Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone deacetylase inhibitors reduce the number of herpes simplex virus-1 genomes initiating expression in individual cells

Although many viral particles can enter a single cell, the number of viral genomes per cell that establish infection is limited. However, mechanisms underlying this restriction were not explored in depth. For herpesviruses, one of the possible mechanisms suggested is chromatinization and silencing of the incoming genomes. To test this hypothesis, we followed infection with three herpes simplex virus 1 (HSV-1) fluorescence-expressing recombinants in the presence or absence of histone deacetylases inhibitors (HDACi’s). Unexpectedly, a lower number of viral genomes initiated expression in the presence of these inhibitors. This phenomenon was observed using several HDACi: Trichostatin A (TSA), Suberohydroxamic Acid (SBX), Valporic Acid (VPA) and Suberoylanilide Hydoxamic Acid (SAHA). We found that HDACi presence did not change the progeny outcome from the infected cells but did alter the kinetic of the infection. Different cell types (HFF, Vero and U2OS), which vary in their capability to activate intrinsic and innate immunity, show a cell specific basal average number of viral genomes establishing infection. Importantly, in all cell types, treatment with TSA reduced the number of viral genomes. ND10 nuclear bodies are known to interact with the incoming herpes genomes and repress viral replication. The viral immediate early protein, ICP0, is known to disassemble the ND10 bodies and to induce degradation of some of the host proteins in these domains. HDACi treated cells expressed higher levels of some of the host ND10 proteins (PML and ATRX), which may down regulate the number of viral genomes initiating expression per cell. Corroborating this hypothesis, infection with three HSV-1 recombinants carrying a deletion in the gene coding for ICP0, show a reduction in the number of genomes being expressed in U2OS cells. We suggest that alterations in the levels of host proteins involved in intrinsic antiviral defense may result in differences in the number of genomes that initiate expression.
Dynamics of Visual Perceptual Decision-Making in Freely Behaving Mice

Abstract The temporal dynamics of perceptual decisions offer a key window into the cognitive processes contributing to decision-making. Investigating perceptual dynamics in a genetically tractable animal model can facilitate the subsequent unpacking of the underlying neural mechanisms. Here, we investigated the time course as well as fundamental psychophysical constants governing visual perceptual decision-making in freely behaving mice. We did so by analyzing response accuracy against reaction time (RT), i.e., conditional accuracy, in a series of two-alternative forced choice (2-AFC) orientation discrimination tasks in which we varied target size, luminance, duration, and presence of a foil. Our results quantified two distinct stages in the time course of mouse visual decision-making: a “sensory encoding” stage in which conditional accuracy exhibits a classic trade-off with response speed, and a subsequent “short-term memory (STM)-dependent” stage in which conditional accuracy exhibits a classic asymptotic decay following stimulus offset. We estimated the duration of visual sensory encoding as 200–320 ms across tasks, the lower bound of the duration of STM as ∼1700 ms, and the briefest duration of visual stimulus input that is informative as ≤50 ms. Separately, by varying stimulus onset delay, we demonstrated that the conditional accuracy function (CAF) and RT distribution can be independently modulated, and found that the duration for which mice naturally withhold from responding is a quantitative metric of impulsivity. Taken together, our results establish a quantitative foundation for investigating the neural circuit bases of visual decision dynamics in mice.
Spatial integration during active tactile sensation drives elementary shape perception

Active haptic sensation is critical for object identification and manipulation, such as for tool use in humans, or prey capture in rodents. The neural circuit basis for recognizing objects through active touch alone is poorly understood. To address this gap, we combined optogenetics, two photon imaging, and high-speed behavioral tracking in mice solving a novel surface orientation discrimination task with their whiskers. We found that orientation discrimination required animals to summate input from multiple whiskers specifically along the whisker arc. Many animals discriminated the orientation of the stimulus per se, as their performance was invariant to the specific location of the presented stimulus. Two photon imaging showed that populations of neurons in the barrel cortex encoded each of the discriminated orientations, and this coding depended on integration over the whisker array. Finally, acute optogenetic inactivation of the barrel cortex strongly impaired surface orientation discrimination, and even cell-type specific optogenetic suppression of layer 4 excitatory neurons degraded performance, implying a role for superficial layers in this computation. These data suggest a model in which spatial summation over an active haptic array generates representations of an object’s surface orientations. These computations may facilitate the encoding of complex three-dimensional objects during active exploration.
Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2

Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of coronavirus SARS-CoV-2. Existing direct-acting antiviral (DAA) drugs cannot be applied immediately to new viruses because of virus-specificity, and the development of new DAA drugs from the beginning is not timely for outbreaks. Thus, host-targeting antiviral (HTA) drugs have many advantages to fight against a broad spectrum of viruses, by blocking the viral replication and overcoming the potential viral mutagenesis simultaneously. Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knocking-out cells. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. Notably, S416 is reported to be the most potent inhibitor with an EC50 of 17nM and SI value >5882 in SARS-CoV-2-infected cells so far. This work demonstrates that both our self-designed candidates and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-repression may have clinical potentials not only to influenza but also to COVID-19 circulating worldwide, no matter such viruses mutate or not.
The Rate of Molecular Evolution When Mutation May Not Be Weak

One of the most fundamental rules of molecular evolution is that the rate of neutral evolution equals the mutation rate and is independent of effective population size. This result lies at the heart of the Neutral Theory, and is the basis for numerous analytic approaches that are widely applied to infer the action of natural selection across the genome and through time, and for dating divergence events using the molecular clock. However, this result was derived under the assumption that evolution is strongly mutation-limited, and it has not been known whether it generalizes across the range of mutation pressures or the spectrum of mutation types observed in natural populations. Validated by both simulations and exact computational analyses, we present a direct and transparent theoretical analysis of the Wright-Fisher model of population genetics, which shows that some of the most important rules of molecular evolution are fundamentally changed by considering recurrent mutation’s full effect. Surprisingly, the rate of the neutral molecular clock is found to have population-size dependence and to not equal the mutation rate in general. This is because, for increasing values of the population mutation rate parameter (θ), the time spent waiting for mutations quickly becomes smaller than the cumulative time mutants spend segregating before a substitution, resulting in a net deceleration compared to classical theory that depends on the population mutation rate. Furthermore, selection exacerbates this effect such that more adaptive alleles experience a greater deceleration than less adaptive alleles, introducing systematic bias in a wide variety of methods for inferring the strength and direction of natural selection from across-species sequence comparisons. Critically, the classical weak mutation approximation performs well only when θ< 0.1, a threshold that many biological populations seem to exceed.
Nepotism masks evidence for reciprocity in cooperation networks

15 Nepotism and reciprocity are not mutually exclusive explanations for cooperation; helping 16 decisions can depend on both kinship cues and past reciprocal help. The importance of these two 17 factors can therefore be difficult to disentangle with observational data. We developed a 18 resampling procedure for inferring the statistical power to detect observational evidence of 19 nepotism and reciprocity, and applied this procedure to simulated and real datasets. We simulated 20 datasets resulting from perfect reciprocity, where the probability and duration of helping events 21 from individual A to B equaled B to A. We also simulated varying degrees of simultaneous 22 nepotism. We then assessed how nepotism and sampling effort influenced the probability of 23 detecting evidence of reciprocity. We applied the same analysis to empirical data on food sharing 24 in vampire bats and allogrooming in mandrills and Japanese macaques. Nepotism consistently 25 masked evidence for reciprocity. With perfect reciprocity and imperfect nepotism, nepotism was 26 more likely to be detected and overestimated. We explain the causes and consequences. To 27 compare the relative importance of genetic and social ties, researchers should measure the relative 28 reliability of both estimates. We provide R scripts to allow others to assess the reliability of 29 kinship and reciprocal help estimates in their own datasets. 30 3
Investigating within-host diversity of Mycobacterium tuberculosis reveals novel super-spreaders in the Canadian North

