title: Average beta burst duration profiles provide a signature of dynamical changes between the ON and OFF medication states in Parkinson's disease

abstract:
Parkinsons disease motor symptoms are associated with an increase in subthalamic nucleus beta band oscillatory power. However, these oscillations are phasic, and there is a growing body of evidence suggesting that beta burst duration may be of critical importance to motor symptoms. This makes insights into the dynamics of beta bursting generation valuable, in particular to refine closed-loop deep brain stimulation in Parkinsons disease. In this study, we ask the question "Can average burst duration reveal how dynamics change between the ON and OFF medication states?". Our analysis of local field potentials from the subthalamic nucleus demonstrates using linear surrogates that the system generating beta oscillations is more likely to act in a non-linear regime OFF medication and that the change in a non-linearity measure is correlated with motor impairment. In addition, we pinpoint the simplest dynamical changes that could be responsible for changes in the temporal patterning of beta oscillations between medication states by fitting to data biologically inspired models, and simpler beta envelope models. Finally, we show that the non-linearity can be directly extracted from average burst duration profiles under the assumption of constant noise in envelope models. This reveals that average burst duration profiles provide a window into burst dynamics, which may underlie the success of burst duration as a biomarker. In summary, we demonstrate a relationship between average burst duration profiles, dynamics of the system generating beta oscillations, and motor impairment, which puts us in a better position to understand the pathology and improve therapies such as deep brain stimulation.

Author summaryIn Parkinsons disease, motor impairment is associated with abnormal oscillatory activity of neurons in deep motor regions of the brain. These oscillations come in the shape of bursts, and the duration of these bursts has recently been shown to be of importance to motor symptoms. To better understand the disease and refine therapies, we relate the duration of these bursts to properties of the system generating them in the pathological state and in a proxy of the healthy state. The data suggest that the system generating bursts involves more complexity in the pathological state, and we show that a measure of this complexity is associated with motor impairment. We propose biologically inspired models and simpler models that can generate the burst patterns observed in the pathological and healthy state. The models confirm what was observed in data, and tell us how burst generation mechanisms could differ in the disease. Finally, we identify a mathematical link allowing us to infer properties of the burst generating system from burst duration measurements in patient recordings. This sheds some light on the significance of burst duration as a marker of pathology.


title: A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

abstract: The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. "in silico analysis"), and arranged on a 5-level validation scale from "incomplete" to "operational" with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.

category: molecular biology


title: On a Reef Far, Far Away: Anthropogenic Impacts Following Extreme Storms Affect Sponge Health and Bacterial Communities

abstract: Terrestrial runoff can negatively impact marine ecosystems through stressors including excess nutrients, freshwater, sediments, and contaminants. Severe storms, which are increasing with global climate change, generate massive inputs of runoff over short timescales (hours to days); such runoff impacted offshore reefs in the northwest Gulf of Mexico (NW GoM) following severe storms in 2016 and 2017. Several weeks after coastal flooding from these events, NW GoM reef corals, sponges, and other benthic invertebrates -185 km offshore experienced mortality (2016 only) and/or sub-lethal stress (both years). To assess the impact of storm-derived runoff on reef filter feeders, we characterized the bacterial communities of two sponges, Agelas clathrodes and Xestospongia muta, from offshore reefs during periods of sub-lethal stress and no stress over a three-year period (2016-2018). Sponge-associated bacterial communities were altered during both flood years. Additionally, we found evidence of wastewater contamination (based on 16S rRNA gene libraries and quantitative PCR) in offshore sponges following these flood years, but not during the no-flood year. We show that flood events from severe storms have the capacity to reach offshore reef ecosystems and impact resident benthic organisms. Such impacts are most readily detected if baseline data on organismal physiology and associated microbiome composition are available. This highlights the need for molecular and microbial time series of benthic organisms in near- and offshore reef ecosystems, and the continued mitigation of stormwater runoff and climate change impacts.

category: microbiology


title: Titration of in-cellula affinities of protein-protein interactions

abstract: A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. In-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.

category: biochemistry


title: Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful

abstract:
Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from non-coding DNA. Proteins are more likely to be born from non-coding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to "first, do no harm", we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent dataset of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.

