in a double burden for LDEs. Our results show that ensuring best practice in asset production while prioritizing well-being outcomes is essential in addressing global inequalities and protecting the environment. Achieving this requires a paradigm shift in sustainability science and policy, as well as in green finance decision-making, to move beyond the focus on the resource use and emissions of daily operations of the assets and instead take into account the long-term environmental footprints of capital accumulation. Show less
Globalizing economies and long-distance trade rely on individuals from different cultural groups to negotiate agreement on what to give and take. In such settings, individuals often lack insight... Show moreGlobalizing economies and long-distance trade rely on individuals from different cultural groups to negotiate agreement on what to give and take. In such settings, individuals often lack insight into what interaction partners deem fair and appropriate, potentially seeding misunderstandings, frustration, and conflict. Here, we examine how individuals decipher distinct rules of engagement and adapt their behavior to reach agreements with partners from other cultural groups. Modeling individuals as Bayesian learners with inequality aversion reveals that individuals, in repeated ultimatum bargaining with responders sampled from different groups, can be more generous than needed. While this allows them to reach agreements, it also gives rise to biased beliefs about what is required to reach agreement with members from distinct groups. Preregistered behavioral (N = 420) and neuroimaging experiments (N = 49) support model predictions: Seeking equitable agreements can lead to overly generous behavior toward partners from different groups alongside incorrect beliefs about prevailing norms of what is appropriate in groups and cultures other than one’s own. Show less
Seifinejad, A.; Ramosaj, M.; Shan, L.; Li, S.; Possovre, M.L.; Pfister, C.; ... ; Tafti, M. 2023
Narcolepsy with cataplexy is a sleep disorder caused by deficiency in the hypothalamic neuropeptide hypocretin/orexin (HCRT), unanimously believed to result from autoimmune destruction of... Show moreNarcolepsy with cataplexy is a sleep disorder caused by deficiency in the hypothalamic neuropeptide hypocretin/orexin (HCRT), unanimously believed to result from autoimmune destruction of hypocretin-producing neurons. HCRT deficiency can also occur in secondary forms of narcolepsy and be only temporary, suggesting it can occur without irreversible neuronal loss. The recent discovery that narcolepsy patients also show loss of hypothalamic (corticotropin-releasing hormone) CRH-producing neurons suggests that other mechanisms than cell-specific autoimmune attack, are involved. Here, we identify the HCRT cell-colocalized neuropeptide QRFP as the best marker of HCRT neurons. We show that if HCRT neurons are ablated in mice, in addition to Hcrt,Qrfp transcript is also lost in the lateral hypothalamus, while in mice where only the Hcrt gene is inactivated Qrfp is unchanged. Similarly, postmortem hypothalamic tissues of narcolepsy patients show preserved QRFP expression, suggesting the neurons are present but fail to actively produce HCRT. We show that the promoter of the HCRT gene of patients exhibits hypermethylation at a methylation-sensitive and evolutionary-conserved PAX5:ETS1 transcription factor-binding site, suggesting the gene is subject to transcriptional silencing. We show also that in addition to HCRT, CRH and Dynorphin (PDYN) gene promoters, exhibit hypermethylation in the hypothalamus of patients. Altogether, we propose that HCRT, PDYN, and CRH are epigenetically silenced by a hypothalamic assault (inflammation) in narcolepsy patients, without concurrent cell death. Since methylation is reversible, our findings open the prospect of reversing or curing narcolepsy. Show less
Heuvel, D. van den; Kim, M.; Wondergem, A.P.; Meer, P.J. van der; Witkamp, M.; Lambregtse, F.; ... ; Luijsterburg, M.S. 2023
XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways.... Show moreXPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum ( XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPAH244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (similar to 50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER. Show less
Fan, J.; Hale V.L.; Lelieveld, L.T.; Whitworth, L.J.; Busch-Nentwich, E.M.; Troll, M.; ... ; Ramakrishnan, L. 2023
Straightforward manufacturing pathways toward large-scale, uniformly layered composites may enable the next generation of materials with advanced optical, thermal, and mechanical properties.... Show moreStraightforward manufacturing pathways toward large-scale, uniformly layered composites may enable the next generation of materials with advanced optical, thermal, and mechanical properties. Reaction-diffusion systems are attractive candidates to this aim, but while layered composites theoretically could spontaneously arise from reaction-diffusion, in practice randomly oriented patches separated by defects form, yielding nonuniformly patterned materials. A propagating reaction front can prevent such nonuniform patterning, as is the case for Liesegang processes, in which diffusion drives a reaction front to produce layered precipitation patterns. However, while diffusion is crucial to control patterning, it slows down transport of reactants to the front and results in a steady increase of the band spacing as the front advances. Here, we circumvent these diffusive limitations by embedding the Liesegang process in mechanically responsive hydrogels. The coupling between a moving reaction front and hydrogel contraction induces the formation of a self-regulated transport channel that ballistically carries reactants toward the area where patterning occurs. This ensures rapid and uniform patterning. Specifically, large-scale ([Formula: see text]5-cm) uniform banding patterns are produced with tunable band distance (d = 60 to 160 µm) of silver dichromate crystals inside responsive gelatin-alginate hydrogels. The generality and applicability of our mechanoreaction-diffusion strategy are demonstrated by forming patterns of precipitates in significantly smaller microscopic banding patterns (d = 10 to 30 µm) that act as self-organized diffraction gratings. By circumventing the inherent limitations of diffusion, our strategy unlocks the potential of reaction-diffusion processes for the manufacturing of uniformly layered materials. Show less
