Miracle-dz/UniFAR-FTUs huggingface dataset:
EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action

The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to identify species for conservation action that embody large amounts of threatened evolutionary history. In 2017, we convened a workshop to update the EDGE metric to incorporate advances in the field of phylogenetically-informed conservation. Building on that workshop, we devised the metric ‘EDGE2’, which we present here. EDGE2 uses a modular, tiered approach to provide priority rankings—and associated measures of uncertainty in both phylogenetic and extinction risk data—for all species in a clade. EDGE2 takes into account the extinction risk of closely-related species to better reflect the contribution a species is expected to make to overall PD in the future. We applied EDGE2 to the world’s mammals to identify an updated list of priority EDGE species and compare the results with the original EDGE approach. Despite similarity in the priority lists produced between EDGE and EDGE2, EDGE2 places greater priority on species with fewer close relatives on the Tree of Life. As we approach a crossroads for global biodiversity policy, EDGE2 exemplifies how academic and applied conservation biologists can collaborate to guide effective priority-setting to conserve the most irreplaceable components of biodiversity upon which humanity depends.
Single cell analysis of the dorsal V-SVZ reveals differential quiescence of postnatal pallial and subpallial neural stem cells driven by TGFbeta/BMP-signalling

The ventricular-subventricular zone (V-SVZ) is the largest neurogenic region of the postnatal forebrain, containing neural stem cells (NSCs) that emerge from both the embryonic pallium and subpallium. Despite of this dual origin, glutamatergic neurogenesis declines rapidly after birth, while gabaergic neurogenesis persists throughout life. Here, we performed single-cell RNA-sequencing (scRNA-Seq) of the postnatal dorsal V-SVZ for unravelling the mechanisms leading to pallial lineage germinal activity silencing. We identify cell lineage-specific NSCs primed for the generation of neurons or glial cells, as well as a large population of so far uncharacterized quiescent NSCs (qNSC). Pallial qNSCs enter a state of deep quiescence, characterized by persistent TGFbeta/BMP signalling, reduced transcriptional activity and Hopx expression, whilst in contrast, subpallial qNSCs remain transcriptionally primed for activation. Induction of deep pallial quiescence is paralleled by a rapid blockade of glutamatergic neuron production and differentiation. Finally, manipulation of the TGFbeta/BMP receptor Bmpr1a demonstrate its key role in mediating these effects at early postnatal times. Together, our results highlight a central role of TGFbeta/BMP-signalling in synchronizing quiescence induction and blockade of neuronal differentiation to rapidly silence pallial germinal activity after birth.
Differences in Gut Microbiota Assembly Alter Its Ability to Metabolize Dietary Polysaccharides and Resist Clostridioides difficile Colonization

The mammalian gut is home to a vibrant community of microbes. As the gut microbiota has evolved, its members have formed a complex yet stable relationships that prevent non-indigenous microorganisms, such as Clostridioides difficile, from establishing within the gut. Using a bioreactor model of the gut, we characterize how variation in microbial community assembly changes its ability to resist C. difficile. We established diluted microbial communities from healthy human stool in a bioreactor gut model and subsequently challenged them with vegetative C. difficile. 16S rRNA-gene sequencing and selective plating revealed that dilution progressively increases microbiota variability and decreases C. difficile colonization resistance. Using Dirichlet Multinomial Mixtures and linear discriminant analysis of effect size, we identified 19 bacterial taxa, including Bifidobacterium, Bacteroides and Lachnospiraceae, that associate with more resistant community types. Since these taxa are associated with butyrate production, which is tied to C. difficile colonization resistance, we performed another reactor experiment where we increased inulin concentrations prior to C. difficile challenge. Diluted communities concurrently lost their ability to produce additional butyrate in response to inulin, as measured by high performance liquid chromatography, and resist C. difficile colonization. These data demonstrate that a similar level of microbiota cohesiveness is required to prevent C. difficile colonization and metabolize inulin. It also suggests that metabolic activity of butyrate-producing microbes is tied to colonization resistance. Future work can leverage these findings to develop treatments that leverage knowledge of these ecological dynamics to improve efficacy. Importance The microbes living in the human large intestine helps create an environment that is resistant to organisms that do not normally reside there, such as the pathogen Clostridioides difficile. Differences in ways in which microbial communities make an environment their home can change their ability to provide that resistance. To study those differences, we use a model of the intestine that incorporates only microbial variables (i.e. no host is involved). By diluting microbial communities to decrease their complexity, we show that communities lose their ability to resist C. difficile at a particular point and, at the same time, their ability to use inulin, a common dietary fiber, in ways that make the environment more toxic to C. difficile. These findings will help future researchers dissect the microbial components that create a resistant intestinal environment.
Bees differentiate sucrose solution from water at a distance