Significance statementProteins are sometimes born de novo. In an experiment to reproduce this process in Escherichia coli, we were able to predict 15% of the variation in random peptide fitness effects from their amino acid frequencies. In contrast, which order the amino acids are in seems to make no difference, adding no predictive power on top of simple amino acid frequencies. Amino acids that are smaller and promote intrinsic structural disorder have more benign fitness effects.

category: evolutionary biology


title: Plant pathogen infection risk tracks global crop yields under climate change

abstract: Global food security is strongly determined by crop production. Climate change-induced losses to production can occur directly, or indirectly, including via the distributions and impacts of plant pathogens. However, the likely changes in pathogen pressure in relation to global crop production are poorly understood. Here we show that temperature-dependent infection risk, r(T), for 80 fungal and oomycete crop pathogens will track projected yield changes in 12 crops over the 21st Century. For most crops, both yields and r(T) are likely to increase at high latitudes. In contrast, while the tropics will see little or no productivity gains, r(T) is also likely to decline. In addition, the USA, Europe and China may experience major changes in pathogen assemblages. The benefits of yield gains may therefore be tempered by the increased burden of crop protection due to increased and unfamiliar pathogens.

category: ecology


title: Evolutionary analysis of the LORELEI gene family in angiosperms reveals regulatory subfunctionalization

abstract:
A signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, reproduction, immunity, and stress responses in Arabidopsis. Genes encoding these proteins are members of multi-gene families in most angiosperms and could generate thousands of signaling complex variants. However, the link(s) between expansion of these gene families and the functional diversification of this critical signaling complex as well as the evolutionary factors underlying the maintenance of gene duplicates remain unknown. Here, we investigated LLG gene family evolution, function, and expression in angiosperms. We found that LLGs in monocots and eudicots are descendants of a duplication early in angiosperm evolution and that both ancient and recent LLG duplicates are retained. Complementation and expression analysis showed that expression divergence of LLGs (regulatory subfunctionalization), rather than functional divergence, explains the retention of paralogs in Brassicales. All but one extant monocot and eudicot species examined maintained an LLG copy with preferential expression in male reproductive tissues, with the other duplicate copies showed highest levels of expression in female or vegetative tissues. Interestingly, the single LLG copy in Amborella (sister to all other angiosperms) is expressed vastly higher in male compared to female reproductive or vegetative tissues. Reconstruction of expression evolution showed that the highest inferred expression levels for the single copy ancestral angiosperm LLG was in male reproductive tissues. We propose that expression divergence played an important role in maintenance of LLG duplicates in angiosperms.

One Sentence SummaryExpression divergence played an important role in maintenance of two sub-groups of LLG duplicates in angiosperms

category: plant biology


title: Evolutionary Genetic Species Detected in Prokaryotes by Applying the K/θ Ratio to DNA Sequences

abstract: Previous papers in this series described the "evolutionary genetic species concept" which is based on population genetic theory and should be applicable to any organism. Also described was a species criterion, the K/{theta} ratio, that delimits independently evolving evolutionary species based on single-gene sequences, and its application to sexual and asexual eukaryotes was illustrated. Here, we show how the evolutionary genetic species concept and the K/{theta} ratio can be applied to bacteria, using the sequences from some genes of the core genome that are rarely, if ever, transferred horizontally between different species. This completes the demonstration that K/{theta} is a general method for species delimitation, applicable to all organisms. Also, it adds to the evidence that bacteria have species in the most general sense, even though they have the ability to exchange genes across species boundaries. Finally, we show that a published critique of the use of K/{theta} [≥] 4 as a criterion for independently evolving species rests on two errors in the application of population/evolutionary genetic theory.


