eLife
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In the ciliate Tetrahymena, telomeres of the germline micronucleus (MIC) are removed and replaced by de novo telomere addition during somatic macronuclear (MAC) development. In this study, we investigated the kinetics and mechanism of the MIC telomere elimination. Comparison of the MIC and MAC genome sequences indicated that the MIC telomeres are excised from chromosomes as part of larger MIC-limited sequences (MLSs) through chromosomal breakage. We confirmed this using an optimized oligo-FISH protocol and found that their elimination occurs in parallel with other programmed DNA elimination processes. CRISPR-Cas9 disruption of a MLS-associated Chromosome Breakage Sequence (CBS) showed that elimination of the MLS was not blocked but instead led to loss of its adjacent MAC-destined sequence (MDS), suggesting abnormal co-elimination. In biparental crosses of the CBS mutant, however, both MLS and MDS were retained, DNA elimination was broadly disrupted, and no viable progeny were produced. These findings indicate that chromosome breakage at MLS-associated CBSs is essential for the proper separation of MLSs and MDSs, ensuring correct DNA elimination and successful sexual progeny development. We propose that the MIC telomere elimination is subsumed within the broader process of programmed DNA elimination.
A new diffusion MRI approach offers a glimpse of the anomalies of cellular architecture underlying basal ganglia degeneration in Huntington’s disease.
Nucleic acid aptamers hold promise for clinical applications, yet understanding their molecular binding mechanisms to target proteins, and efficiently optimizing their binding affinities, remain challenging. Here, we present CAAMO (Computer-Aided Aptamer Modeling and Optimization), which integrates in silico aptamer design with experimental validation to accelerate the development of aptamer-based RNA therapeutics. Starting from the sequence information of a reported RNA aptamer, Ta, for the SARS-CoV-2 spike protein, our CAAMO method first determines its binding mode with the spike protein’s receptor binding domain (RBD) through a multi-strategy computational approach. We then optimize its binding affinity via structure-based rational design. Among the six designed candidates, five were experimentally verified and exhibited enhanced binding affinities compared to the original Ta sequence. Furthermore, we directly compared the binding properties of the RNA aptamers to neutralizing antibodies and found that the designed aptamer TaG34C demonstrated a comparable binding affinity to the RBD compared to the representative neutralizing antibodies analyzed in this study. This highlights its potential as an alternative to existing COVID-19 antibodies. Our work provides a robust approach for the efficient design of a relatively large number of high-affinity aptamers with complicated topologies. This approach paves the way for the development of aptamer-based RNA diagnostics and therapeutics.
Elucidating the neuronal circuits that govern appetite requires precise, high-resolution monitoring of the microstructure of solid food consumption, a need unmet by existing tools, which are either costly or lack the temporal resolution to align feeding events with neuronal activity. To overcome this, we developed the Crunchometer, a low-cost, open-source acoustic system that uses computational algorithms to generate high-resolution feeding ethograms from the sounds produced during solid food consumption. Validation across energy states (hunger/satiety) confirmed its sensitivity to changes in feeding microstructure, and the system reliably detected semaglutide-induced suppression of intake and reduced preference for a high-fat diet. Leveraging its seamless integration with in vivo recordings in freely behaving mice, we paired the Crunchometer with lateral hypothalamus (LH) electrophysiology to identify ‘meal-related’ neurons that track entire meals rather than individual bouts. Calcium imaging further revealed that distinct subsets of LH GABAergic and glutamatergic neurons were tuned to feeding only, to licking only, or to both behaviors. Thus, LH neuronal ensembles differentially encode the consumption of solid food versus liquid sucrose. These findings demonstrate that the Crunchometer is a robust, accessible platform for dissecting the neural correlates of feeding behavior at the resolution of a single bite.
