Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic comparison of culture media uncovers phenotypic shift of human microglia defined by reduced reliance to CSF1R signaling

Efforts to understand microglia function in health and diseases have been hindered by the lack of culture models that recapitulate in situ cellular properties. In recent years, the use of serum-free media with brain-derived growth factors (CSF1R ligands and TGF-β1/2) have been favored for the maintenance of rodent microglia as they promote morphological features observed in situ. Here we study the functional and transcriptomic impacts of such media on human microglia. Media formulation had little impact on microglia transcriptome assessed by RNA sequencing which was sufficient to significantly alter microglia capacity to phagocytose myelin debris and to elicit an inflammatory response to lipopolysaccharide. When compared to immediately ex vivo microglia from the same donors, the addition of fetal bovine serum to culture media, but not growth factors, was found to aid in the maintenance of key signature genes including those involved in phagocytic processes. A phenotypic shift characterized by CSF1R downregulation in culture correlated with a lack of reliance on CSF1R signaling for survival. Consequently, no improvement in cell survival was observed following culture supplementation with CSF1R ligands. Our study provides better understanding of human microglia in culture, with observations that diverge from those previously made in rodent microglia. Graphical abstract
Predicting expression divergence and its evolutionary parameters between single-copy genes in two species

Predicting gene expression divergence and its evolutionary parameters is integral to understanding the emergence of new gene functions and associated traits. Whereas several sophisticated methods have been developed for these tasks, their applications are either limited to duplicate genes or require expression data from more than two species. Thus, here we present PiXi, the first machine learning framework for predicting expression divergence and its evolutionary parameters between single-copy genes in two species. In particular, PiXi models gene expression evolution as an Ornstein-Uhlenbeck process, and overlays this model with multi-layer neural network, random forest, and support vector machine architectures for making predictions. We show that PiXi has high power and accuracy in predicting gene expression divergence and its underlying parameters across a wide range of evolutionary scenarios, with the globally best performance achieved by a multi-layer neural network. Moreover, application of our best performing PiXi predictor to empirical data from single-copy genes residing at different loci in two species of Drosophila reveals that expression divergence occurs in approximately 20% of these positionally relocated genes and is driven by a combination of neutral and selective forces. Further analysis shows that several of these genes are involved in the electron transport chain of the mitochondrial membrane, suggesting that new chromatin environments may impact energy production in Drosophila. Thus, by providing a toolkit for predicting expression divergence and its evolutionary parameters between single-copy genes in two species, PiXi can shed light on the origins of novel phenotypes across diverse biological processes and study systems.
Evolution of the regulation of developmental gene expression in blind Mexican cavefish

Changes in gene expression regulation during development are considered the main drivers of morphological evolution and diversification. Here, we analysed the embryonic transcriptomes of surface-dwelling and blind cave-adapted morphs of the species Astyanax mexicanus and their reciprocal F1 hybrids at tailbud stage. Comparing gene expression in parents and allelic expression ratios in hybrids, we found that ∼20% of the transcriptome is differentially expressed and that cis-regulatory changes are the main contributors to variations in early developmental gene expression in the two morphs. We provide a list of 108 cis-regulated genes that could contribute to cavefish developmental evolution, and further explore the regulatory mechanisms controlling the cellular and regional expression of rx3, a “master eye gene”. Using quantitative embryology approaches after fluorescent in situ hybridisation, cell transplantations and interference with signalling pathways, we show that rx3 cellular levels -controlling optic cell fates-are regulated in cis and in a cell-autonomous manner, whereas the size of rx3 domain -controlling eye size-depends on non-autonomous Wnt signalling. Altogether, we reveal how distinct mechanisms and regulatory modules can regulate developmental gene expression and shape developmental evolution, with negligible contribution of coding mutations.
Within-species differences in vocal production learning in a songbird are associated with differences in flexible rhythm pattern perception