title: Cell-free DNA Profiling Informs Major Complications of Hematopoietic Cell Transplantation

abstract: Allogeneic hematopoietic cell transplantation (HCT) provides effective treatment for hematologic malignancies and immune disorders. Monitoring of post-transplant complications is critical, yet current diagnostic options are limited. Here, we show that cell-free DNA (cfDNA) in blood is a highly versatile analyte for monitoring of the most important complications that occur after HCT: graft-versus-host disease (GVHD), a frequent immune complication of HCT; infection; relapse of underlying disease; and graft failure. We demonstrate that these different therapeutic complications can be informed from a single assay, low-coverage bisulfite sequencing of cfDNA, followed by disease-specific bioinformatic analyses. To inform GVHD, we profile cfDNA methylation marks to trace the cfDNA tissues-of-origin and to quantify tissue-specific injury. To inform on infections, we implement metagenomic cfDNA profiling. To inform cancer relapse, we implement analyses of tumor-specific genomic aberrations. Finally, to detect graft failure we quantify the proportion of donor and recipient specific cfDNA. We applied this assay to 170 plasma samples collected from 27 HCT recipients at predetermined time points before and after allogeneic HCT. We found that the abundance of solid-organ derived cfDNA in the blood at one-month after HCT is an early predictor of acute graft-versus-host disease (area under the curve, 0.88). Metagenomic profiling of cfDNA revealed the frequent occurrence of viral reactivation in this patient population. The fraction of donor specific cfDNA was indicative of cell chimerism, relapse and remission, and the fraction of tumor specific cfDNA was informative of cancer relapse. This proof-of-principle study shows that cfDNA has the potential to improve the care of allogeneic HCT recipients by enabling earlier detection and better prediction of the complex array of complications that occur after HCT.

category: genomics


title: DNA damage independent inhibition of NF-κB transcription by anthracyclines

abstract: Anthracyclines are among the most used and effective anticancer drugs. Their activity has been attributed to DNA double-strand breaks resulting from topoisomerase II poisoning and to eviction of histones from select sites in the genome. Here we show that the extensively used anthracyclines Doxorubicin, Daunorubicin and Epirubicin, decrease the transcription of nuclear factor kappa B (NF-{kappa}B)-dependent gene targets, but not interferon responsive genes. Using an NMR-based structural approach, we demonstrate that anthracyclines disturb the complexes formed between the NF-{kappa}B subunit RelA and its DNA binding sites. The variant anthracyclines Aclarubicin, Doxorubicinone and the newly developed Dimethyl-doxorubicin, which share anticancer properties with the other anthracyclines but do not induce DNA damage, also suppressed inflammation, thus uncoupling DNA damage from the effects on inflammation. These findings have implications for anticancer therapy and for the development of novel anti-inflammatory drugs with limited side effects for life-threatening conditions such as sepsis.

category: immunology


title: Geometric model incorporating prey's turn and predator attack endpoint explains multiple preferred escape trajectories

abstract: The escape trajectory (ET) of prey - measured as the angle relative to the predators approach path - plays a major role in avoiding predation. Previous geometric models predict a single ET; however, many species show highly variable ETs with multiple preferred directions. Although such a high ET variability may confer unpredictability to avoid predation, the reasons why animals prefer specific multiple ETs remain unclear. Here, we constructed a novel geometric model that incorporates the time required for prey to turn and the predators position at the end of its attack. The optimal ET was determined by maximizing the time difference of arrival at the edge of the safety zone between the prey and predator. By fitting the model to the experimental data of fish Pagrus major we show that the model can clearly explain the observed multiple preferred ETs. By using the same model, we were able to explain different patterns of ETs empirically observed in other species (e.g., insects and frogs): a single preferred ET and multiple preferred ETs at small (20-50{degrees}) and large (150-180{degrees}) angles from the predator. Our results open new avenues of investigation for understanding how animals choose their ETs from behavioral and neurosensory perspectives.

category: animal behavior and cognition


title: The impact of purifying and background selection on the inference of population history: problems and prospects

abstract: Current procedures for inferring population history generally assume complete neutrality - that is, they neglect both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects (DFE) and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the DFE as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites can be used to infer demographic histories with reasonable accuracy.


title: Parental population range expansion before secondary contact promotes heterosis

abstract: Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.


