Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Automated Approach for Improving Standardization of the Marble Burying Test Enables Quantification of Burying Bouts and Activity Characteristics

Abstract The marble burying test is a commonly used paradigm to describe phenotypes in mouse models of neurodevelopmental and psychiatric disorders. The current methodological approach relies predominantly on reporting the number of buried marbles at the end of the test. By measuring the proxy of the behavior (buried marbles), many important characteristics regarding the temporal aspect of this assay are lost. Here, we introduce a novel, automated method to quantify mouse behavior during the marble burying test with the focus on the burying bouts and movement dynamics. Using open-source software packages, we trained a supervised machine learning algorithm (the “classifier”) to distinguish burying behavior in freely moving mice. In order to confirm the classifier’s accuracy and characterize burying events in high detail, we performed the marble burying test in three mouse models: Ube3am-/p+ [Angelman syndrome (AS) model], Shank2−/− (autism model), and Sapap3−/− [obsessive-compulsive disorder (OCD) model] mice. The classifier scored burying behavior accurately and consistent with the previously reported phenotype of the Ube3am-/p+ mice, which showed decreased levels of burying compared with controls. Shank2−/− mice showed a similar pattern of decreased burying behavior, which was not found in Sapap3−/− mice. Tracking mouse behavior throughout the test revealed hypoactivity in Ube3am-/p+ and hyperactivity in the Shank2−/− mice, indicating that mouse activity is unrelated to burying behavior. Reducing activity with midazolam in Shank2−/− mice did not alter the burying behavior. Together, we demonstrate that our classifier is an accurate method for the analysis of the marble burying test, providing more information than currently used methods.
The pathogenic R5L mutation disrupts formation of Tau complexes on the microtubule by altering local N-terminal structure

Significance The microtubule-associated protein Tau is strongly linked to a number of neurological diseases. Disease onset is typically associated with weakened interaction with the microtubule, but this widely accepted model is based on hyperphosphorylation or mutations within the C-terminal microtubule-binding domain of Tau. Here, we find that an N-terminal disease-associated mutation in Tau, R5L, does not reduce Tau affinity for microtubules but instead, modifies the N-terminal structure, altering Tau’s behavior and ability to condense on the microtubule surface. Our findings challenge the current paradigms of both how mutations in Tau lead to disease and the functional role of the N-terminal region of Tau. The microtubule-associated protein (MAP) Tau is an intrinsically disordered protein (IDP) primarily expressed in axons, where it functions to regulate microtubule dynamics, modulate motor protein motility, and participate in signaling cascades. Tau misregulation and point mutations are linked to neurodegenerative diseases, including progressive supranuclear palsy (PSP), Pick’s disease, and Alzheimer’s disease. Many disease-associated mutations in Tau occur in the C-terminal microtubule-binding domain of the protein. Effects of C-terminal mutations in Tau have led to the widely accepted disease-state theory that missense mutations in Tau reduce microtubule-binding affinity or increase Tau propensity to aggregate. Here, we investigate the effect of an N-terminal arginine to leucine mutation at position 5 in Tau (R5L), associated with PSP, on Tau–microtubule interactions using an in vitro reconstituted system. Contrary to the canonical disease-state theory, we determine that the R5L mutation does not reduce Tau affinity for the microtubule using total internal reflection fluorescence microscopy. Rather, the R5L mutation decreases the ability of Tau to form larger-order complexes, or Tau patches, at high concentrations of Tau. Using NMR, we show that the R5L mutation results in a local structural change that reduces interactions of the projection domain in the presence of microtubules. Altogether, these results challenge both the current paradigm of how mutations in Tau lead to disease and the role of the projection domain in modulating Tau behavior on the microtubule surface.
Brain Functional Connectome Defines a Transdiagnostic Dimension Shared by Cognitive Function and Psychopathology in Preadolescents

Background Cognitive dysfunction and high-order psychopathologic dimensions are two main classes of transdiagnostic factors related to psychiatric disorders. They may link to common or distinct core brain networks underlying developmental risk of psychiatric disorders. Method The current study is a longitudinal investigation with 11,875 youths aged 9-to 10-years-old at study onset, from the Adolescent Brain Cognitive Development study. A machine-learning approach based on canonical correlation analysis was used to identify latent dimensional associations of the resting-state functional connectome with multi-domain behavioral assessments of cognitive functions and psychopathological problems. For the latent rsFC factor showing a robust behavioral association, its ability to predict psychiatric disorders was assessed using two-year follow-up data and its genetic association was evaluated using twin data from the same cohort. Result A latent functional connectome pattern was identified that showed a strong and generalizable association with the multi-domain behavioral assessments (5-fold cross validation: ρ = 0.68~0.73, for the training set (N = 5096); ρ = 0.56 ~ 0.58, for the test set (N = 1476)). This functional connectome pattern was highly heritable (h2 = 74.42%, 95% CI: 56.76%-85.42%), exhibited a dose-response relationship with cumulative number of psychiatric disorders assessed concurrently and 2-years post-MRI-scan, and predicted the transition of diagnosis across disorders over the 2-year follow-up period. Conclusion These findings provide preliminary evidence for a transdiagnostic connectome-based measure that underlies individual differences in developing psychiatric disorders in early adolescence.
Sucrose promotes D53 accumulation and tillering in rice.