Bees are perhaps the most important model for studying complex cognition in invertebrates, showing a variety of impressive abilities. Many experiments employ a training procedure in which the animal associates a characteristic of a “flower” (neutral stimulus) to sucrose solution (positive stimulus) over multiple foraging bouts. We hypothesized that sucrose solution might appear different from water to the bee sensorium, rendering it superfluous for the animal to learn the intended experimental cues. To test this hypothesis, we presented bumblebees simultaneously with 1.6M sucrose and water on artificial flowers. We presented the solutions in three conditions, to identify the most likely recognition mechanism: in drop form, inside cotton-plugged centrifuge tubes, and soaked into raised cigarette filters. The bumblebees chose to contact the sucrose solution significantly more often in all three conditions, confirming their ability to discriminate sucrose from water at a distance, with spectral differences being the most likely mechanism for this differentiation. These results have large implications for the design of training procedures, as the presence of an alternative cue may mask the learning of challenging tasks. This may force us to re-examine much of the literature and unpublished ‘negative results’ on bee cognition: weakening some claims, but strengthening others.
Ectodermal Wnt signaling, cell fate determination, and polarity of the skate gill arch skeleton

The gill skeleton of cartilaginous fishes (sharks, skates, rays and holocephalans) exhibits a striking anterior–posterior polarity, with a series of fine appendages called branchial rays projecting from the posterior margin of the gill arch cartilages. We previously demonstrated in the skate (Leucoraja erinacea) that branchial rays derive from a posterior domain of pharyngeal arch mesenchyme that is responsive to Shh signalling from a distal gill arch epithelial ridge (GAER) signalling centre. However, how branchial ray progenitors are specified exclusively within posterior gill arch mesenchyme is not known. Here we show that genes encoding several Wnt ligands are expressed in the ectoderm immediately adjacent to the skate GAER, and that these Wnt signals are transduced largely in the anterior arch environment. Using pharmacological manipulation, we show that inhibition of Wnt signalling results in an anterior expansion of Shh signal transduction in developing skate gill arches, and in the formation of ectopic anterior branchial ray cartilages. Our findings demonstrate that ectodermal Wnt signalling contributes to gill arch skeletal polarity in skate by restricting Shh signal transduction and chondrogenesis to the posterior arch environment and highlights the importance of signalling interactions at embryonic tissue boundaries for cell fate determination in vertebrate pharyngeal arches.
Prelimbic cortex neural encoding dynamically tracks expected outcome value

Animals must modify their behavior based on updated expected outcomes in a changing environment. Prelimbic cortex (PrL) neural encoding during learning predicts and is necessary for appropriately altering behavior based on new expected outcome value following devaluation. We aimed to determine how PrL neural activity encodes reward predictive cues after the expected outcome value of those cues is decreased following conditioned taste aversion. In one post- devaluation session, rats were tested under extinction to determine their ability alter their behavior to the expected outcome values (i.e., extinction test). In a second post-devaluation session, rats were tested with the newly devalued outcome delivered so that the rats experienced the updated outcome value within the session (i.e., re-exposure test). We found that PrL neural encoding to the cue associated with the devalued reward predicted the ability of rats to suppress behavior in the extinction test session, but not in the re-exposure test session. While all rats were able to successfully devalue the outcome during conditioned taste aversion, a subset of rats continued to consume the devalued outcome in the re-exposure test session. We found differential patterns of PrL neural encoding in the population of rats that did not avoid the devalued outcome during the re-exposure test compared to the rats that successfully avoided the devalued outcome. Our findings suggest that PrL neural encoding dynamically tracks expected outcome values, and differential neural encoding in the PrL to reward predictive cues following expected outcome value changes may contribute to distinct behavioral phenotypes.
Maximum a posteriori natural scene reconstruction from retinal ganglion cells with deep denoiser priors