title: Relative salience signaling within a thalamo-orbitofrontal circuit governs learning rate

abstract: Learning to predict rewards is essential for the sustained fitness of animals. Contemporary views suggest that such learning is driven by a reward prediction error (RPE) -- the difference between received and predicted rewards. The magnitude of learning induced by an RPE is proportional to the product of the RPE and a learning rate. Here we demonstrate using two- photon calcium imaging and optogenetics in mice that certain functionally distinct subpopulations of ventral/medial orbitofrontal cortex (vmOFC) neurons signal learning rate control. Consistent with learning rate control, trial-by-trial fluctuations in vmOFC activity positively correlates with behavioral updating when RPE is positive, and negatively correlates with behavioral updating when RPE is negative. Learning rate is affected by many variables including the salience of a reward. We found that the average reward response of these neurons signals the relative salience of a reward, as it decreases after reward prediction learning or the introduction of another highly salient aversive stimulus. The relative salience signaling in vmOFC is sculpted by medial thalamic inputs. These results support emerging theoretical views that the prefrontal cortex encodes and controls learning parameters.

category: neuroscience


title: On the fitness of informative cues in complex environments

abstract: To be able to deal with uncertainty is of primary importance to most living organisms. When cues provide information about the state of the environment, organisms can use them to respond flexibly. Life forms have evolved complex adaptations and sensory mechanisms to use these environmental cues and extract valuable information about the environment. Previous work has shown a theoretical limit to the amount of fitness benefit possible to be extracted from the cues. We show that the previously used information theoretical approaches can be generalised to scenarios involving any potential relationship between the number of possible phenotypes and environmental states. Such cases are relevant when physiological constraints or complex ecological scenarios lead to the number of environmental states exceeding potential phenotypes. We illustrate cases in which these scenarios can emerge: along environmental gradients, such as geographical transects or complex environments, where organisms adopt different bet-hedging strategies, switching stochastically between phenotypes or developing intermediate ones. In conclusion, we develop an information-theoretic extensible approach for investigating and quantifying fitness in ecological studies.


title: Baseline Resting-State Functional Connectivity Determines Subsequent Pain Ratings to a Tonic Ecologically Valid Experimental Model of Orofacial Pain

abstract: Pain is a subjective experience with significant individual differences. Laboratory studies investigating pain thresholds and experimental acute pain have identified structural and functional neural correlates. However, these types of pain stimuli have limited ecological validity to real-life pain experiences. Here, we use an orthodontic procedure--the insertion of an elastomeric separator between teeth--which typically induces mild to moderate pain that peaks within 2 days and lasts several days. We aimed to determine whether the baseline structure and resting-state functional connectivity (rsFC) of key regions along the trigeminal nociceptive and pain modulatory pathways correlate with subsequent peak pain ratings. Twenty-six healthy individuals underwent structural and resting-state functional (rs-fMRI) scanning prior to the placement of a separator between the first and second molars, which was kept in place for five days. Participants recorded pain ratings three times daily on a 100-mm visual analogue scale. Peak pain was not significantly correlated with diffusion metrics of the trigeminal nerve, or grey matter volume of any brain region. Peak pain did, however, positively correlate with baseline rsFC between the thalamus contralateral to the separator and bilateral insula, and negatively correlated with connectivity between the periaqueductal gray (PAG) and core nodes of the default mode network (medial prefrontal and posterior cingulate cortices). The ascending (thalamic) nociceptive and the descending (PAG) pain modulatory pathways at baseline each explained unique variation in peak pain intensity ratings. In sum, pre-interventional functional neural architecture of both systems determined the individual pain experience to a subsequent ecologically valid pain stimulus.