All living systems use an almost identical standard genetic code (SGC), in which 20 amino acids are assigned non-randomly. According to the error minimization theory, amino acids are arranged to minimize the mutational effect on protein function, while experimental verification remains limited. Here, we constructed 10 non-standard genetic codes (non-SGCs) in vitro by reassigning three amino acids (Ala, Ser, and Leu) in vacant codons of the minimal genetic code consisting of 21 tRNAs. Most of these non-SGCs have a higher cost of amino acid replacement than the SGC, calculated based on three amino acid properties: polar requirement (PR), molecular volume (MV), and hydropathy index (HI). The protein function of three reporter genes expressed using these non-SGCs decreased similarly when random mutations were introduced into the genes, implying that the effect of mutations was similar across all the non-SGCs tested here. This result provides direct experimental evidence that mutational robustness does not significantly change in individual reporter protein activity within the range of mutational cost tested in this study (CostPR: 5.29–5.77, CostMV: 1848–2348, and CostHI: 3.27–5.10), which covers approximately 18.4% (PR), 37.6% (MV), and 50.8% (HI) of the possible cost range achievable among one million randomly-generated genetic codes.
Stress granules are large cytoplasmic bodies formed in response to environmental insults by eukaryotic cells. Stress granule formation is key for post-stress recovery, and many diseases and infections are characterized by dysregulation of these membraneless organelles. How specific and non-specific macromolecular interactions drive the formation of stress granules and other large assemblies is an area of active research. Stress granules are comprised of dense, ~200 nm cores, and these are known to contain numerous RNAs and proteins. Now, we have discovered that more than half of the nucleic acid content of stress granule cores is circular, double-stranded DNA. We demonstrate cytologically that these extrachromosomal circular DNAs (eccDNAs) colocalize cytoplasmically with canonical stress granule marker proteins in HEK293T cells, and through CRISPR targeting in budding yeast, that they are required for stress granule formation upon stress. This discovery thus reveals a key function for eccDNA in the eukaryotic stress response.
Several theoretical studies have concluded that heterozygote advantage makes at most a minor contribution to MHC diversity. Siljestam and Rueffler (2024) recently presented models in which heterozygote advantage alone can lead to realistically high diversity. Here I argue that heterozygote advantage cannot by itself explain MHC diversity, and that its contribution to diversity is unlikely to be large in most species. I first show that the high diversity reported by Siljestam and Rueffler is so sensitive to parameter values that the underlying phenomenon cannot explain the widespread diversity of MHC genes. I then consider a fundamental problem with explaining MHC diversity by heterozygote advantage alone: selective forces that favored heterozygotes would lead to the evolution of haplotypes having much higher fitness when homozygous, diminishing or eliminating heterozygote advantage. Diversity maintained by another force, however, might bring about adaptation to the more common heterozygous state at the expense of homozygous fitness. Thus, substantial heterozygote advantage may arise as a consequence of MHC diversity.
The key elements for fear extinction learning are unexpected omissions of expected aversive events, which are considered to be rewarding. Given its reception of reward information, we tested the hypothesis that the cerebellum contributes to reward-like prediction error processing driving extinction learning via its connections with the ventral tegmental area (VTA). Forty-three young and healthy participants performed a three-day fear conditioning paradigm in a 7T MR scanner. The cerebellum and VTA were active during unexpected omissions of aversive unconditioned stimuli in the initial extinction trials and in other learning phases, in line with the proposed role of prediction-error processing. Increased functional connectivity was observed between the cerebellum and VTA, indicating that they are functionally coupled during fear extinction learning. These results suggest that an interaction between the cerebellum and VTA should be incorporated into the existing model of the fear extinction network.