-Shoot branching is regulated by multiple signals. Previous studies have indicated that sucrose may promote shoot branching through suppressing the inhibitory effect of the hormone strigolactone (SL). However, the molecular mechanisms underlying this effect are unknown. -Here we used molecular and genetic tools to identify the molecular targets underlying the antagonistic interaction between sucrose and SL. -We showed that sucrose antagonises the suppressive action of SL on tillering in rice and on the degradation of D53, a major target of SL signalling. Sucrose inhibits the gene expression of D3, the orthologue of the arabidopsis F-box MAX2 required for SL signalling. Over-expression of D3 antagonises sucrose inhibition of D53 degradation and enabled the SL inhibition of tillering under high sucrose. Sucrose prevents SL-induced degradation of D14, the SL receptor involved in D53 degradation. In contrast with D3, D14 over-expression enhances D53 protein levels and sucrose-induced tillering, even in the presence of SL. -Our results show that sucrose inhibits SL response by affecting key components of SL signalling and, together with previous studies reporting the inhibition of SL synthesis by nitrate and phosphate, demonstrate the central role played by strigolactones in the regulation of plant architecture by nutrients.
The evolution of stomatal traits along the trajectory toward C4 photosynthesis.

C4 photosynthesis optimizes plant carbon and water relations, allowing high photosynthetic rates with low stomatal conductance. Stomata have long been considered a part of the C4 syndrome. However, it remains unclear how stomatal traits evolved along the path from C3 to C4. Here, we examined stomata in the Flaveria genus, a model used for C4 evolutionary study. Comparative, transgenic, and semi-in-vitro experiments were performed to study the molecular basis that underlies the changes of stomatal traits in C4 evolution. The evolution from C3 to C4 species is accompanied by a gradual rather than an abrupt change in stomatal traits. The initial change appears near the Type I intermediate stage. Co-evolution of the photosynthetic pathway and stomatal traits is supported. On the road to C4, stomata tend to be fewer in number but larger in size, and stomatal density dominates changes in anatomical maximum stomatal conductance (gsmax). Reduction of FSTOMAGEN expression underlies decreased gsmaxin Flaveria and likely occurs in other C4 lineages. Decreased gsmax contributes to the increase in intrinsic water use efficiency in C4 evolution. This work highlights the stomatal traits in the current C4 evolutionary model. Our study provides insights into the pattern, mechanism, and role of stomatal evolution along the road towards C4.
Maternal behavioral thermoregulation facilitated evolutionary transitions from egg laying to live birth

Abstract Live birth is a key innovation that has evolved from egg-laying ancestors over 100 times in reptiles. However, egg-laying lizards and snakes can have preferred body temperatures that are lethal to developing embryos, which should select against prolonged egg retention. Here, we demonstrate that thermal mismatches between mothers and offspring are widespread across the squamate phylogeny. This mismatch is resolved by gravid females adjusting their body temperature towards the thermal optimum of their embryos. We find that the same response occurs in both live-bearing and egg-laying species, despite the latter only retaining embryos during the early stages of development. Importantly, phylogenetic reconstructions suggest this thermoregulatory behavior in gravid females evolved in egg-laying species prior to the evolution of live birth. Maternal thermoregulatory behavior, therefore, bypasses the constraints imposed by a slowly evolving thermal physiology and has likely been a key facilitator in the repeated transition to live birth.
Cellular perception of growth rate and the mechanistic origin of bacterial growth law

