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Targeted protein degradation is a drug modality represented by compounds that recruit a target to an E3 ubiquitin ligase to promote target ubiquitination and proteasomal degradation. Historically, the field distinguishes monovalent degraders from bifunctional degraders (PROTACs) that connect target and ligase via separate binding ligands joined via a linker1–4. Here, we elucidate the mechanism of action of a PROTAC-like degrader of the transcriptional coactivator BRD4, composed of a BRD4 ligand linked to a ligand for the E3 ligase CRL4DCAF15. Using orthogonal CRISPR/Cas9 screens we identify the degrader activity is independent of DCAF15, and relies on a different CRL4 substrate receptor, DCAF16. We demonstrate an intrinsic affinity between BRD4 and DCAF16, which is dependent on the tandem bromodomains of BRD4 and further increased by the degrader without physically engaging DCAF16 in isolation. Structural characterization of the resulting ternary complex reveals both BRD4 bromodomains are bivalently engaged in cis by the degrader and are bound to DCAF16 through several interfacial BRD4-DCAF16 and degrader-DCAF16 contacts. Our findings demonstrate that intramolecularly bridging domains can confer glue-type stabilization of intrinsic target-E3 interactions, and we propose this as a general strategy to modulate the surface topology of target proteins to nucleate co-opting of E3 ligases or other cellular effector proteins for effective proximity-based pharmacology.
Glutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signaling pathways. Achieving a detailed understanding of intracellular GSH trafficking and regulation depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Herein, we present a new GSH sensing platform, TRaQ-G, for live-cell imaging. This small-molecule/protein hybrid sensor possesses a unique reactivity turn-on mechanism that ensures that the small molecule is only sensitive to GSH in the desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein of choice to give a ratiometric response. Using TRaQ-G-mGold, we demonstrated that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. We also used this sensor, in combination with roGFP, to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor.
Tracking influenza a virus infection in the lung from hematological data with machine learning
(2022)
The tracking of pathogen burden and host responses with minimal-invasive methods during respiratory infections is central for monitoring disease development and guiding treatment decisions. Utilizing a standardized murine model of respiratory Influenza A virus (IAV) infection, we developed and tested different supervised machine learning models to predict viral burden and immune response markers, i.e. cytokines and leukocytes in the lung, from hematological data. We performed independently in vivo infection experiments to acquire extensive data for training and testing purposes of the models. We show here that lung viral load, neutrophil counts, cytokines like IFN-γ and IL-6, and other lung infection markers can be predicted from hematological data. Furthermore, feature analysis of the models shows that blood granulocytes and platelets play a crucial role in prediction and are highly involved in the immune response against IAV. The proposed in silico tools pave the path towards improved tracking and monitoring of influenza infections and possibly other respiratory infections based on minimal-invasively obtained hematological parameters.
We have investigated the systematic differences introduced when performing a Bayesian-inference analysis of the equation of state of neutron stars employing either variable- or constant-likelihood functions. The former have the advantage that it retains the full information on the distributions of the measurements, making an exhaustive usage of the data. The latter, on the other hand, have the advantage of a much simpler implementation and reduced computational costs. In both approaches, the EOSs have identical priors and have been built using the sound-speed parameterization method so as to satisfy the constraints from X-ray and gravitationalwaves observations, as well as those from Chiral Effective Theory and perturbative QCD. In all cases, the two approaches lead to very similar results and the 90%-confidence levels are essentially overlapping. Some differences do appear, but in regions where the probability density is extremely small and are mostly due to the sharp cutoff set on the binary tidal deformability Λ˜ ≤ 720 employed in the constant-likelihood analysis. Our analysis has also produced two additional results. First, a clear inverse correlation between the normalized central number density of a maximally massive star, nc,TOV/ns, and the radius of a maximally massive star, RTOV. Second, and most importantly, it has confirmed the relation between the chirp mass Mchirp and the binary tidal deformability Λ˜. The importance of this result is that it relates a quantity that is measured very accurately, Mchirp, with a quantity that contains important information on the micro-physics, Λ˜. Hence, once Mchirp is measured in future detections, our relation has the potential of setting tight constraints on Λ˜.
Viewpoint effects on object recognition interact with object-scene consistency effects. While recognition of objects seen from “accidental” viewpoints (e.g., a cup from below) is typically impeded compared to processing of objects seen from canonical viewpoints (e.g., the string-side of a guitar), this effect is reduced by meaningful scene context information. In the present study we investigated if these findings established by using photographic images, generalise to 3D models of objects. Using 3D models further allowed us to probe a broad range of viewpoints and empirically establish accidental and canonical viewpoints. In Experiment 1, we presented 3D models of objects from six different viewpoints (0°, 60°, 120°, 180° 240°, 300°) in colour (1a) and grayscaled (1b) in a sequential matching task. Viewpoint had a significant effect on accuracy and response times. Based on the performance in Experiments 1a and 1b, we determined canonical (0°-rotation) and non-canonical (120°-rotation) viewpoints for the stimuli. In Experiment 2, participants again performed a sequential matching task, however now the objects were paired with scene backgrounds which could be either consistent (e.g., a cup in the kitchen) or inconsistent (e.g., a guitar in the bathroom) to the object. Viewpoint interacted significantly with scene consistency in that object recognition was less affected by viewpoint when consistent scene information was provided, compared to inconsistent information. Our results show that viewpoint-dependence and scene context effects generalize to depth rotated 3D objects. This supports the important role object-scene processing plays for object constancy.
