Miracle-dz/UniFAR-FTUs huggingface dataset:
MSH2-MSH3 promotes DNA end resection during HR and blocks TMEJ through interaction with SMARCAD1 and EXO1

DNA double strand break (DSB) repair by Homologous recombination (HR) is initiated by the end resection, a process during which 3’ ssDNA overhangs are generated by the nucleolytic degradation. The extent of DNA end resection determines the choice of the DSB repair pathway. The role of several proteins including nucleases for end resection has been studied in detail. However, it is still unclear how the initial, nicked DNA generated by MRE11-RAD50-NBS1 is recognized and how subsequent proteins including EXO1 are recruited to DSB sites to facilitate extensive end resection. We found that the MutSβ (MSH2-MSH3) mismatch repair (MMR) complex is recruited to DSB sites by recognizing the initial nicked DNA at DSB sites through the interaction with the chromatin remodeling protein SMARCAD1. MSH2-MSH3 at DSB sites helps to recruit EXO1 for long-range resection and enhances its enzymatic activity. MSH2-MSH3 furthermore inhibits the access of DNA polymerase θ (POLQ), which promotes polymerase theta-mediated end-joining (TMEJ) of DSB. Collectively, our data show a direct role for MSH2-MSH3 in the initial stages of DSB repair by promoting end resection and influencing DSB repair pathway by favoring HR over TMEJ. Our findings extend the importance of MMR in DSB repair beyond established role in rejecting the invasion of sequences not perfectly homologous to template DNA during late-stage HR.
Convergent, functionally independent signaling by mu and delta opioid receptors in hippocampal parvalbumin interneurons

Functional interactions between G protein-coupled receptors are poised to enhance neuronal sensitivity to neuromodulators and therapeutic drugs. Mu and Delta opioid receptors (MORs and DORs) can interact when overexpressed in the same cells, but whether co-expression of endogenous MORs and DORs in neurons leads to functional interactions is unclear. Here, we show that both MORs and DORs inhibit parvalbumin-expressing basket cells (PV-BCs) in hippocampal CA1 through partially occlusive signaling pathways that terminate on somato-dendritic potassium channels and presynaptic calcium channels. Using photoactivatable opioid neuropeptides, we find that DORs dominate the response to enkephalin in terms of both ligand-sensitivity and kinetics, which may be due to relatively low expression levels of MOR. Opioid-activated potassium channels do not show heterologous desensitization, indicating that MORs and DORs signal independently. In a direct test for heteromeric functional interactions, the DOR antagonist TIPP-Psi does not alter the kinetics or potency of either the potassium channel or synaptic responses to photorelease of the MOR agonist DAMGO. Thus, despite largely redundant and convergent signaling, MORs and DORs do not functionally interact in PV-BCs. These findings imply that crosstalk between MORs and DORs, either in the form of physical interactions or synergistic intracellular signaling, is not a preordained outcome of co-expression in neurons.
Perfecting and extending the near-infrared biological window

In vivo fluorescence imaging in the second near-infrared window (NIR-II) has been considered as a promising technique for visualizing the mammals. However, the definition of the NIR-II region and the mechanism accounting for the excellent performance still need to be perfected. Herein, we simulated bioimaging in the NIR spectral range (to 2340 nm), confirmed the positive contribution of moderate light absorption by water in intravital imaging and perfected the NIR-II window as 900-1880 nm, where the 1400-1500 nm was defined as NIR-IIx region and the 1700-1880 nm was defined as NIR-IIc region, respectively. Moreover, the 2080-2340 nm was newly proposed as the third near-infrared (NIR-III) window, which was believed to provide the best imaging quality. The wide-field fluorescence microscopy in brain, in addition, was performed around NIR-IIx region with excellent optical sectioning strength and the largest imaging depth of in vivo NIR-II fluorescence microscopy to date. We also proposed 1400 nm long-pass detection in off-peak NIR-II imaging whose profits exceeded those of NIR-IIb imaging, using bright fluorophores with short peak emission wavelength.
CRISPR/Cas9 modified An. gambiae carrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and interaction with metabolic enzymes