Background Tuberculosis disproportionately affects the Canadian Inuit population. To address this problem, it is imperative we understand transmission dynamics. Here, we investigate whether ‘deep’ sequencing provides additional resolution compared to standard sequencing, with implications for TB control in high-transmission environments. Methods 48/50 samples from an outbreak (2011-2012), and 14/15 samples from the preceding five years from an Arctic village, were deep sequenced (to ∼500-1000x) using Illumina HiSeq. Reads were aligned to a novel local reference genome, generated using PacBio SMRT sequencing. Consensus single nucleotide polymorphisms (cSNPs) and heterogeneous alleles (hSNPs, where the alternative allele was in > 5% and < 95% of reads) were identified. Core cSNPs were used to calculate genetic distances, and hSNPs were reviewed between samples. Findings In contrast with previous genomic analyses using ∼50x depth, deep sequencing allowed us to identify a novel super-spreader. This case, previously thought to have transmitted to four others, likely transmitted to up to 17 other cases during the outbreak (35% of all cases that year). 76% attended the same community gathering houses as the putative source, supporting a major role for these social venues in the outbreak. hSNP analysis also helped confirm other transmission events, and discriminate relapse from re-infection in TB recurrence. Interpretation Deep sequencing and investigation of within-host diversity may be critical to accurately identify super-spreaders and corresponding transmission clusters. We propose – at a minimum - targeted deep sequencing of highly contagious cases, in addition to routine sequencing, to facilitate public health investigations. Funding National Institutes of Health.
Closed-loop stimulation of the medial septum terminates epileptic seizures

Temporal lobe epilepsy with distributed hippocampal seizure foci is often intractable and its secondary generalization might lead to sudden death. Early termination through spatially extensive hippocampal intervention is not feasible directly, due to its large size and irregular shape. In contrast, the medial septum (MS) is a promising target to govern hippocampal oscillations through its divergent connections to both hippocampi. Combining this ‘proxy intervention’ concept and precisely timed stimulation, we report here that closed-loop MS electrical stimulation can quickly terminate intrahippocampal seizures and suppress secondary generalization in a rat kindling model. Precise stimulus timing governed by internal seizure rhythms was essential. Cell-type-specific stimulation revealed that precisely timed activation of MS GABAergic neurons underlay the effects. Our concept of phase-targeted proxy stimulation for intervening pathological oscillations can be extrapolated to other neurological and psychiatric disorders, and its current embodiment can be directly translated into clinical application.
Embryo-Like Features in Developing Bacillus subtilis Biofilms

Correspondence between evolution and development has been discussed for more than two centuries1. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity2–10. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes6, 10–12. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure13–16. For instance, it has been increasingly recognized that multicellular behaviour underlies biofilm formation in bacteria13, 14, 17–19. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes14–16, 18, 20. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed towards later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos11, 21. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants and fungi. Given that most cells on Earth reside in the form of biofilms22 and that biofilms represent the oldest known fossils23, we anticipate that the widely-adopted vision of the first life as a single-cell and free-living organism needs rethinking.
Food Insecurity is Linked to Dietary Intake but not Growth of Children in the Caribbean

Objective: To examine food insecurity and its relationship with children’s nutritional health. Methods: Data for 390 children aged 7-12 years and their caregivers, recruited from eight schools in Trinidad and seven schools in St. Kitts in 2013-14 from a study dealing with food and nutrition security. Food insecurity, assessed using the USDA’s Household Food Security Survey Module, and 24-hour dietary recall of children were assessed in home interviews. Height and weight were measured and a capillary blood sample was collected at school. Results: Overall, 41.5% of caregivers reported household food insecurity, with 15% of the children living in households with very low food security. Daily intakes of protein and zinc were higher among children from “food secure” vs. “food insecure” households (protein, 59.6 ± 31.5 g vs. 50.9 ± 24.4 g, p=0.003; zinc, 7.33 ± 5.02 mg vs. 6.20 ± 3.47 mg, p=0.004, respectively). There were no other differences in dietary intake. Children’s BMI z-score, weight status, and height-for-age z-score were not associated with food insecurity, and there was no evidence of stunting in either group. Anemia, however, was prevalent (30%) and higher among children from food insecure households (39% vs. 23%; p=0.002). Conclusion: Household food insecurity was reflected in some lower intakes of some nutrients and anemia rates were higher among children living in food insecure households but food insecurity was not related to indicators of growth or weight status.
Implementation of a pre- and in-scan system to minimize head motion in pediatric participants undergoing fMRI scans