In a dynamic environment, the already limited information that human working memory can maintain needs to be constantly updated to optimally guide behaviour. Indeed, previous studies showed that working memory representations are continuously being transformed during delay periods leading up to a response. This goes hand-in-hand with the removal of task-irrelevant items. However, does such removal also include veridical, original stimuli, as they were prior to transformation? Here we aimed to assess the neural representation of task-relevant transformed representations, compared to the no-longer-relevant veridical representations they originated from. We applied multivariate pattern analysis to electroencephalographic data during maintenance of orientation gratings with and without mental rotation. During maintenance, we perturbed the representational network by means of a visual impulse stimulus, and were thus able to successfully decode veridical as well as imaginary, transformed orientation gratings from impulse-driven activity. On the one hand, the impulse response reflected only task-relevant (cued), but not task-irrelevant (uncued) items, suggesting that the latter were quickly discarded from working memory. By contrast, even though the original cued orientation gratings were also no longer task-relevant after mental rotation, these items continued to be represented next to the rotated ones, in different representational formats. This seemingly inefficient use of scarce working memory capacity was associated with reduced probe response times and may thus serve to increase precision and flexibility in guiding behaviour in dynamic environments.
Background: Blood donation saves lives. Provided they are in good health, male volunteers can donate as often as six times per year from the age of 18 into their late sixties. The burden of blood donation is very unevenly distributed, with a small minority of altruistic individuals providing this critical resource. While the consequences of persistent iron depletion in blood donors have been studied in the context of cancer and coronary heart disease, potential effects of the erythropoietic stress from repetitive large-volume phlebotomy remain unexplored. We sought to investigate if and how repeated blood donations affect the clonal composition of the hematopoietic stem and progenitor cell (HSPC) compartment.
Methods: 105 healthy, male individuals with an extensive blood donation history (median of 120 donations per donor; median age of 66 yrs.) were screened for the presence of clonal hematopoiesis (CH) using a sequencing panel covering 141 genes commonly mutated in human myeloid neoplasms. The control cohort consisted of 103 healthy, male donors with a median of 5 donations per donor and a median age of 63. Donors positive for CH were subsequently studied longitudinally. The pathogenicity of detected variants was compared using established scoring systems. Finally, to assess the functional consequences of blood-donation induced CH, selected CH mutations were introduced by CRISPR-mediated editing into HSPCs from human cord blood (CB) or bone marrow (BM). The effect of these mutations was tested under different stress stimuli using functional ex vivo long-term culture initiating cells (LTC-IC) assays.
Results: Compared to the control cohort, frequent donors were significantly more likely to have mutations in genes encoding for epigenetic modifiers (44.7 vs. 22.3 %), most specifically in the two genes most commonly mutated in CH, DNMT3A and TET2 (35.2 vs. 20.3 %). However, no difference in the variant allele frequency (VAF) of detected mutations was found between the groups. Longitudinal analysis revealed that the majority of the mutations remained at a stable VAF over an observation period of approximately one year. Three DNMT3A variants from the frequent donor cohort were introduced into healthy HSPCs and functionally analyzed: All expanded in response to EPO, but none responded to LPS or IFNγ stimulation. This contrasted with the leukemogenic DNMT3A R882H mutation, which did not expand in the presence of EPO but instead responded strongly to inflammatory stimuli.
Conclusions: Frequent whole blood donation is associated with a higher prevalence of CH driven by mutations in genes encoding for epigenetic modifiers, with DNMT3A and TET2 being the most common. This increased CH prevalence is not associated with a higher pathogenicity of the associated variants and is likely a result of the selection of clones with improved responsiveness to EPO under the condition of bleeding stress. Our data show that even highly frequent blood donations over many years is not increasing the risk for malignant clones further underscoring the safety of repetitive blood donations. To our knowledge, this is the first CH study analyzing a cohort of individuals known for their superior health and survival, able to donate blood until advanced age. Thus, our analysis possibly identified mutations associated with beneficial outcomes, rather than a disease condition, such as mutations in DNMT3A that mediated the improved expansion of HSPCs in EPO enriched environments. Our data support the notion of ongoing Darwinian evolution in humans at the somatic stem cell level and present EPO as one of the environmental factors to which HSPCs with specific mutations may respond with superior fitness.
Selective attention implements preferential routing of attended stimuli, likely through increasing the influence of the respective synaptic inputs on higher-area neurons. As the inputs of competing stimuli converge onto postsynaptic neurons, presynaptic circuits might offer the best target for attentional top-down influences. If those influences enabled presynaptic circuits to selectively entrain postsynaptic neurons, this might lead to selective routing. Indeed, when two visual stimuli induce two gamma rhythms in V1, only the gamma induced by the attended stimulus entrains gamma in V4. Here, we modeled this selective entrainment with a Dynamic Causal Model for Cross-Spectral Densities and found that it can be explained by attentional modulation of intrinsic V1 connections. Specifically, local inhibition was decreased in the granular input layer and increased in the supragranular output layer of the V1 circuit that processed the attended stimulus. Thus, presynaptic attentional influences and ensuing entrainment were sufficient to mediate selective routing.