Humans readily recognize a familiar rhythmic pattern, such as isochrony (equal timing between events) across a wide range of rates. This ability reflects a facility with perceiving the relative timing of events, not just absolute interval durations. Several lines of evidence suggest that this ability is supported by precise temporal predictions that arise from forebrain auditory-motor interactions. We have shown previously that male zebra finches, which possess specialized auditory-motor networks and communicate with rhythmically patterned sequences, share our ability to recognize isochrony independent of rate. To test the hypothesis that flexible rhythm pattern perception is linked to vocal learning, we ask whether female zebra finches, which do not learn to sing, can also recognize global temporal patterns. We find that non-singing females can flexibly recognize isochrony but perform slightly worse than males on average. These findings are consistent with recent work showing that while females have reduced forebrain song regions, the overall network connectivity of vocal premotor regions is similar to that in males and supports predictions of upcoming events. Comparative studies of male and female songbirds thus offer an opportunity to study how individual differences in auditory-motor connectivity influence perception of relative timing, a hallmark of human music perception.
Innexin-Mediated Adhesion between Glia Is Required for Axon Ensheathment in the Peripheral Nervous System

Glia are essential to protecting and enabling nervous system function and a key glial function is the formation of the glial sheath around peripheral axons. Each peripheral nerve in the Drosophila larva is ensheathed by three glial layers, which structurally support and insulate the peripheral axons. How peripheral glia communicate with each other and between layers is not well established and we investigated the role of Innexins in mediating glial function in the Drosophila periphery. Of the eight Drosophila Innexins, we found two (Inx1 and Inx2) are important for peripheral glia development. In particular loss of Inx1 and Inx2 resulted in defects in the wrapping glia leading to disruption of the glia wrap. Of interest loss of Inx2 in the subperineurial glia also resulted in defects in the neighboring wrapping glia. Inx plaques were observed between the subperineurial glia and the wrapping glia suggesting that gap junctions link these two glial cell types. We found Inx2 is key to Ca2+ pulses in the peripheral subperineurial glia but not in the wrapping glia, and we found no evidence of gap junction communication between subperineurial and wrapping glia. Rather we have clear evidence that Inx2 plays an adhesive and channel-independent role between the subperineurial and wrapping glia to ensure the integrity of the glial wrap. SIGNIFICANCE STATEMENT Gap junctions are critical for glia communication and formation of myelin in myelinating glia. However, the role of gap junctions in non-myelinating glia is not well studied, yet non-myelinating glia are critical for peripheral nerve function. We found the Innexin gap junction proteins are present between different classes of peripheral glia in Drosophila. Here Innexins form junctions to facilitate adhesion between the different glia but do so in a channel-independent manner. Loss of adhesion leads to disruption of the glial wrap around axons and leads to fragmentation of the wrapping glia membranes. Our work points to an important role for gap junction proteins in mediating insulation by non-myelinating glia.
Urban birds’ tolerance towards humans was largely unaffected by increased variation in human levels due to COVID-19 shutdowns

The coronavirus disease 2019 (COVID-19) pandemic dramatically altered human activities, and, during shutdowns. Here, we evaluated whether urban birds from five countries changed their tolerance towards humans during the COVID-19 shutdowns. We collected 6369 flight initiation distance estimates for 147 bird species and found that human numbers in parks (at a given hour, day, week or year - before and during the COVID-19 shutdowns) had a little effect on birds’ tolerance of approaching humans. Apart from the actual human numbers in the area (hourly scale), the effect of human activity at other temporal scales centered around zero. The results were similar across countries, for most species or when we restricted our analyses only to species sampled both before and during the COVID-19 shutdowns. As expected, the level of daily human presence in parks (measured by Google Mobility Reports) correlated negatively with the stringency of governmental restrictions (a weekly proxy for human presence) and was overall lower during COVID-19 shutdowns than during the post-shutdown year (2022). Our results highlight the resilience of birds to changes in human numbers on multiple temporal scales, the complexities of linking animal fear responses to human behavior, and the challenge of quantifying both simultaneously in situ.
EEG frequency tagging evidence of intact social interaction recognition in adults with autism