Glutaminyl cyclase (QC) modifies N-terminal glutamine or glutamic acid residues of target proteins into cyclic pyroglutamic acid (pGlu). Here, we report the biochemical and functional analysis of P...Show moreGlutaminyl cyclase (QC) modifies N-terminal glutamine or glutamic acid residues of target proteins into cyclic pyroglutamic acid (pGlu). Here, we report the biochemical and functional analysis of Plasmodium QC. We show that sporozoites of QC-null mutants of rodent and human malaria parasites are recognized by the mosquito immune system and melanized when they reach the hemocoel. Detailed analyses of rodent malaria QC-null mutants showed that sporozoite numbers in salivary glands are reduced in mosquitoes infected with QC-null or QC catalytically dead mutants. This phenotype can be rescued by genetic complementation or by disrupting mosquito melanization or phagocytosis by hemocytes. Mutation of a single QC-target glutamine of the major sporozoite surface protein (circumsporozoite protein; CSP) of the rodent parasite Plasmodium berghei also results in melanization of sporozoites. These findings indicate that QC-mediated posttranslational modification of surface proteins underlies evasion of killing of sporozoites by the mosquito immune system. Show less
Pattern recognition molecules (PRMs) form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The... Show morePattern recognition molecules (PRMs) form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The pentraxin family of soluble PRMs comprises long and short pentraxins, with the former containing unique N-terminal regions unrelated to other proteins or each other. No complete high-resolution structural information exists about long pentraxins, unlike the short pentraxins, where there is an abundance of both X-ray and cryoelectron microscopy (cryo-EM)-derived structures. This study presents a high-resolution structure of the prototypical long pentraxin, PTX3. Cryo-EM yielded a 2.5-angstrom map of the C-terminal pentraxin domains that revealed a radically different quaternary structure compared to other pentraxins, comprising a glycosylated D4 symmetrical octameric complex stabilized by an extensive disulfide network. The cryo-EM map indicated a-helices that extended N terminal of the pentraxin domains that were not fully resolved. AlphaFold was used to predict the remaining N-terminal structure of the octameric PTX3 complex, revealing two long tetrameric coiled coils with two hinge regions, which was validated using classification of cryo-EM two-dimensional averages. The resulting hybrid cryo-EM/AlphaFold structure allowed mapping of ligand binding sites, such as C1q and fibroblast growth factor-2, as well as rationalization of previous biochemical data. Given the relevance of PTX3 in conditions ranging from COVID-19 prognosis, cancer progression, and female infertility, this structure could be used to inform the understanding and rational design of therapies for these disorders and processes. Show less
Boer, C. de; Armstrong, Z.W.B; Lit, V.A.J.; Barash, U.; Ruijgrok, G.; Boyango, I.; ... ; Wu, L. 2022
Heparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG... Show moreHeparan sulfate proteoglycans (HSPGs) mediate essential interactions throughout the extracellular matrix (ECM), providing signals that regulate cellular growth and development. Altered HSPG composition during tumorigenesis strongly aids cancer progression. Heparanase (HPSE) is the principal enzyme responsible for extracellular heparan sulfate catabolism and is markedly up-regulated in aggressive cancers. HPSE overactivity degrades HSPGs within the ECM, facilitating metastatic dissemination and releasing mitogens that drive cellular proliferation. Reducing extracellular HPSE activity reduces cancer growth, but few effective inhibitors are known, and none are clinically approved. Inspired by the natural glycosidase inhibitor cyclophellitol, we developed nanomolar mechanism-based, irreversible HPSE inhibitors that are effective within physiological environments. Application of cyclophellitol-derived HPSE inhibitors reduces cancer aggression in cellulo and significantly ameliorates murine metastasis. Mechanism-based irreversible HPSE inhibition is an unexplored anticancer strategy. We demonstrate the feasibility of such compounds to control pathological HPSE-driven malignancies. Show less