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large messenger ribonucleoprotein particle (mRNP) assemblies, these proteins often function in. Using UV-induced RNA-protein crosslinking and subsequent mass spectrometric analysis, we first identified more than 100 in vivo RNA crosslinks in 16 nuclear mRNP components in S. cerevisiae. For functional analysis, we chose Npl3, for which we determined crosslinks in its two RNA recognition motifs (RRM) and in the flexible linker region connecting the two. Using NMR and structural analyses, we show that both RRM domains and the linker uniquely contribute to RNA recognition. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains of Npl3. Notably, the npl3-Linker mutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of further mRNP components into nuclear mRNPs, establishing a function of Npl3 in nuclear mRNP assembly. Taken together, we determined the specific function of the RNA-binding activity of the nuclear mRNP component Npl3, an approach that can be applied to many RBPs in any RNA metabolic process.
Vaccines are central to controlling the coronavirus disease 2019 (COVID-19) pandemic but the durability of protection is limited for currently approved COVID-19 vaccines. Further, the emergence of variants of concern (VoCs) that evade immune recognition has reduced vaccine effectiveness, compounding the problem. Here, we show that a single dose of a murine cytomegalovirus (MCMV)-based vaccine, which expresses the spike (S) protein of the virus circulating early in the pandemic (MCMVS), protects highly susceptible K18-hACE2 mice from clinical symptoms and death upon challenge with a lethal dose of D614G SARS-CoV-2. Moreover, MCMVS vaccination controlled two immune-evading VoCs, the Beta (B.1.135) and the Omicron (BA.1) variants in BALB/c mice, and S-specific immunity was maintained for at least 5 months after immunization, where neutralizing titers against all tested VoCs were higher at 5-months than at 1-month post-vaccination. Thus, cytomegalovirus (CMV)-based vector vaccines might allow for long-term protection against COVID-19.
The free energy of TAP-solutions for the SK-model of mean field spin glasses can be expressed as a nonlinear functional of local terms: we exploit this feature in order to contrive abstract REM-like models which we then solve by a classical large deviations treatment. This allows to identify the origin of the physically unsettling quadratic (in the inverse of temperature) correction to the Parisi free energy for the SK-model, and formalizes the true cavity dynamics which acts on TAP-space, i.e. on the space of TAP-solutions. From a non-spin glass point of view, this work is the first in a series of refinements which addresses the stability of hierarchical structures in models of evolving populations.
The Kitaev material α-RuCl3 is among the most prominent candidates to host a quantum spin-liquid state endowed with fractionalized excitations. Recent experimental and theoretical investigations have separately revealed the importance of both the magnetoelastic coupling and the magnetic anisotropy, in dependence of the applied magnetic field direction. In this combined theoretical and experimental research, we investigate the anisotropic magnetic and magnetoelastic properties for magnetic fields applied along the main crystallographic axes as well as for fields canted out of the honeycomb plane. We found that the magnetostriction anisotropy is unusually large compared to the anisotropy of the magnetization, which is related to the strong magnetoelastic Γ′˜-type coupling in our \textit{ab-initio} derived model. We observed large, non-symmetric magnetic anisotropy for magnetic fields canted out of the honeycomb ab-plane in opposite directions, namely towards the +c∗ or −c∗ axes, respectively. The observed directional anisotropy is explained by considering the relative orientation of the magnetic field with respect to the co-aligned RuCl6 octahedra. Magnetostriction measurements in canted fields support this non-symmetric magnetic anisotropy, however these experiments are affected by magnetic torque effects. Comparison of theoretical predictions with experimental findings allow us to recognize the significant contribution of torque effects in experimental setups where α-RuCl3 is placed in canted magnetic fields.
The phase diagram of the (1+1)-dimensional Gross-Neveu model is reanalyzed for (non-)zero chemical potential and (non-)zero temperature within the mean-field approximation. By investigating the momentum dependence of the bosonic two-point function, the well-known second-order phase transition from the Z2 symmetric phase to the so-called inhomogeneous phase is detected. In the latter phase the chiral condensate is periodically varying in space and translational invariance is broken. This work is a proof of concept study that confirms that it is possible to correctly localize second-order phase transition lines between phases without condensation and phases of spatially inhomogeneous condensation via a stability analysis of the homogeneous phase. To complement other works relying on this technique, the stability analysis is explained in detail and its limitations and successes are discussed in context of the Gross-Neveu model. Additionally, we present explicit results for the bosonic wave-function renormalization in the mean-field approximation, which is extracted analytically from the bosonic two-point function. We find regions -- a so-called moat regime -- where the wave function renormalization is negative accompanying the inhomogeneous phase as expected.
The phase diagram of the (1+1)-dimensional Gross-Neveu model is reanalyzed for (non-)zero chemical potential and (non-)zero temperature within the mean-field approximation. By investigating the momentum dependence of the bosonic two-point function, the well-known second-order phase transition from the Z2 symmetric phase to the so-called inhomogeneous phase is detected. In the latter phase the chiral condensate is periodically varying in space and translational invariance is broken. This work is a proof of concept study that confirms that it is possible to correctly localize second-order phase transition lines between phases without condensation and phases of spatially inhomogeneous condensation via a stability analysis of the homogeneous phase. To complement other works relying on this technique, the stability analysis is explained in detail and its limitations and successes are discussed in context of the Gross-Neveu model. Additionally, we present explicit results for the bosonic wave-function renormalization in the mean-field approximation, which is extracted analytically from the bosonic two-point function. We find regions -- a so-called moat regime -- where the wave function renormalization is negative accompanying the inhomogeneous phase as expected.
The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing, and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately-100-kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA- and RNA-binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerise, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
Background: Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion.
Results: By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species’ genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations (≤ 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern.
Conclusion: Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the population’s phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species’ invasion into colder ecoregions worldwide that way expanding their climate niche.