To explain the social difficulties in autism, a large amount of research has been conducted on the neural correlates of social perception. However, this research has mostly used basic social stimuli (e.g. eyes, faces, hands, single agent), not resembling the complexity of what we encounter in our daily social lives, and as such, the situations people with autism experience difficulties in. A more complex stimulus that we do come across often and is also highly relevant for social functioning is that of third-party social interactions. Here, we investigated if individuals with and without autism process third-party social interactions differently. More specifically, we measured neural responses to social scenes depicting either social interaction or not with an electroencephalogram (EEG) frequency tagging task and compared these responses between adults with and without autism (N = 61). The results revealed an enhanced response to social scenes with interaction, replicating previous findings in a neurotypical sample (Oomen et al., 2022). Crucially, this effect was found in both groups with no difference between them. This suggest that social interaction recognition is not anomalous in adults with autism and cannot explain the social difficulties adults with autism experience. Lay abstract People with autism have social difficulties and are thought to experience the world differently. To better understand these differences, research has studied how the brain of people with and without autism processes social stimuli. However, this research has mostly used basic social stimuli (e.g. eyes, faces, hands, and single agents). Such stimuli do not resemble the complexity of daily life, where we typically do not come across isolated body parts, but instead have to make sense of complex social scenes with multiple people. To do so, it is imperative that we are able to recognize social interaction. Hence, if social interaction processing is anomalous, this could have pervasive consequences for social functioning more generally. Here, we used brain imaging to test if adults with autism process social interaction scenes differently than adults without autism. In line with previous findings from a neurotypical sample (Oomen et al. (2022), we found that social scenes depicting interaction elicited stronger brain responses than social scenes not depicting interaction. Crucially, this effect was found in both groups with no difference between them. These findings suggest that the fundamental process of social interaction recognition is not anomalous in adults with autism.
Audiovisual integration in the human brain: a coordinate-based meta-analysis

People can seamlessly integrate a vast array of information from what we see and hear in the noisy and uncertain world. However, the neural underpinnings of audiovisual integration continue to be the topic of debate. Using strict inclusion criteria, we performed activation likelihood estimation meta-analysis on 121 neuroimaging experiments with a total of 2,092 participants. We found that audiovisual integration is linked with the coexistence of multiple integration sites including early cortical, subcortical, and higher association areas. Although activity was consistently found within the superior temporal cortex, different portions of this cortical region were identified depending on the analytical contrast used, complexity of the stimuli, and modality within which attention was directed. The context-dependent neural activity related to audiovisual integration suggests a flexible rather than fixed neural pathway for audiovisual integration. Together, our findings highlight a flexible multiple pathways model for audiovisual integration, with superior temporal cortex as the central node in these neural assemblies.
Intense light unleashes male–male courtship behaviour in wild-type Drosophila

Drosophila courtship studies have elucidated several principles of the neurogenetic organization of complex behavior. Through an integration across sensory modalities, males perform stereotypic patterns of chasing, courtship song production, and copulation attempts. Here we report a serendipitous finding that intense light not only enhances courtship toward female targets but also triggers unexpected courtship behaviors among male flies. Strikingly, in wild-type male-only chambers, we observed extreme behavioral manifestations, such as “chaining” and “wheeling”, resembling previously reported male-male courtship behaviors in fruitless mutants and in transformants with ectopic mini-white+ overexpression. This male-male courtship was greatly diminished in a variety of visual system mutants, including disrupted phototransduction (norpA), eliminated eye-color screening pigments (white), or deletion of the R7 photoreceptor cells (sevenless). However, light-induced courtship was unhampered in wing-cut flies, despite their inability to produce courtship song, a major acoustic signal during courtship. Unexpectedly the olfactory mutants orco and sbl displayed unrestrained male-male courtship. Particularly, orco males attained maximum courtship scores under either dim or intense light conditions. Together, our observations support the notion that the innate male courtship behavior is restrained by olfactory cues under normal conditions but can be unleashed by strong visual stimulation in Drosophila.
Microstructural and crystallographic evolution of palaeognath (Aves) eggshells

The avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).
GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations

Cellular response to genetic perturbation is central to numerous biomedical applications from identifying genetic interactions involved in cancer to methods for regenerative medicine. However, the combinatorial explosion in the number of possible multi-gene perturbations severely limits experimental interrogation. Here, we present GEARS, a method that can predict transcriptional response to both single and multi-gene perturbations using single-cell RNA-sequencing data from perturbational screens. GEARS is uniquely able to predict outcomes of perturbing combinations consisting of novel genes that were never experimentally perturbed by leveraging geometric deep learning and a knowledge graph of gene-gene relationships. GEARS has higher precision than existing approaches in predicting five distinct genetic interaction subtypes and can identify the strongest interactions more than twice as well as prior approaches. Overall, GEARS can discover novel phenotypic outcomes to multi-gene perturbations and can thus guide the design of perturbational experiments.
Differences in single-motor and multi-motor motility properties across the kinesin-6 family