Insecticide resistance in Anopheles mosquitoes is a major obstacle in maintaining the momentum in reducing the malaria burden; mitigating strategies require improved understanding of the underlying mechanisms. Mutations in the target site of insecticides (the voltage gated sodium channel for the most widely used pyrethroid class) and over-expression of detoxification enzymes are commonly reported, but their relative contribution to phenotypic resistance remain poorly understood. Here we present a genome editing pipeline to introduce single nucleotide polymorphisms in An. gambiae which we have used to study the effect of the classical kdr mutation L1014F (L995F based on An. gambiae numbering), one of the most widely distributed resistance alleles. Introduction of 1014F in an otherwise fully susceptible genetic background increased levels of resistance to all tested pyrethroids and DDT ranging from 9.9-fold for permethrin to >24-fold for DDT. The introduction of the 1014F allele was sufficient to reduce mortality of mosquitoes after exposure to deltamethrin treated bednets, even as the only resistance mechanism present. When 1014F was combined with over-expression of glutathione transferase Gste2, resistance to permethrin increased further demonstrating the critical combined effect between target site resistance and detoxification enzymes in vivo. We also show that mosquitoes carrying the 1014F allele in homozygosity showed fitness disadvantages including increased mortality at the larval stage and a reduction in fecundity and adult longevity, which can have consequences for the strength of selection that will apply to this allele in the field. Author Summary Escalation of pyrethroid resistance in Anopheles mosquitoes threatens to reduce the effectiveness of our most important tools in malaria control. Studying the mechanisms underlying insecticide resistance is critical to design mitigation strategies. Here, using genome modified mosquitoes, we functionally characterize the most prevalent mutation in resistant mosquitoes, showing that it confers substantial levels of resistance to all tested pyrethroids and undermines the performance of pyrethroid-treated nets. Furthermore, we show that combining this mutation with elevated levels of a detoxification enzyme further increases resistance. The pipeline we have developed provides a robust approach to quantifying the contribution of different combinations of resistance mechanisms to the overall phenotype, providing the missing link between resistance monitoring and predictions of resistance impact.
Rich and lazy learning of task representations in brains and neural networks

How do neural populations code for multiple, potentially conflicting tasks? Here, we used computational simulations involving neural networks to define “lazy” and “rich” coding solutions to this multitasking problem, which trade off learning speed for robustness. During lazy learning the input dimensionality is expanded by random projections to the network hidden layer, whereas in rich learning hidden units acquire structured representations that privilege relevant over irrelevant features. For context-dependent decision-making, one rich solution is to project task representations onto low-dimensional and orthogonal manifolds. Using behavioural testing and neuroimaging in humans, and analysis of neural signals from macaque prefrontal cortex, we report evidence for neural coding patterns in biological brains whose dimensionality and neural geometry are consistent with the rich learning regime.
Capturing membrane trafficking events during 3D angiogenic development in vitro

Objectives Mechanisms that govern angiogenesis are paramount to our understanding of how blood vessels are formed embryonically, maintained in adulthood and manifest disease. Akin to transcriptional regulation of endothelial-specific genes, vesicular trafficking events dictate protein localization, functional activity, and half-life, providing a critically important regulatory step. However, there is little information detailing endothelial-specific trafficking signatures. This is due, in part, by limitations in visualizing trafficking events in endothelial tissues. Our aim in this investigation was to explore the use of a 3-dimensional (3D) in vitro sprouting model to image and evaluate membrane trafficking events compared to the conventional 2-dimensional (2D)-based culture method. Methods Primary Human endothelial cells were challenged to make multicellular sprouts using a fibrin-bead assay. An assortment of cell polarity and Rab proteins were quantified via immunocytochemistry and live-imaging to compare their localization between 3D sprouts and 2D culture. Results Our results show that sprouts generated from the fibrin-bead assay grow close to the imaging plane allowing for an orthogonal view of apical and basal membrane domains. Compared with 2D culture in which the apical and basal domains are in the axial orientation, limiting resolution, 3D sprouts are acquired in the X-Y plane providing high-resolution for viewing trafficking events. Second, we demonstrate that fibrin-bead generated sprouts have a strong apicobasal polarity axis. Third, we directly compare imaging of trafficking mediators podocalyxin and Rab35 between 3D sprouts and 2D culture. Here, we show that 3D sprouting structures are well-suited to capture trafficking events that are not present in 2D culture due to the lack of a defined apical domain. Lastly, we compared exocytic events of von Willebrand Factor between 3D sprouting and 2D culture. Our results demonstrate a distinct imaging advantage for monitoring these trafficking programs in 3D sprouts as compared with conventional 2D culture. Conclusions In general, our results establish that the fibrin-bead sprouting assay is well-suited for sub-cellular imaging of trafficking events during angiogenic growth. Additionally, the 2D endothelial culture does not enforce the formation of an apicobasal polarity axis.
Dopamine desynchronizes the retinal clock through a melanopsin-dependent regulation of acetylcholine retinal waves during development