Objects that are congruent with a scene are recognised more efficiently than objects that are incongruent. Further, semantic integration of incongruent objects elicits a stronger N300/N400 EEG component. Yet, the time course and mechanisms of how contextual information supports access to semantic object information is unclear. We used computational modelling and EEG to test how context influences semantic object processing. Using representational similarity analysis, we established that EEG patterns dissociated between objects in congruent or incongruent scenes from around 300 ms. By modelling semantic processing of objects using independently normed properties, we confirm that the onset of semantic processing of both congruent and incongruent objects is similar (∼150 ms). Critically, after ∼275 ms, we discover a difference in the duration of semantic integration, lasting longer for incongruent compared to congruent objects. These results constrain our understanding of how contextual information supports access to semantic object information.
Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
Neuroscience studies in non-human primates (NHP) often follow the rule of thumb that results observed in one animal must be replicated in at least one other. However, we lack a statistical justification for this rule of thumb, or an analysis of whether including three or more animals is better than including two. Yet, a formal statistical framework for experiments with few subjects would be crucial for experimental design, ethical justification, and data analysis. Also, including three or four animals in a study creates the possibility that the results observed in one animal will differ from those observed in the others: we need a statistically justified rule to resolve such situations. Here, I present a statistical framework to address these issues. This framework assumes that conducting an experiment will produce a similar result for a large proportion of the population (termed ‘representative’), but will produce spurious results for a substantial proportion of animals (termed ‘outliers’); the fractions of ‘representative’ and ‘outliers’ animals being defined by a prior distribution. I propose a procedure in which experimenters collect results from M animals and accept results that are observed in at least N of them (‘N-out-of-M’ procedure). I show how to compute the risks α (of reaching an incorrect conclusion) and β (of failing to reach a conclusion) for any prior distribution, and as a function of N and M. Strikingly, I find that the N-out-of-M model leads to a similar conclusion across a wide range of prior distributions: recordings from two animals lowers the risk α and therefore ensures reliable result, but leaves a large risk β; and recordings from three animals and accepting results observed in two of them strikes an efficient balance between acceptable risks α and β. This framework gives a formal justification for the rule of thumb of using at least two animals in NHP studies, suggests that recording from three animals when possible markedly improves statistical power, provides a statistical solution for situations where results are not consistent between all animals, and may apply to other types of studies involving few animals.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ∼70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Our lives (and deaths) have by now been dominated for two years by COVID-19, a pandemic that has caused hundreds of millions of disease cases, millions of deaths, trillions in economic costs, and major restrictions on our freedom. Here we suggest a novel tool for controlling the COVID-19 pandemic. The key element is a method for a population-scale PCR-based testing, applied on a systematic and repeated basis. For this we have developed a low cost, highly sensitive virus-genome-based test. Using Germany as an example, we demonstrate by using a mathematical model, how useful this strategy could have been in controlling the pandemic. We show using real-world examples how this might be implemented on a mass scale and discuss the feasibility of this approach.
Mollusca is the second-largest animal phylum with over 100,000 species among eight distinct taxonomic classes. Across 1000 living species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess “shell eyes”, true eyes with a lens and retina that are embedded within the dorsal shells, which represent the most recent evolution of animal eyes. The phylogeny of major chiton clades is mostly well established, in a set of superfamily and higher-level taxa supported by various approaches including multiple gene markers, mitogenome-phylogeny and phylotranscritomic approaches as well as morphological studies. However, one critical lineage has remained unclear: Schizochiton was controversially suggested as a potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assembly of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. Phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. A consistent robust topology was generated with protein coding genes using different models and methods. Our results support Schizochitonoidea is a sister group to other Chitonoidea in Chitonina, in agreement with established classification. This suggests that the earliest origin of shell eyes is in Schizochitonoidea, which were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding on the evolution of Polyplacophora.
In meditation practices that involve focused attention to a specific object, novice practitioners often experience moments of distraction (i.e., mind wandering). Previous studies have investigated the neural correlates of mind wandering during meditation practice through Electroencephalography (EEG) using linear metrics (e.g., oscillatory power). However, their results are not fully consistent. Since the brain is known to be a chaotic/nonlinear system, it is possible that linear metrics cannot fully capture complex dynamics present in the EEG signal. In this study, we assess whether nonlinear EEG signatures can be used to characterize mind wandering during breath focus meditation in novice practitioners. For that purpose, we adopted an experience sampling paradigm in which 25 participants were iteratively interrupted during meditation practice to report whether they were focusing on the breath or thinking about something else. We compared the complexity of EEG signals during mind wandering and breath focus states using three different algorithms: Higuchi’s fractal dimension (HFD), Lempel-Ziv complexity (LZC), and Sample entropy (SampEn). Our results showed that EEG complexity was generally reduced during mind wandering relative to breath focus states. We conclude that EEG complexity metrics are appropriate to disentangle mind wandering from breath focus states in novice meditation practitioners, and therefore, they could be used in future EEG neurofeedback protocols to facilitate meditation practice.
When speech is too fast, the tracking of the acoustic signal along the auditory pathway deteriorates, leading to suboptimal speech segmentation and decoding of speech information. Thus, speech comprehension is limited by the temporal constraints of the auditory system. Here we ask whether individual differences in auditory-motor coupling strength in part shape these temporal constraints. In two behavioral experiments, we characterize individual differences in the comprehension of naturalistic speech as function of the individual synchronization between the auditory and motor systems and the preferred frequencies of the systems. Obviously, speech comprehension declined at higher speech rates. Importantly, however, both higher auditory-motor synchronization and higher spontaneous speech motor production rates were predictive of better speech-comprehension performance. Furthermore, performance increased with higher working memory capacity (Digit Span) and higher linguistic, model-based sentence predictability – particularly so at higher speech rates and for individuals with high auditory-motor synchronization. These findings support the notion of an individual preferred auditory– motor regime that allows for optimal speech processing. The data provide evidence for a model that assigns a central role to motor-system-dependent individual flexibility in continuous speech comprehension.