In the current era of T cell-based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens,... Show moreIn the current era of T cell-based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens, chimeric peptides are generated through proteasome-catalyzed peptide splicing (PCPS). Whether such spliced peptides are abundantly presented by MHC is highly disputed because of disagreement in computational analyses of mass spectrometry data of MHC-eluted peptides. Moreover, such mass spectrometric analyses cannot elucidate how much spliced peptides contribute to the pool of immunogenic antigens. In this Perspective, we explain the significance of knowing the contribution of spliced peptides for accurate analyses of peptidomes on one hand, and to serve as a potential source of targetable tumor antigens on the other hand. Toward a strategy for mass spectrometry independent estimation of the contribution of PCPS to the immunopeptidome, we first reviewed methodologies to identify MHC-presented spliced peptide antigens expressed by tumors. Data from these identifications allowed us to compile three independent datasets containing 103, 74, and 83 confirmed T cell antigens from cancer patients. Only 3.9%, 1.4%, and between 0% and 7.2% of these truly immunogenic antigens are produced by PCPS, therefore providing a marginal contribution to the pool of immunogenic tumor antigens. We conclude that spliced peptides will not serve as a comprehensive source to expand the number of targetable antigens for immunotherapies. Show less
When moderating content online, two key values may come into conflict: protecting freedom of expression and preventing harm. Robust rules based in part on how citizens think about these moral... Show moreWhen moderating content online, two key values may come into conflict: protecting freedom of expression and preventing harm. Robust rules based in part on how citizens think about these moral dilemmas are necessary to deal with the unprecedented scale and urgency of this conflict in a principled way. Yet little is known about people’s judgments and preferences around content moderation. We examined such moral dilemmas in a conjoint survey experiment where respondents (N=2,564) indicated whether they would remove problematic social media posts on election denial, anti-vaccination, Holocaust denial, and climate change denial and whether they would take punitive action against the accounts. Respondents were shown key information about the user and their post, as well as the consequences of the misinformation. The majority preferred quashing harmful misinformation over protecting free speech. Respondents were more likely to remove posts and suspend accounts if the consequences were severe and if it was a repeated offence. Features related to the account itself (the person behind the account, their partisanship, and the number of followers) had little to no effect on respondents’ decisions. Content moderation of harmful misinformation was a partisan issue: Across all four scenarios, Republicans were consistently less willing than Democrats or Independents to delete posts or penalize the accounts that posted them. Our results can inform the design of transparent rules of content moderation for human and algorithmic moderators. Show less
Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity toward other antibiotics, offers treatment opportunities to constrain or reverse the evolution of... Show moreCollateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity toward other antibiotics, offers treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here, we address this issue in the gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles and their combinations that confer resistance to fluoroquinolones. We integrated these results in a mathematical model that allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects to different antibiotics and suggest that these need to be considered in models examining CS-based therapies. Show less
Madrigal-Matute, J.; Bruijn, J. de; Kuijk, K. van; Riascos-Bernal, D.F.; Diaz, A.; Tasset, I.; ... ; Cuervo, A.M. 2022
Chaperone-mediated autophagy (CMA) contributes to regulation of energy homeostasis by timely degradation of enzymes involved in glucose and lipid metabolism. Here, we report reduced CMA activity in... Show moreChaperone-mediated autophagy (CMA) contributes to regulation of energy homeostasis by timely degradation of enzymes involved in glucose and lipid metabolism. Here, we report reduced CMA activity in vascular smooth muscle cells and macrophages in murine and human arteries in response to atherosclerotic challenges. We show that in vivo genetic blockage of CMA worsens atherosclerotic pathology through both systemic and cell-autonomous changes in vascular smooth muscle cells and macrophages, the two main cell types involved in atherogenesis. CMA deficiency promotes dedifferentiation of vascular smooth muscle cells and a proinflammatory state in macrophages. Conversely, a genetic mouse model with up-regulated CMA shows lower vulnerability to proatherosclerotic challenges. We propose that CMA could be an attractive therapeutic target against cardiovascular diseases. Show less
In modern society, the widespread use of artificial light at night disrupts the suprachiasmatic nucleus (SCN), which serves as our central circadian clock. Existing models describe excitatory... Show moreIn modern society, the widespread use of artificial light at night disrupts the suprachiasmatic nucleus (SCN), which serves as our central circadian clock. Existing models describe excitatory responses of the SCN to primarily blue light, but direct measures in humans are absent. The combination of state-of-the-art neuroimaging techniques and custom-made MRI compatible light-emitting diode devices allowed to directly measure the light response of the SCN. In contrast to the general expectation, we found that blood oxygen level-dependent (BOLD) functional MRI signals in the SCN were suppressed by light. The suppressions were observed not only in response to narrowband blue light (lambda max: 470 nm) but remarkably, also in response to green (lambda max: 515 nm) and orange (lambda max: 590 nm), but not to violet light (lambda max: 405 nm). The broadband sensitivity of the SCN implies that strategies on light exposure should be revised: enhancement of light levels during daytime is possible with wavelengths other than blue, while during nighttime, all colors are potentially disruptive. Show less