Dopamine (DA) plays a critical role in retinal physiology, including resetting of the retinal circadian clock that in turn regulates DA release. DA acts on major classes of retinal cells by reconfiguring electrical and chemical synapses. Although a bidirectional regulation between intrinsically photosensitive melanopsin ganglion cells (ipRGCs) and dopaminergic cells has been demonstrated during development and adulthood, DA involvement in the ontogeny of the retinal clock is still unknown. Using wild-type Per2Luc and melanopsin knockout (Opn4-/-::Per2Luc) mice at different postnatal stages, we found that the retina can generate self-sustained circadian rhythms from postnatal day 5 that emerge in the absence of external time cues in both genotypes. Intriguingly, DA lengthens the endogenous period only in wild-type retinas, suggesting that this desynchronizing effect requires melanopsin. Furthermore, blockade of cholinergic retinal waves in wild-type retinas induces a shortening of the period, similarly to Opn4-/-::Per2Luc explants. Altogether, these data suggest that DA desynchronizes the retinal clock through a melanopsin-dependent regulation of acetylcholine retinal waves, thus offering a new role of melanopsin in setting the period of the retinal clock during development.
Reduced visitation to the buzz-pollinated Cyanella hyacinthoides in the presence of other pollen sources in the hyperdiverse Cape Floristic Region

Many plant species have floral morphologies that restrict access to floral resources, such as pollen or nectar, and only a subset of floral visitors can perform the complex handling behaviours required to extract restricted resources. Due to the time and energy required to extract resources from morphologically complex flowers, these plant species potentially compete for pollinators with co-flowering plants that have more easily accessible resources. A widespread floral mechanism restricting access to pollen is the presence of tubular anthers that open through small pores or slits (poricidal anthers). Some bees have evolved the capacity to remove pollen from poricidal anthers using vibrations, giving rise to the phenomenon of buzz-pollination. These bee vibrations that are produced for pollen extraction are presumably energetically costly, and to date, few studies have investigated whether buzz-pollinated flowers may be at a disadvantage when competing for pollinators’ attention with plant species that present unrestricted pollen resources. Here, we studied Cyanella hyacinthoides (Tecophilaeaceae), a geophyte with poricidal anthers in the hyperdiverse Cape Floristic Region of South Africa, to assess how the composition and relative abundance of flowers with easily accessible pollen affect bee visitation to a buzz-pollinated plant. We found that the number of pollinator species was not influenced by community composition. However, visitation rates to C. hyacinthoides were negatively related to the abundance of flowers with more accessible resources. Visitation rates were strongly associated with petal colour, showing that flower colour is important in mediating these interactions. We conclude that buzz-pollinated plants might be at a competitive disadvantage when many easily accessible pollen sources are available, particularly when competitor species share its floral signals.
Nanoparticle Internalization Promotes the Survival of Primary Macrophages

Macrophages, a class of tissue resident innate immune cells, are responsible for sequestering foreign objects through the process of phagocytosis, making them a promising target for immune-modulation via particulate engineering. Here, we report that nanoparticle (NP) dosing and cellular internalization via phagocytosis significantly enhances survival of ex vivo cultures of primary bone marrow-derived, alveolar, and peritoneal macrophages over particle-free controls. The enhanced survival is attributed to suppression of caspase-dependent apoptosis and is linked to phagocytosis and lysosomal signaling, which was also found to occur in vivo. Uniquely, poly(ethylene glycol)-based NP treatment does not alter macrophage polarization or lead to inflammatory effects. The enhanced survival phenomenon is also applicable to NPs of alternative chemistries, indicating the potential universality of this phenomenon with relevant drug delivery particles. These findings provide a framework for extending the lifespan of primary macrophages ex vivo for drug screening, vaccine studies, and cell therapies and has implications for any in vivo particulate immune-engineering applications.
A push-pull system of repressors matches levels of glucose transporters to extracellular glucose in budding yeast

A common cellular task is to match gene expression dynamically to a range of concentrations of a regulatory molecule. Studying glucose transport in budding yeast, we determine mechanistically how such matching occurs for seven hexose transporters. By combining time-lapse microscopy with mathematical modelling, we find that levels of transporters are history-dependent and are regulated by a push-pull system comprising two types of repressors. Repression by these two types varies with glucose in opposite ways, and not only matches the expression of transporters by their affinity to a range of glucose concentrations, but also the expression of some to how glucose is changing. We argue that matching is favoured by a rate-affinity trade-off and that the regulatory system allows yeast to import glucose rapidly enough to starve competitors. Matching expression to a pattern of input is fundamental, and we believe that push-pull repression is widespread.
General object-based features account for letter perception