In this work, we study for the first time the thermal evolution of twin star pairs, i.e., stars that present the same mass but different radius and compactness. We collect available equations of state that give origin to a second branch of stable compact stars with quarks in their core. For each equation of state, we investigate the particle composition inside stars and how differently each twin evolves over time, which depends on the central density/pressure and consequent crossing of the threshold for the Urca cooling process. We find that, although the general stellar thermal evolution depends on mass and particle composition, withing one equation of state, only twin pairs that differ considerably on compactness can be clearly distinguished by how they cool down.
Although new advances in neuroscience allow the study of vocal communication in awake animals, substantial progress in the processing of vocalizations has been made from brains of anaesthetized preparations. Thus, understanding how anaesthetics affect neuronal responses is of paramount importance. Here, we used electrophysiological recordings and computational modelling to study how the auditory cortex of bats responds to vocalizations under anaesthesia and in wakefulness. We found that multifunctional neurons that process echolocation and communication sounds were affected by ketamine anaesthesia in a manner that could not be predicted by known anaesthetic effects. In wakefulness, acoustic contexts (preceding echolocation or communication sequences) led to stimulus-specific suppression of lagging sounds, accentuating neuronal responses to sound transitions. However, under anaesthesia, communication contexts (but not echolocation) led to a global suppression of responses to lagging sounds. Such asymmetric effect was dependent on the frequency composition of the contexts and not on their temporal patterns. We constructed a neuron model that could replicate the data obtained in vivo. In the model, anaesthesia modulates spiking activity in a channel-specific manner, decreasing responses of cortical inputs tuned to high-frequency sounds and increasing adaptation in the respective cortical synapses. Combined, our findings obtained in vivo and in silico reveal that ketamine anaesthesia does not reduce uniformly the neurons’ responsiveness to low and high frequency sounds. This effect depends on combined mechanisms that unbalance cortical inputs and ultimately affect how auditory cortex neurons respond to natural sounds in anaesthetized preparations.
The knowledge that brain functional connectomes are both unique and reliable has enabled behaviourally relevant inferences at a subject level. However, it is unknown whether such “fingerprints” persist under altered states of consciousness. Ayahuasca is a potent serotonergic psychedelic which elicits a widespread dysregulation of functional connectivity. Used communally in religious ceremonies, its shared use may highlight relevant novel interactions between mental state and FC inherency. Using 7T fMRI, we assessed resting-state static and dynamic FCs for 21 Santo Daime members after collective ayahuasca intake in an acute, within-subject study. Here, connectome fingerprinting revealed a shared functional space, accompanied by a spatiotemporal reallocation of keypoint edges. Importantly, we show that interindividual differences in higher-order FCs motifs are relevant to experiential phenotypes, given that they can predict perceptual drug effects. Collectively, our findings offer an example as to how individualised connectivity markers can be used to trace a subject’s functional connectome across altered states of consciousness.
In this article we provide a stack-theoretic framework to study the universal tropical Jacobian over the moduli space of tropical curves. We develop two approaches to the process of tropicalization of the universal compactified Jacobian over the moduli space of curves -- one from a logarithmic and the other from a non-Archimedean analytic point of view. The central result from both points of view is that the tropicalization of the universal compactified Jacobian is the universal tropical Jacobian and that the tropicalization maps in each of the two contexts are compatible with the tautological morphisms. In a sequel we will use the techniques developed here to provide explicit polyhedral models for the logarithmic Picard variety.
Intraspecific genomic variability affects a species’ adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.
Moving in synchrony to external rhythmic stimuli is an elementary function that humans regularly engage in. It is termed “sensorimotor synchronization” and it is governed by two main parameters, the period and the phase of the movement with respect to the external rhythm. There has been an extensive body of research on the characteristics of these parameters, primarily once the movement synchronization has reached a steady-state level. Particular interest has been shown about how these parameters are corrected when there are deviations for the steady-state level. However, little is known about the initial “tuning-in” interval, when one aligns the movement to the external rhythm from rest. The current work investigates this “tuning-in” period for each of the four limbs and makes various novel contributions in the understanding of sensorimotor synchronization. The results suggest that phase and period alignment appear to be separate processes. Phase alignment involves limb-specific somatosensory memory in the order of minutes while period alignment has very limited memory usage. Phase alignment is the primary task but then the brain switches to period alignment where it spends most its resources. In overall this work suggests a central, cognitive role of period alignment and a peripheral, sensorimotor role of phase alignment.
Research on psychopathy has so far been largely limited to the investigation of high-level processes, such as emotion perception and regulation. In the present work, we investigate whether psychopathy has an effect on the estimation of fundamental physical parameters, which are computed in the brain during early stages of sensory processing. We employed a simple task in which participants had to estimate their interpersonal distance from a moving avatar and stop it at a given distance. The face expression of the avatars were positive, negative, or neutral. Participants carried out the task online on their home computers. We measured the psychopathy level via a self-report questionnaire. Regardless of the degree of psychopathy, the facial expression of the avatars showed no effect on distance estimation. Our results show that individuals with a high degree of psychopathy underestimate distance of approaching avatars significantly less (let the avatar approach them significantly closer) than did participants with a lesser degree of psychopathy. Moreover, participants who scored high in Self-Centered Impulsivity underestimate the distance to approaching avatars significantly less (let the avatar approach closer) than participants with a low score. Distance estimation is considered an automatic process performed at early stages of visual processing. Therefore, our results imply that psychopathy affects basic early sensory processes, such as feature extraction, in the visual cortex.