Kinesin motor proteins are responsible for orchestrating a variety of microtubule-based processes including intracellular transport, cell division, cytoskeletal organization, and cilium function. During cell division, members of the kinesin-6 family play critical roles in anaphase and cytokinesis, however little is known about their motility properties. We find that truncated versions of MKLP1 (HsKIF23), MKLP2 (HsKIF20A), and HsKIF20B predominately display non-processive behavior as single molecules although slow, processive motility was occasionally observed, most prominently for MKLP2. Despite their non-processive nature, all kinesin-6 proteins were able to work in teams to drive microtubule gliding. MKLP1 and KIF20B were also able to work in teams to drive robust transport of both peroxisomes, a low-load cargo, and Golgi, a high-load cargo, in cells. In contrast, MKLP2 showed minimal transport of peroxisomes and was unable to drive Golgi dispersion. These results indicate that while all three mammalian kinesin-6 motor proteins are generally non-processive as single motors, they differ in their ability to work in teams and generate forces needed to drive cargo transport in cells.
POLLINATOR GROOMING BEHAVIOR ALTERS POLLEN LANDSCAPES ON BEES’ BODIES AND INCREASES POLLEN CARRYOVER TO OTHER FLOWERS

Pollen participates both as the carrier of male gametes in the reproduction of flowering plants and as a key resource exploited by floral visitors, especially bees. Pollinator behavior significantly alters the patterns of pollen removal and deposition, often called pollen fates. To date, few theoretical investigations have attempted to jointly model patterns of pollen transfer and pollinator behavior, and empirical studies are restricted to species to which pollen movement can be tracked. Here we use a spatially explicit agent-based modeling approach, to determine how bee grooming behavior may alter pollen fates and affect plant reproduction. Specifically, we asked whether pollen mixing and removal during pollen grooming may change the “pollen landscape” on a bee’s body consequently affecting both pollen export by the anthers and deposition onto stigmas. Our model shows that both mixing and removal behaviors restructure the “pollen landscape” on the bee’s body, increasing pollen carryover (deposition in consecutive visits), and increasing pollen diversity (number of pollen donors) onto stigmas in sequential flower visits. Our results counterintuitively show that pollen grooming may have a positive effect on both male and female finesses during plant reproduction.
Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter

Protein clustering plays numerous roles in cell physiology and disease. However, protein oligomers can be difficult to detect because they are often too small to appear as puncta in conventional fluorescence microscopy. Here we describe a fluorescent reporter strategy that detects protein clusters with high sensitivity, called CluMPS (Clusters Magnified by Phase Separation). A CluMPS reporter detects and visually amplifies even small clusters of a binding partner, generating large, quantifiable fluorescence condensates. We use computational modeling and optogenetic clustering to demonstrate that CluMPS can detect small oligomers and behaves rationally according to key system parameters. CluMPS detected small aggregates of pathological proteins where the corresponding GFP fusions appeared diffuse. CluMPS also detected and tracked clusters of unmodified and tagged endogenous proteins, and orthogonal CluMPS probes could be multiplexed in cells. CluMPS provides a powerful yet straightforward approach to observe higher-order protein assembly in its native cellular context.
Dietary protection against the visual and motor deficits induced by experimental autoimmune encephalomyelitis

Five to eight percent of the world population currently suffers from at least one autoimmune disorder. Despite multiple immune modulatory therapies for autoimmune demyelinating diseases of the central nervous system, these treatments can be limiting for subsets of patients due to adverse effects and expense. To circumvent these barriers, we investigated a nutritional intervention in mice undergoing experimental autoimmune encephalomyelitis (EAE). This model of autoimmune-mediated demyelination induces visual and motor pathologies similar to those experienced by people with multiple sclerosis (MS). Here, we report that limiting dietary carbohydrates by feeding mice a ketogenic diet (KD) enriched in medium chain triglycerides, α-linolenic acid, and fiber is effective at mitigating EAE-induced optic neuritis and motor deficits. The KD was efficacious when fed as a preventive regimen prior to EAE immunization as well as when initiated as an interventional regimen following the onset of EAE symptoms. The KD minimally impacted body weight during the experimental time course, increased circulating ketones, prevented motor and ocular deficits, preserved myelination of the optic nerve, and reduced infiltration of immune cells to optic nerves. The KD also increased anti-inflammatory-associated omega-3 fatty acids in the plasma and reduced select cytokines in the circulation associated with EAE-mediated pathological inflammation. In light of ongoing clinical trials using dietary strategies to treat people with MS, these findings support that a KD promotes a systemic anti-inflammatory milieu and ameliorates autoimmune-induced demyelinating visual and motor deficits.