Bacteria organize many activities according to their grow rate via the ppGpp signaling system. Yet it is not clear how this signaling system “knows” how fast cells grow. Through quantitative experiments, we show that ppGpp responds inversely to the rate of translational elongation in E. coli. Together with its roles in inhibiting ribosome biogenesis and activity, ppGpp closes a key regulatory circuit that enables the cell to perceive and control the rate of its growth across conditions. The celebrated linear growth law relating the ribosome content and growth rate emerges as a consequence of keeping a supply of ribosome reserves while maintaining elongation rate in slow growth conditions. Further analysis suggests the elongation rate itself is detected by sensing the ratio of dwelling and translocating ribosomes, a strategy employed to collapse the complex, high-dimensional dynamics of the molecular processes underlying cell growth to perceive the physiological state of the whole.
An Optimal Policy Model for Concurrent Uncertainty Estimation During Decision Making

We often postpone or even avoid making decisions when we feel uncertain. Uncertainty estimation is not an afterthought of decision making but a dynamic process that accompanies decision making in parallel and affects decision making. To study concurrent uncertainty estimation during decision making, we adapted the classic random-dots motion direction discrimination task to allow a reaction-time measure of uncertainty responses. Subjects were asked to judge whether a patch of random dots was moving left or right. In addition, they could seek assistance by choosing to look at a second stimulus that had the same direction but high coherence any time during the task. The task allows us to measure the reaction time of both the perceptual decisions and the uncertainty responses. The subjects were more likely to choose the uncertainty response when the motion coherence was low, while their reaction times of the uncertainty responses showed individual variations. To account for the subjects’ behavior, we created an optimal policy decision model in which decisions are based on the value functions computed from the accumulated evidence using a drift-diffusion process. Model simulations captured key features of the subjects’ choices, reaction times, and proportions of uncertainty responses. Varying model parameters explained individual variations in the subjects and the correlations between decision accuracy, proportions of uncertainty responses, and reaction times at the individual level. Our model links perceptual decisions and value-based decisions and indicates that concurrent uncertainty estimation may be based on comparisons between values of uncertainty responses and perceptual decisions, both of which may be derived from the same evidence accumulation process during decision making. It provides a theoretical framework for future investigations, including the ones that aim at the underlying neural mechanism.
Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon

Mexico has considerable population substructure due to pre-Columbian diversity and subsequent variation in admixture levels from trans-oceanic migrations, primarily from Europe and Africa, but also, to a lesser extent, from Asia. Detailed analyses exploring sub-continental structure remain limited and post-Columbian demographic dynamics within Mexico have not been inferred with genomic data. We analyze the distribution of ancestry tracts to infer the timing and number of pulses of admixture in ten regions across Mexico, observing older admixture timings in the first colonial cities and more recent timings moving outward into southern and southeastern Mexico. We characterize the specific origin of the heterogeneous Native American ancestry in Mexico: a widespread western-central Native Mesoamerican component in northern Aridoamerican states and a central-eastern Nahua contribution in Guerrero (southern Mexico) and Veracruz to its north. Yucatan shows lowland Mayan ancestry, while Sonora exhibits a unique northwestern native Mexican ancestry matching no sampled reference, each consistent with localized indigenous cultures. Finally, in Acapulco, Guerrero a notable proportion of East Asian ancestry was observed, an understudied heritage in Mexico. We identified the source of this ancestry within Southeast Asia—specifically western Indonesian and non-Negrito Filipino—and dated its arrival to approximately thirteen generations ago (1620 CE). This points to a genetic legacy from the 17th century Manila Galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco in Spanish Mexico. Although this piece of the colonial Spanish trade route from China to Europe appears in historical records, it has been largely ignored as a source of genetic ancestry in Mexico, neglected due to slavery, assimilation as “Indios” and incomplete historical records.
Single-cell Networks Reorganise to Facilitate Whole-brain Supercritical Dynamics During Epileptic Seizures

Excitation-inhibition (EI) balance may be required for the organisation of brain dynamics to a phase transition, criticality, which confers computational benefits. Brain pathology associated with EI imbalance may therefore occur due to a deviation from criticality. However, evidence linking critical dynamics with EI imbalance-induced pathology is lacking. Here, we studied the effect of EI imbalance-induced epileptic seizures on brain dynamics, using in vivo whole-brain 2-photon imaging of GCaMP6s larval zebrafish at single-neuron resolution. We demonstrate the importance of EI balance for criticality, with EI imbalance causing a loss of whole-brain critical statistics. Using network models we show that a reorganisation of network topology drives this loss of criticality. Seizure dynamics match theoretical predictions for networks driven away from a phase transition into disorder, with the emergence of chaos and a loss of network-mediated separation, dynamic range and metastability. These results demonstrate that EI imbalance drives a pathological deviation from criticality.
Connexin hemichannels with prostaglandin release in anabolic function of bone to mechanical loading