After years of experience, humans become experts at perceiving letters. Is this visual capacity attained by learning specialized letter features, or by reusing general visual features previously learned in service of object categorization? To explore this question, we first measured the perceptual similarity of letters in two behavioral tasks, visual search and letter categorization. Then, we trained deep convolutional neural networks on either 26-way letter categorization or 1000-way object categorization, as a way to operationalize possible specialized letter features and general object-based features, respectively. We found that the general object-based features more robustly correlated with the perceptual similarity of letters. We then operationalized additional forms of experience-dependent letter specialization by altering object-trained networks with varied forms of letter training; however, none of these forms of letter specialization improved the match to human behavior. Thus, our findings reveal that it is not necessary to appeal to specialized letter representations to account for perceptual similarity of letters. Instead, we argue that it is more likely that the perception of letters depends on domain-general visual features. AUTHOR SUMMARY For over a century, scientists have conducted behavioral experiments to investigate how the visual system recognizes letters, but it has proven difficult to propose a model of the feature space underlying this capacity. Here we leveraged recent advances in machine learning to model a wide variety of features ranging from specialized letter features to general object-based features. Across two large-scale behavioral experiments we find that general object-based features account well for letter perception, and that adding letter specialization did not improve the correspondence to human behavior. It is plausible that the ability to recognize letters largely relies on general visual features unaltered by letter learning.
The forest avifauna of Arabuko Sokoke Forest and adjacent modified habitats

Arabuko Sokoke Forest (ASF) is the largest area of coastal forest remaining in East Africa and a major Important Bird Area in mainland Kenya. The study analysed data from point count surveys over 15 months in three land use types; primary forest (PF), plantation forest (PL), and farmlands (FM), and compared these to the first comprehensive bird checklist for the forest, as well as recent surveys from other studies. Avifaunal diversity and abundance were compared using multivariate analysis to determine bird responses to different land use characteristics. The primary forest held a distinctive bird community, while the bird communities of farmlands and plantation forest were more similar to each other. Land use had a significant effect on overall avian diversity and abundance. The current forest avifauna was divided into forest specialists (16 species), forest generalists (26 species) and forest visitors (30 species). Seven species of forest specialist and generalists recorded prior to 1980 may no longer occur in the forest. Of 38 specialists and generalists recorded in our point counts, 19 were also recorded on farmland and 28 in plantations. One forest specialist, the Green Barbet, was most encountered outside the forest. Future research should focus on habitat use by these bird species, and the extent of movement by forest birds between the remaining patches of coastal forest. Patterns of habitat use by birds in the area suggest that vegetation heterogeneity and habitat complexity are especially significant in sustaining diverse and abundant bird populations. The management of plantations and farmland will be critical for the conservation of forest generalists and forest visitors.
Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae: Hypostomus) from the central Brazilian Shield

River capture is a geological process of potentially great importance in shaping the genetic diversity, distributions, and community composition of freshwater taxa. Using phylogeographic analyses of ddRAD-seq data from suckermouth armored catfish (Hypostomus sp. 2) populations, we tested for predicted genetic effects of headwater river capture events in central Brazil, previously supported by geological and community ecological data. We analyzed 227 ddRAD tags (3829 SNP loci) across 42 samples. Molecular results strongly supported six Hypostomus genetic clusters/lineages, with the deepest divergence ∼1.25 million years ago in the early Pleistocene between a clade from the Upper Paraná and Upper São Francisco river basins versus all other lineages. Consistent with the ‘Paraná Capture Hypothesis’, several lines of evidence supported mid-Pleistocene colonization and vicariant isolation of Hypostomus populations from an ancestral Upper Paraná population, including: (1) significant phylogeographic structure, with predicted phylogenetic patterns, (2) higher Paraná lineage diversity, (3) ancestral geographic locations reconstructed in the Paraná basin, and (4) non-random interdrainage dispersal and vicariance events, indicating river captures primarily into the Tocantins and Upper São Francisco basins c. ∼220,000–145,500 years ago. Phylogeographic inference was complicated by lack of lineage monophyly across loci and lineages distributed in multiple basins, the latter of which lent support to the non-mutually exclusive ‘Frequent Interdrainage Dispersal Hypothesis’. However, species tree and demographic modeling results suggested these were artefacts of incomplete sorting of alleles in large ancestral populations over a geologically recent timeframe of divergence. Qualitative and quantitative sensitivity analyses demonstrated that our downstream genetic results were robust to effects of varying ddRAD-seq assembly parameters, which heavily influenced the number of output loci. We predict that codistributed freshwater taxa in Central Brazil may not exhibit phylogeographic patterns similar to Hypostomus sp. 2 due to complex patterns of superimposed river capture events, or if smaller ancestral population sizes have allowed more complete lineage sorting in other taxa.