The neural mechanisms that unfold when humans form a large group defined by an overarching context, such as audiences in theater or sports, are largely unknown and unexplored. This is mainly due to the lack of availability of a scalable system that can record the brain activity from a significantly large portion of such an audience simultaneously. Although the technology for such a system has been readily available for a long time, the high cost as well as the large overhead in human resources and logistic planning have prohibited the development of such a system. However, during the recent years reduction in technology costs and size have led to the emergence of low-cost, consumer-oriented EEG systems, developed primarily for recreational use. Here by combining such a low-cost EEG system with other off-the-shelve hardware and tailor-made software, we develop in the lab and test in a cinema such a scalable EEG hyper-scanning system. The system has a robust and stable performance and achieves accurate unambiguous alignment of the recorded data of the different EEG headsets. These characteristics combined with small preparation time and low-cost make it an ideal candidate for recording large portions of audiences.
Neuronal hyperexcitability is a feature of Alzheimer’s disease (AD). Three main mechanisms have been proposed to explain it: i), dendritic degeneration leading to increased input resistance, ii), ion channel changes leading to enhanced intrinsic excitability, and iii), synaptic changes leading to excitation-inhibition (E/I) imbalance. However, the relative contribution of these mechanisms is not fully understood. Therefore, we performed biophysically realistic multi-compartmental modelling of excitability in reconstructed CA1 pyramidal neurons of wild-type and APP/PS1 mice, a well-established animal model of AD. We show that, for synaptic activation, the excitability promoting effects of dendritic degeneration are cancelled out by excitability decreasing effects of synaptic loss. We find an interesting balance of excitability regulation with enhanced degeneration in the basal dendrites of APP/PS1 cells potentially leading to increased excitation by the apical but decreased excitation by the basal Schaffer collateral pathway. Furthermore, our simulations reveal that three additional pathomechanistic scenarios can account for the experimentally observed increase in firing and bursting of CA1 pyramidal neurons in APP/PS1 mice. Scenario 1: increased excitatory burst input; scenario 2: enhanced E/I ratio and scenario 3: alteration of intrinsic ion channels (IAHP down-regulated; INap, INa and ICaT up-regulated) in addition to enhanced E/I ratio. Our work supports the hypothesis that pathological network and ion channel changes are major contributors to neuronal hyperexcitability in AD. Overall, our results are in line with the concept of multi-causality and degeneracy according to which multiple different disruptions are separately sufficient but no single disruption is necessary for neuronal hyperexcitability.
The ability to extract regularities from the environment is arguably an adaptive characteristic of intelligent systems. In the context of speech, statistical learning is thought to be an important mechanism for language acquisition. By considering individual differences in speech auditory-motor synchronization, an independent component analysis of fMRI data revealed that the neural substrates of statistical word form learning are not fully shared across individuals. While a network of auditory and superior pre/motor regions is universally activated in the process of learning, a fronto-parietal network is instead additionally and selectively engaged by some individuals, boosting their performance. Furthermore, interfering with the use of this network via articulatory suppression (producing irrelevant speech during learning) normalizes performance across the entire sample. Our work provides novel insights on language-related statistical learning and reconciles previous contrasting findings, while highlighting the need to factor in fundamental individual differences for a precise characterization of cognitive phenomena.
Research points to neurofunctional differences underlying fluent speech production in stutterers and non-stutterers. There has been considerably less work focusing on the processes that underlie stuttered speech, primarily due to the difficulty of reliably eliciting stuttering in the unnatural contexts associated with neuroimaging experiments. We used magnetoencephalography (MEG) to test the hypothesis that stuttering events result from global motor inhibition–a “freeze” response typically characterized by increased beta power in nodes of the action-stopping network. We leveraged a novel clinical interview to develop participant-specific stimuli in order to elicit a comparable amount of stuttered and fluent trials. Twenty-nine adult stutterers participated. The paradigm included a cue prior to a go signal, which allowed us to isolate processes associated with stuttered and fluent trials prior to speech initiation. During this pre-speech time window, stuttered trials were associated with greater beta power in the right pre-supplementary motor area, a key node in the action-stopping network, compared to fluent trials. Beta power in the right pre-supplementary area was related to a clinical measure of stuttering severity. We also found that anticipated words identified independently by participants were stuttered more often than those generated by the researchers, which were based on the participants’ reported anticipated sounds. This suggests that global motor inhibition results from stuttering anticipation. This study represents the largest comparison of stuttered and fluent speech to date. The findings provide a foundation for clinical trials that test the efficacy of neuromodulation on stuttering. Moreover, our study demonstrates the feasibility of using our approach for eliciting stuttering during MEG and functional magnetic resonance imaging experiments so that the neurobiological bases of stuttered speech can be further elucidated.