Mechanical stimulation, such as physical exercise, is essential for bone formation and health. Here, we demonstrate the critical role of osteocytic Cx43 hemichannels in anabolic function of bone in response to mechanical loading. Two transgenic mouse models, R76W and Δ130-136, expressing dominant-negative Cx43 mutants in osteocytes were adopted. Mechanical loading of tibial bone increased cortical bone mass and mechanical properties in wild-type and gap junction-impaired R76W mice through increased PGE2, endosteal osteoblast activity, and decreased sclerostin. These anabolic responses were impeded in gap junction/hemichannel-impaired Δ130-136 mice and accompanied by increased endosteal osteoclast activity. Specific inhibition of Cx43 hemichannels by Cx43(M1) antibody suppressed PGE2 secretion and impeded loading-induced endosteal osteoblast activity, bone formation and anabolic gene expression. PGE2 administration rescued the osteogenic response to mechanical loading impeded by impaired hemichannels. Together, osteocytic Cx43 hemichannels could be a potential new therapeutic target for treating bone loss and osteoporosis.
TRPV1-Lineage Somatosensory Fibers Communicate with Taste Neurons in the Mouse Parabrachial Nucleus

Trigeminal neurons convey somatosensory information from craniofacial tissues. In mouse brain, ascending projections from medullary trigeminal neurons arrive at taste neurons in the parabrachial (PB) nucleus, suggesting that taste neurons participate in somatosensory processing. However, the cell types that support this convergence were undefined. Using Cre-directed optogenetics and in vivo neurophysiology in anesthetized mice of both sexes, here we studied whether transient receptor potential vanilloid 1 (TRPV1)-lineage nociceptive and thermosensory fibers are primary neurons that drive trigeminal circuits reaching PB taste cells. We monitored spiking activity in individual PB neurons during photoexcitation of the terminals of TRPV1-lineage fibers arriving at the dorsal trigeminal nucleus caudalis, which relays orofacial somatosensory messages to the PB area. We also recorded PB neural responses to oral delivery of taste, chemesthetic, and thermal stimuli. We found that optical excitation of TRPV1-lineage fibers elicited responses in traditionally defined taste neurons in lateral PB nuclei. The tuning of neurons across diverse tastes associated with their sensitivity to TRPV1-lineage fiber stimulation, which only sparingly engaged neurons oriented to preferred tastes like sucrose. Moreover, neurons responsive to photostimulation of TRPV1-lineage afferents showed strong responses to temperature including noxious heat, which predominantly excited PB bitter taste cells. Multivariate and machine learning analyses revealed the PB confluence of TRPV1-lineage signals with taste captured sensory valence information shared across aversive gustatory, nociceptive, and thermal stimuli. Our results reveal that TRPV1-lineage fibers, which have defined roles in thermosensation and pain, communicate with PB taste neurons. This multisensory convergence supports dependencies between gustatory and somatosensory hedonic representations in the brain. SIGNIFICANCE STATEMENT The parabrachial (PB) nucleus participates in autonomic and integrative neural processing for diverse sensory modalities. We recently found in mice that trigeminal neurons supplying craniofacial somatosensation project to PB neurons sensitive to tastes. Here, we show that trigeminal projections to PB gustatory cells are driven by a genetic class of thermosensory and nociceptive fiber. Input from these fibers was associated with PB neural sensitivity to aversive oral temperatures and tastes and supported a multimodal neural representation of sensory valence across gustatory, nociceptive, and thermal stimuli. These results reveal gustation and somatosensation to be only components of a larger PB code that captures sensory value. Defining this circuit has implications for understanding the neural representation of taste, temperature, and also pain-related phenomena.
Hair phenotype diversity across Indriidae lemurs

Objectives Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution— serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials and Methods Our analyses consider multiple phylogenetic scales (family-level, genus-level) and hypotheses (e.g., Gloger’s rule, the body cooling hypotheses). We obtain hair color and density from museum and/or wild animals, opsin genotypes from wild animals, and climate data from WorldClim. To analyze our data, we use phylogenetic generalized linear mixed models (PGLMM) using Markov chain Monte Carlo algorithms. Results Our results show that across the Indriidae family, darker hair is typical in wetter regions. However, within Propithecus, dark black hair is common in colder forest regions. Results also show pelage redness increases in populations exhibiting enhanced color vision. Lastly, we find follicle density on the crown and limbs increases in dry and open environments. Discussion This study highlights how different selective pressures across distinct phylogenetic scales have likely acted on primate hair evolution. Specifically, our data across Propithecus may implicate thermoregulation and is the first empirical evidence of Bogert’s rule in mammals. Our study also provides rare empirical evidence supporting an early hypothesis on hominin hair evolution.