Environmental changes necessitate adaptive responses, and thus the ability to monitor one’s actions and their connection to specific cues and outcomes is crucial for survival. The anterior cingulate cortex (ACC) is implicated in these processes, yet its precise role in action monitoring vs. outcome tracking remains unclear. To investigate this, we developed a novel discrimination–avoidance task for mice, designed with clear temporal separation between actions and outcomes. Our findings show that ACC neurons primarily encode post-action variables over extended periods, reflecting the animal’s preceding actions rather than the outcomes or values of those actions. Specifically, we identified two distinct subpopulations of ACC neurons: one encoding the action state (whether an action was taken) and the other encoding the action content (which action was taken). Importantly, increased post-action ACC activity was associated with better performance in subsequent trials. These findings suggest that the ACC supports complex associative learning through extended signaling of rich action-relevant information, thereby bridging cue, action, and outcome associations.
The cerebral cortex is a multi-layered structure generated through the migration of neural precursors from their birthplace in the ventricular zone to their destination within the cortical plate. Neuronal migration defects are responsible for many human pathologies collectively called neuronal migration disorders, which include subcortical band heterotopia and cobblestone brain (COB) malformation. One example of a protein involved in a neuronal migration disorder is the echinoderm microtubule-associated protein-like 1 (EML1) protein, one of six members of the mammalian EML family. Absence of EML1 protein results in subcortical band heterotopia in mice and humans. Here, we report that the absence of the paralogous protein EML3 leads to delayed embryonic development and small size, and a COB-like phenotype with neuronal ectopias in the dorsal telencephalon. We found that EML3 is expressed in the neuroepithelium and meningeal mesenchyme when those tissues participate in pial basement membrane (PBM) formation. Transmission electron microscopy demonstrated that the extracellular matrix of the PBM is structurally abnormal in Eml3 null mice when the first radially migrating neurons arrive. The reduced structural integrity of the PBM leads to focal over-migration of neurons into the subarachnoid space. These findings strengthen the link between the EML protein family and cortical neuronal migration defects by identifying Eml3 as the first EML family member whose absence leads to over-migration of neuroblasts. Moreover, we report the first COB-like phenotype with PBM structural defects when a single microtubule-associated protein is deleted.
Funding agencies use a variety of mechanisms to fund research. The National Institutes of Health in the United States, for example, employs scientists to perform research at its own laboratories (intramural research), and it also awards grants to pay for research at external institutions such as universities (extramural research). Here, using data from 1594 intramural grants and 97,054 extramural grants funded between 2009 and 2019, we compare the scholarly outputs from these two funding mechanisms in terms of number of publications, Relative Citation Ratio, and clinical metrics. We find that extramural awards are more cost-effective for producing outputs commonly used for academic evaluation, such as publications and citations (per dollar), while intramural awards are more cost-effective for generating research that influences future clinical work, more closely in line with the agency’s health goals. These findings provide evidence that institutional incentives associated with different funding mechanisms drive their comparative strengths.
Viral infection triggers a robust DNA damage response (DDR), reshaping the host chromatin landscape to facilitate viral replication. Here, we uncover a novel mechanism by which alphaherpesviruses exploit the DDR pathway. We demonstrated that herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) induced selective degradation of class I histone deacetylases (HDAC1/2), leading to histone hyperacetylation and subsequent DDR activation. Strikingly, viral infection promoted nuclear export of HDAC1/2, followed by MDM2-mediated K63-linked polyubiquitination and proteasomal degradation in the cytoplasm. Pharmacological inhibition of either DDR signaling or HDAC1/2 nuclear export significantly affected viral replication in vitro and in vivo. Our findings reveal a unique viral strategy to hijack host epigenetic regulation for efficient replication, and identify potential therapeutic targets for alphaherpesvirus infections.