Speech imagery (the ability to generate internally quasi-perceptual experiences of speech) is a fundamental ability linked to cognitive functions such as inner speech, phonological working memory, and predictive processing. Speech imagery is also considered an ideal tool to test theories of overt speech. The study of speech imagery is challenging, primarily because of the absence of overt behavioral output as well as the difficulty in temporally aligning imagery events across trials and individuals. We used magnetoencephalography (MEG) paired with temporal-generalization-based neural decoding and a simple behavioral protocol to determine the processing stages underlying speech imagery. We monitored participants’ lip and jaw micromovements during mental imagery of syllable production using electromyography. Decoding participants’ imagined syllables revealed a sequence of task-elicited representations. Importantly, participants’ micromovements did not discriminate between syllables. The decoded sequence of neuronal patterns maps well onto the predictions of current computational models of overt speech motor control and provides evidence for hypothesized internal and external feedback loops for speech planning and production, respectively. Additionally, the results expose the compressed nature of representations during planning which contrasts with the natural rate at which internal productions unfold. We conjecture that the same sequence underlies the motor-based generation of sensory predictions that modulate speech perception as well as the hypothesized articulatory loop of phonological working memory. The results underscore the potential of speech imagery, based on new experimental approaches and analytical methods, and further pave the way for successful non-invasive brain-computer interfaces.
We study the μ-μ45-T phase diagram of the 2+1-dimensional Gross-Neveu model, where μ denotes the ordinary chemical potential, μ45 the chiral chemical potential and T the temperature. We use the mean-field approximation and two different lattice regularizations with naive chiral fermions. An inhomogeneous phase at finite lattice spacing is found for one of the two regularizations. Our results suggest that there is no inhomogeneous phase in the continuum limit. We show that a chiral chemical potential is equivalent to an isospin chemical potential. Thus, all results presented in this work can also be interpreted in the context of isospin imbalance.
A prototype of a new type of calorimeter has been designed and constructed, based on a silicon-tungsten sampling design using pixel sensors with digital readout. It makes use of the Alpide MAPS sensor developed for the ALICE ITS upgrade. A binary readout is possible due to the pixel size of ≈30×30μm2. This prototype has been successfully tested with cosmic muons and with test beams at DESY and the CERN SPS. We report on performance results obtained at DESY, showing good energy resolution and linearity, and compare to detailed MC simulations. Also shown are preliminary results of the high-energy performance as measured at the SPS. The two-shower separation capabilities are discussed.
Brookshire (2022) claims that previous analyses of periodicity in detection performance after a reset event suffer from extreme false-positive rates. Here we show that this conclusion is based on an incorrect implemention of a null-hypothesis of aperiodicity, and that a correct implementation confirms low false-positive rates. Furthermore, we clarify that the previously used method of shuffling-in-time, and thereby shuffling-in-phase, cleanly implements the null hypothesis of no temporal structure after the reset, and thereby of no phase locking to the reset. Moving from a corresponding phase-locking spectrum to an inference on the periodicity of the underlying process can be accomplished by parameterizing the spectrum. This can separate periodic from non-periodic components, and quantify the strength of periodicity.
Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.
Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.
After myocardial infarction in the adult heart the remaining, non-infarcted tissue adapts to compensate the loss of functional tissue. This adaptation requires changes in gene expression networks, which are mostly controlled by transcription regulating proteins. Long non-coding transcripts (lncRNAs) are now recognized for taking part in fine-tuning such gene programs. We identified and characterized the cardiomyocyte specific lncRNA Sweetheart RNA (Swhtr), an approximately 10 kb long transcript divergently expressed from the cardiac core transcription factor coding gene Nkx2-5. We show that Swhtr is dispensable for normal heart development and function, but becomes essential for the tissue adaptation process after myocardial infarction. Re-expressing Swhtr from an exogenous locus rescues the Swhtr null phenotype. Genes depending on Swhtr after cardiac stress are significantly occupied, and therefore most likely regulated by NKX2-5. Our results indicate a synergistic role for Swhtr and the developmentally essential transcription factor NKX2-5 in tissue adaptation after myocardial injury.
The discovery of superconductivity in layered vanadium-based kagome metals AV3Sb5 (A: K, Rb, Cs) has added a new family of materials to the growing class of possible unconventional superconductors. However, the nature of the superconducting pairing in these materials remains elusive. We present a microscopic theoretical study of the leading superconducting instabilities on the kagome lattice based on spin- and charge-fluctuation mediated Cooper pairing. The applied methodology includes effects of both on-site and nearest-neighbor repulsive Coulomb interactions. Near the upper van Hove filling -- relevant for the AV3Sb5 materials -- we find a rich phase diagram with several pairing symmetries being nearly degenerate. In particular, while a substantial fraction of the phase diagram is occupied by a spin-singlet order parameter transforming as a two-dimensional irreducible representation of the point group, several nodal spin-triplet pairing states remain competitive. We compute the band and interaction parameter-dependence of the hierarchy of the leading superconducting instabilities, and determine the detailed momentum dependence of the resulting preferred gap structures. Crucially, for moderate values of the interaction parameters, the individual pairing states depend strongly on momentum and exhibit multiple nodes on the Fermi surface. We discuss the properties of these superconducting gap structures in light of recent experimental developments of the AV3Sb5 materials.
The electrical and computational properties of neurons in our brains are determined by a rich repertoire of membrane-spanning ion channels and elaborate dendritic trees. However, the precise reason for this inherent complexity remains unknown. Here, we generated large stochastic populations of biophysically realistic hippocampal granule cell models comparing those with all 15 ion channels to their reduced but functional counterparts containing only 5 ion channels. Strikingly, valid parameter combinations in the full models were more frequent and more stable in the face of perturbations to channel expression levels. Scaling up the numbers of ion channels artificially in the reduced models recovered these advantages confirming the key contribution of the actual number of ion channel types. We conclude that the diversity of ion channels gives a neuron greater flexibility and robustness to achieve target excitability.