A fraction of the visual information arriving at the retina is transmitted to the brain by signals in the optic nerve, and the brain must rely solely on these signals to make inferences about the visual world. Previous work has probed the visual information contained in retinal signals by reconstructing images from retinal activity using linear regression and nonlinear regression with neural networks. Maximum a posteriori (MAP) reconstruction offers a more general and principled approach. We develop a novel method for approximate MAP reconstruction by combining a generalized linear model of light responses in retinal neurons and their dependence on spike history and spikes of neighboring cells, with an image prior implicitly embedded in a deep convolutional neural network trained for image denoising. We use this method to reconstruct natural images from ex vivo simultaneously-recorded spikes of hundreds of ganglion cells uniformly sampling a region of the retina. The method produces reconstructions that match or exceed the state-of-the-art in perceptual similarity and exhibit additional fine detail, while using substantially fewer model parameters than previous approaches. The use of more rudimentary encoding models (a linear-nonlinear-Poisson cascade) or image priors (a 1/F spectral model) significantly reduces reconstruction performance, indicating the essential role of both components in achieving high-quality reconstructed images from the retinal signal.
Correcting Modification-Mediated Errors in Nanopore Sequencing by Nucleotide Demodification and in silico Correction

The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modifications untrained in the basecalling models can seriously reduce the quality. This paper reports a set of ONT-sequenced genomes with unexpected low quality (∼Q30) due to extensive new modifications. Demodification by whole-genome amplification (WGA) significantly improved the quality of all genomes (∼Q50-60) while losing the epigenome. We developed a computational method, Modpolish, for correcting modification-mediated errors without WGA. Modpolish produced high-quality genomes and uncovered the underlying modification motifs without loss of epigenome. Our results suggested that novel modifications are prone to ONT errors, which are correctable by WGA or Modpolish without additional short-read sequencing.
AI-guided screen identifies probucol-mediated mitophagy enhancement through modulation of lipid droplets

Failures in mitophagy, a process by which damaged mitochondria are cleared, results in neurodegeneration, while enhancing mitophagy promotes the survival of dopaminergic neurons. Using an artificial intelligence platform, we employed a natural language processing approach to evaluate the semantic similarity of candidate molecules to a set of well-established mitophagy enhancers. Top candidates were screened in a cell-based mitochondrial clearance assay. Probucol, a lipid-lowering drug, was validated across several orthogonal mitophagy assays. In vivo, probucol improved survival, locomotor function and dopaminergic neuron loss in zebrafish and fly models of mitochondrial damage. Probucol functioned independently of PINK1/Parkin but its effects on mitophagy and in vivo depended on ABCA1, which negatively regulated mitophagy following mitochondrial damage. Autophagosome and lysosomal markers were elevated by probucol treatment in addition to increased contact between lipid droplets and mitochondria. Conversely, lipid droplet expansion, which occurs following mitochondrial damage was suppressed by probucol and probucol-mediated mitophagy enhancement required lipid droplets. Probucol-mediated lipid droplet dynamics changes may prime the cell for a more efficient mitophagic response to mitochondrial damage.
Local synaptic inhibition mediates cerebellar pattern separation necessary for learned sensorimotor associations

The cerebellar cortex plays a key role in generating predictive sensorimotor associations. To do so, the granule cell layer is thought to establish unique sensorimotor representations for learning. However, how this is achieved, and how granule cell population responses contribute to behavior, has remained unclear. To address these questions, we have used in vivo calcium imaging and granule cell specific pharmacological manipulation of synaptic inhibition in awake, behaving mice. We find that inhibition sparsens and thresholds sensory responses, limiting overlap between sensory ensembles, and preventing spiking in many granule cells that receive excitatory input. Moreover, we find that inhibition can be recruited in a stimulus-specific manner to powerfully decorrelate multisensory ensembles. Consistent with these results, we find that granule cell inhibition is required for sensory discrimination in a cerebellum-dependent behavior. These data thus reveal new mechanisms for granule cell layer pattern separation beyond those envisioned by classical models.
Robust alignment of single-cell and spatial transcriptomes with CytoSPACE

Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, a method for aligning single-cell and spatial transcriptomes via convex linear optimization. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise-tolerance, accuracy, and efficiency, enabling improved analysis of spatial transcriptomics data at single-cell resolution.
Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking

Quantifying the contributions of possible environmental sources (“sources”) to a specific microbial community (“sink”) is a classical problem in microbiology known as microbial source tracking (MST). Solving the MST problem will not only help us understand how microbial communities were formed, but also have far-reaching applications in pollution control, public health, and forensics. Numerous computational methods, referred to as MST solvers hereafter, have been developed in the past and applied to various real datasets to demonstrate their utility across different contexts. Yet, those MST solvers do not consider microbial interactions and priority effects in microbial communities. Here, we revisit the performance of several representative MST solvers. We show compelling evidence that solving the MST problem using existing MST solvers is impractical when ecological dynamics plays a role in community assembly. In particular, we clearly demonstrate that the presence of either microbial interactions or priority effects will render the MST problem mathematically unsolvable for any MST solver. We further analyze data from fecal microbiota transplantation studies, finding that the state-of-the-art MST solvers fail to identify donors for most of the recipients. Finally, we perform community coalescence experiments to demonstrate that the state-of-the-art MST solvers fail to identify the sources for most of the sinks. Our findings suggest that ecological dynamics imposes fundamental challenges in solving the MST problem using computational approaches.
Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation

Viruses have evolved mechanisms to modulate cellular pathways to facilitate infection. One such pathway is the formation of stress granules (SG), which are ribonucleoprotein complexes that assemble during translation inhibition following cellular stress. Inhibition of SG assembly has been observed under numerous virus infections across species, suggesting a conserved fundamental viral strategy. However, the significance of SG modulation during virus infection is not fully understood. The 1A protein encoded by the model dicistrovirus, Cricket Paralysis Virus (CrPV), is a multifunctional protein that can bind to and degrade Ago-2 in an E3 ubiquitin ligase-dependent manner to block the antiviral RNA interference pathway and inhibit SG formation. Moreover, the R146 residue of 1A is necessary for SG inhibition and CrPV infection in both Drosophila S2 cells and adult flies. Here, we uncoupled CrPV-1A’s functions and provide insight into its underlying mechanism for SG inhibition. CrPV-1A mediated inhibition of SGs requires the E3 ubiquitin-ligase binding domain and the R146 residue, but not the Ago-2 binding domain. Wild-type but not mutant CrPV-1A R146A localizes to the nuclear membrane which correlates with nuclear enrichment of poly(A)+ RNA. Transcriptome changes in CrPV-infected cells are dependent on the R146 residue. Finally, Nup358/RanBP2 is targeted and degraded in CrPV-infected cells in an R146-dependent manner and the depletion of Nup358 blocks SG formation. We propose that CrPV utilizes a multiprong strategy whereby the CrPV-1A protein interferes with a nuclear event that contributes to SG inhibition in order to promote infection. AUTHOR SUMMARY Viruses often inhibit a cellular stress response that leads to the accumulation of RNA and protein condensates called stress granules. How this occurs and why this would benefit virus infection are not fully understood. Here, we reveal a viral protein that can block stress granules and identify a key amino acid residue in the protein that inactivates this function. We demonstrate that this viral protein has multiple functions to modulate nuclear events including mRNA export and transcription to regulate stress granule formation. We identify a key host protein that is important for viral protein mediate stress granule inhibition, thus providing mechanistic insights. This study reveals a novel viral strategy in modulating stress granule formation to promote virus infection.
Rab11 regulates autophagy at dendritic spines in an mTOR- and NMDA-dependent manner

Synaptic plasticity is a process that shapes neuronal connections during neurodevelopment, learning, and memory. Autophagy is a mechanism that allows cells to degrade their unnecessary or dysfunctional components. Autophagosomes appear at dendritic spines in response to plasticity-inducing stimuli. Autophagy defects contribute to altered dendritic spine development, autistic-like behavior in mice, and neurological disease. While several studies explored the involvement of autophagy in synaptic plasticity, the steps preceding autophagosome emergence at the postsynapse remain unknown. Here we show a postsynaptic association of autophagy-related protein 9A (Atg9A), known to be involved in the initial stages of autophagosome formation, with Rab11, a small GTPase that regulates endosomal trafficking. Rab11 activity is necessary for the maintenance of Atg9A-positive structures at dendritic spines. Inhibition of mTOR increased Rab11 and Atg9A interaction and increased the emergence of autophagosomes in dendritic spines when coupled to NMDA receptor stimulation. Dendritic spines with newly formed autophagosomes were more resistant to NMDA-induced morphologic change. These results collectively suggest that autophagy initiation in dendritic spines depends on an activity-dependent Rab11a-Atg9A interaction regulated by mTOR.
mNeonGreen-tagged fusion proteins and nanobodies reveal localization of tropomyosin to patches, cables, and contractile actomyosin rings in live yeast cells

Tropomyosins are structurally conserved α-helical coiled-coil dimeric proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments in non-muscle cells and are essential for calcium regulation of myosin II contractility in the muscle. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live cell imaging tools currently available in many organisms. Here, we report mNeon-Green (mNG) tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin localization and dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8), and Saccharomyces cerevisiae (Tpm1 and Tpm2), in vivo and in isolated S. pombe cell division apparatuses. We extended this approach to also visualize the mammalian TPM2 isoform. Finally, we generated a camelid-nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo without significantly influencing cell growth and dynamics of actin cytoskeleton. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring, and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and actin cables in vivo.