Attention deficit hyperactivity disorder (ADHD) affects 5–7% of children worldwide, yet diagnosis continues to rely on clinical-behavioral assessments. The theta/beta ratio (TBR) derived from electroencephalography (EEG) has long been proposed as a complementary neurobiological marker of ADHD based on reports of elevated TBR in affected children. However, accumulating evidence has raised concerns about the robustness and generalizability of these findings, pointing to a strong sensitivity to methodological choices. Here, we used multiverse analyses to systematically quantify how researcher degrees of freedom shape conclusions about associations between TBR and ADHD. Across two large, independent datasets (Healthy brain network: N=1499; validation sample: N=381), we evaluated 576 theoretically plausible analytical specifications, varying recording conditions, reference scheme, frequency band definitions, treatment of aperiodic (1/f) activity, regions of interest, sample inclusion criteria, and covariate specifications. Across the multiverse, we found that group differences in TBR were highly contingent on analytical choices, with no evidence for robust main effects of diagnosis, indicating no reliable differences between healthy controls, ADHD-inattentive, and ADHD-combined subtypes. Instead, significant effects emerged primarily as interactions with age and individual alpha frequency (IAF), particularly when TBR was derived from aperiodic-uncorrected power or from the aperiodic signal itself. These interaction patterns replicated across both independent samples and were observed using both categorical and dimensional definitions of ADHD. Together, these findings indicate that previously reported TBR effects are largely driven by variability in aperiodic activity and IAF rather than genuine differences in oscillatory theta-beta dynamics. Our results challenge the interpretation of TBR as a reliable standalone biomarker for ADHD and underscore the importance of multiverse approaches for evaluating candidate neurobiological markers in heterogeneous clinical populations.
Astronauts consistently exhibit slower movements in microgravity, even during tasks requiring rapid responses. The sensorimotor mechanisms underlying this general slowing remain debated. Two hypotheses have been proposed: either the sensorimotor system adopts a conservative control strategy for safety and postural stability, or the system underestimates body mass due to reduced inputs from proprioceptive receptors. To dissociate these opinions, we studied 12 taikonauts aboard the China Space Station performing a classical hand-reaching task. Compared to their pre-flight performance and to an age-matched control group, participants showed increased movement durations and altered kinematic profiles in microgravity. Model-based analyses of motor control parameters revealed that these changes stemmed from reduced initial force generation in the feedforward control phase followed by compensatory feedback-based corrections. These findings provide support for the body mass underestimation hypothesis while being inconsistent with the strategic slowing hypothesis. Importantly, the sensory estimate of bodily property in microgravity is biased but immune from sensorimotor adaptation, calling for an extension of existing theories of motor learning.
Accurately estimating relative transmission rates of SARS-CoV-2 variants remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from genetic sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological behavior of SARS-CoV-2. Here, we extend methods for inferring the effective reproduction number of an epidemic using confirmed case data to jointly estimate variant-specific effective reproduction numbers and frequencies of co-circulating variants using cases and sequences across states in the United States from January 2021 to March 2022. Our method can be used to infer structured relationships between effective reproduction numbers across time series, allowing us to estimate fixed variant-specific growth advantages. We use this model to estimate the effective reproduction number of SARS-CoV-2 variants of concern and variants of interest in the United States, and to estimate consistent growth advantages of particular variants across different locations.
Human planning is efficient – it frugally deploys limited cognitive resources to accomplish difficult tasks – and flexible – adapting to novel problems and environments. Computational approaches suggest that people construct simplified mental representations of their environment, balancing the complexity of a task representation with its utility. These models imply a nested optimisation in which planning shapes perception and perception shapes planning – but the perceptual and attentional mechanisms governing how this interaction unfolds remain unknown. Here, we harness virtual maze navigation to characterise how spatial attention controls which aspects of a task representation enter subjective awareness and are available for planning. We find that spatial proximity governs which aspects of a maze are available for planning and that when task-relevant information follows natural (lateralised) contours of attention, people can more easily construct simplified and useful maze representations. This influence of attention varies considerably across individuals, explaining differences in people’s task representations and behaviour. Inspired by the ‘spotlight of attention’ analogy, we incorporate the effects of visuospatial attention into existing computational accounts of value-guided construal. Together, our work bridges computational perspectives on perception and decision-making to better understand how individuals represent their environments in aid of planning.