From early to middle childhood, brain regions that underlie memory consolidation undergo profound maturational changes. However, there is little empirical investigation that directly relates age-related differences in brain structural measures to the memory consolidation processes. The present study examined system-level memory consolidations of intentionally studied object-location associations after one night of sleep (short delay) and after two weeks (long delay) in normally developing 5-to-7-year-old children (n = 50) and young adults (n = 39). Behavioural differences in memory consolidation were related to structural brain measures. Our results showed that children, in comparison to young adults, consolidate correctly learnt object-location associations less robustly over short and long delay. Moreover, using partial least squares correlation method, a unique multivariate profile comprised of specific neocortical (prefrontal, parietal, and occipital), cerebellar, and hippocampal subfield structures was found to be associated with variation in short-delay memory consolidation. A different multivariate profile comprised of a reduced set of brain structures, mainly consisting of neocortical (prefrontal, parietal, and occipital), and selective hippocampal subfield structures (CA1-2 and subiculum) was associated with variation in long-delay memory consolidation. Taken together, the results suggest that multivariate structural pattern of unique sets of brain regions are related to variations in short- and long-delay memory consolidation across children and young adults.
RESEARCH HIGHLIGHTS
* Short- and long-delay memory consolidation is less robust in children than in young adults
* Short-delay brain profile comprised of hippocampal, cerebellar, and neocortical brain regions
* Long-delay brain profile comprised of neocortical and selected hippocampal brain regions.
* Brain profiles differ between children and young adults.
Hydrogen is a promising fuel in a carbon-neutral economy, and many efforts are currently undertaken to produce hydrogen. One of the challenges is to store and transport the highly explosive gas in a safe and easy way. One option that is intensively analyzed by chemists and biologists is the conversion of hydrogen and CO2 to formic acid, the liquid organic hydrogen carrier. Here, we demonstrate for the first time that a bio-based system, using Acetobacterium woodii as the biocatalyst, allows multiple cycles of bi-directional hydrogenation of CO2 to formic acid in one bioreactor. The process was kept running over 2 weeks producing and oxidizing 330 mM formic acid in total. Unwanted side-product formation of acetic acid was prevented through metabolic engineering of the organism. The demonstrated process design can be considered as a future “bio-battery” for the reversible storage of electrons in the form of H2 in formic acid, a versatile compound.
Gasdermin-D (GSDMD) is the ultimate effector of pyroptosis, a form of programmed cell death associated with pathogen invasion and inflammation. After proteolytic cleavage by caspases activated by the inflammasome, the GSDMD N-terminal domain (GSDMDNT) assembles on the inner leaflet of the plasma membrane and induces the formation of large membrane pores. We use atomistic molecular dynamics simulations to study GSDMDNT monomers, oligomers, and rings in an asymmetric plasma membrane mimetic. We identify distinct interaction motifs of GSDMDNT with phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) and phosphatidylserine (PS) head-groups and describe differential lipid binding between the pore and prepore conformations. Oligomers are stabilized by shared lipid binding sites between neighboring monomers acting akin to double-sided tape. We show that already small GSDMDNT oligomers form stable, water-filled and ion-conducting membrane pores bounded by curled beta-sheets. In large-scale simulations, we resolve the process of pore formation by lipid detachment from GSDMDNT arcs and lipid efflux from partial rings. We find that that high-order GSDMDNT oligomers can crack under the line tension of 86 pN created by an open membrane edge to form the slit pores or closed GSDMDNT rings seen in experiment. Our simulations provide a detailed view of key steps in GSDMDNT-induced plasma membrane pore formation, including sublytic pores that explain nonselective ion flux during early pyroptosis.
The heterotetrameric human transfer RNA (tRNA) splicing endonuclease (TSEN) catalyzes the excision of intronic sequences from precursor tRNAs (pre-tRNAs)1. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH)2–8. The three-dimensional (3D) assembly of TSEN/CLP1, the mechanism of substrate recognition, and the molecular details of PCH-associated mutations are not fully understood. Here, we present cryo-electron microscopy structures of human TSEN with intron-containing pre-tRNATyrgta and pre-tRNAArgtct. TSEN exhibits broad structural homology to archaeal endonucleases9 but has evolved additional regulatory elements that are involved in handling and positioning substrate RNA. Essential catalytic residues of subunit TSEN34 are organized for the 3’ splice site which emerges from a bulge-helix configuration. The triple-nucleotide bulge at the intron/3’-exon boundary is stabilized by an arginine tweezer motif of TSEN2 and an interaction with the proximal minor groove of the helix. TSEN34 and TSEN54 define the 3’ splice site by holding the tRNA body in place. TSEN54 adapts a bipartite fold with a flexible central region required for CLP1 binding. PCH-associated mutations are located far from pre-tRNA binding interfaces explaining their negative impact on structural integrity of TSEN without abrogating its catalytic activity in vitro10. Our work defines the molecular framework of pre-tRNA recognition and cleavage by TSEN and provides a structural basis to better understand PCH in the future.
The new variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype strain (B.1) with respect to their interactions with the antiviral type I interferon (IFN-alpha/beta) response in infected cells. Our data indicate that Omicron has gained an elevated capability to suppress IFN-beta induction upon infection and to better withstand the antiviral state imposed by exogenously added IFN-alpha.