Background Performing fMRI scans of children can be a difficult task, as participants tend to move while being scanned. Head motion represents a significant confound in functional magnetic resonance imaging (fMRI) connectivity analyses, and methods to limit the impact of movement on data quality are needed. One approach has been to use shorter MRI protocols, though this potentially reduces the reliability of the results. Objective Here we describe steps we have taken to limit head motion in an ongoing fMRI study of children undergoing a 60 minute MRI scan protocol. Specifically, we have used a mock scan protocol that trains participants to lie still while being scanned. We provide a detailed protocol and describe other in-scanner measures we have implemented, including an incentive system and the use of a weighted blanket. Materials and methods Participants who received a formal mock scan (n = 12) were compared to participants who had an informal mock scan (n = 7). A replication group of participants (n = 16), including five with autism spectrum disorder, who received a formal mock scan were also compared to the informal mock scan group. The primary measure of interest was the mean frame-to-frame displacement across eight functional runs during the fMRI protocol. Results Participants in the formal mock scan and replication group tended to exhibit more low-motion functional scans than the informal mock scan group (P < 0.05). Across different functional scan conditions (i.e. while watching movie clips, performing an attention task, and during resting-state scans), effect sizes tended to be large (Hedge’s g > 0.8). Conclusion Results indicate that with appropriate measures, it is possible to achieve low-motion fMRI data in younger participants undergoing a long scan protocol.
The BBSome assembly is spatially controlled by BBS1 and BBS4 in human cells

Bardet–Biedl syndrome (BBS) is a pleiotropic ciliopathy caused by dysfunction of primary cilia. More than half of BBS patients carry mutations in one of eight genes encoding for subunits of a protein complex, the BBSome, which mediates trafficking of ciliary cargoes. In this study, we elucidated the mechanisms of the BBSome assembly in living cells and how this process is spatially regulated. We generated a large library of human cell lines deficient in a particular BBSome subunit and expressing another subunit tagged with a fluorescent protein. We analyzed these cell lines utilizing biochemical assays, conventional and expansion microscopy, and quantitative fluorescence microscopy techniques: fluorescence recovery after photobleaching and fluorescence correlation spectroscopy. Our data revealed that the BBSome formation is a sequential process. We show that the pre-BBSome is nucleated by BBS4 and assembled at pericentriolar satellites, followed by the translocation of the BBSome into the ciliary base mediated by BBS1. Our results provide a framework for elucidating how BBS-causative mutations interfere with the biogenesis of the BBSome.
Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation

Once described as mere “bags of enzymes”, bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in E. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life. Significance Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.
Altered spike timing-dependent plasticity rules in physiological calcium

Like many forms of long-term synaptic plasticity, spike-timing-dependent plasticity (STDP) depends on intracellular Ca2+ signaling for its induction. Yet, all in vitro studies devoted to STDP used abnormally high external Ca2+ concentration. We measured STDP at the CA3-CA1 hippocampal synapses under different extracellular Ca2+ concentrations and found that the sign, shape and magnitude of plasticity strongly depend on Ca2+. A pre-post protocol that results in robust LTP in high Ca2+, yielded only LTD or no plasticity in the physiological Ca2+ range. LTP could be restored by either increasing the number of post-synaptic spikes or increasing the pairing frequency. A calcium-based plasticity model in which depression and potentiation depend on post-synaptic Ca2+ transients was found to fit quantitatively all the data, provided NMDA receptor-mediated non-linearities were implemented. In conclusion, STDP rule is profoundly altered in physiological Ca2+ but specific activity regimes restore a classical STDP profile.