title: Super-selective reconstruction of causal and direct connectivity with application to in-vitro iPSC neuronal networks

abstract: Despite advancements in the development of cell-based in-vitro neuronal network models, the lack of appropriate computational tools limits their analyses. Methods aimed at deciphering the effective connections between neurons from extracellular spike recordings would increase utility of in-vitro local neural circuits, especially for studies of human neural development and disease based on induced pluripotent stem cells (hiPSC). Current techniques allow statistical inference of functional couplings in the network but are fundamentally unable to correctly identify indirect and apparent connections between neurons, generating redundant maps with limited ability to model the causal dynamics of the network. In this paper, we describe a novel mathematically rigorous, model-free method to map effective - direct and causal - connectivity of neuronal networks from multi-electrode array data. The inference algorithm uses a combination of statistical and deterministic indicators which, first, enables identification of all existing functional links in the network and then, reconstructs the directed and causal connection diagram via a super-selective rule enabling highly accurate classification of direct, indirect and apparent links. Our method can be generally applied to the functional characterization of any in-vitro neuronal networks. Here, we show that, given its accuracy, it can offer important insights into the functional development of in-vitro iPSC-derived neuronal cultures.


title: Connectomes across development reveal principles of brain maturation

abstract: From birth to adulthood, an animals nervous system changes as its body grows and its behaviours mature. The form and extent of circuit remodelling across the connectome is unknown. We used serial-section electron microscopy to reconstruct the full brain of eight isogenic C. elegans individuals across postnatal stages to learn how it changes with age. The overall geometry of the brain is preserved from birth to adulthood. Upon this constant scaffold, substantial changes in chemical synaptic connectivity emerge. Comparing connectomes among individuals reveals substantial connectivity differences that make each brain partly unique. Comparing connectomes across maturation reveals consistent wiring changes between different neurons. These changes alter the strength of existing connections and create new connections. Collective changes in the network alter information processing. Over development, the central decision-making circuitry is maintained whereas sensory and motor pathways substantially remodel. With age, the brain progressively becomes more feedforward and discernibly modular. Developmental connectomics reveals principles that underlie brain maturation.


title: Nano-analytical Characterization of Breast Tissue Biopsies Reveals an Association between Spherical Nano and Micro Particles and Invasive Malignant Breast Tumours.

abstract: The presence of calcifications on mammograms is a widely used diagnostic marker for breast cancer. While the clinicopathological analysis of breast tissue is well-developed, an in-depth characterisation of the properties of calcifications at the micro and nano scale remained elusive. In this work, we use nano-analytical methods to investigate the calcification present in healthy breast tissue, as well as in benign and malignant breast tumour tissue biopsies. While polycrystalline apatite with lower crystallinity can be found in all breast tissue samples, we show that magnesium-containing nano and micro spherical particles are found only in malignant invasive breast cancers. These particles are present exclusively in the vasculature and their concentration increases with cancer progression. The discovery of these spherical particles provides new insights into the characteristics of breast calcification associated with malignant tumours and opens new research pathways to a better understanding of breast tumours and their microenvironment in general.

category: cancer biology


title: Molecular basis for the ATPase-powered substrate translocation by the Lon AAA+ protease

abstract: The Lon AAA+ (adenosine triphosphatases associated with diverse cellular activities) protease (LonA) converts ATP-fuelled conformational changes into sufficient mechanical force to drive translocation of the substrate into a hexameric proteolytic chamber. To understand the structural basis for the substrate translocation process, we have determined the cryo-electron microscopy (cryo-EM) structure of Meiothermus taiwanensis LonA (MtaLonA) at 3.6 [A] resolution in a substrate-engaged state. Substrate interactions are mediated by the dual pore-loops of the ATPase domains, organized in spiral staircase arrangement from four consecutive protomers in different ATP-binding and hydrolysis states; a closed AAA+ ring is nevertheless maintained by two disengaged ADP-bound protomers transiting between the lowest and highest position. The structure reveals a processive rotary translocation mechanism mediated by LonA-specific nucleotide-dependent allosteric coordination among the ATPase domains, which is induced by substrate binding.

category: biophysics


title: New Music System Reveals Spectral Contribution to Statistical Learning

abstract: 1Knowledge of speech and music depends upon the ability to perceive relationships between sounds in order to form a stable mental representation of statistical structure. Although evidence exists for the learning of musical scale structure from the statistical properties of sound events, little research has been able to observe how specific acoustic features contribute to statistical learning independent of the effects of long-term exposure. Here, using a new musical system, we show that spectral content is an important cue for acquiring musical scale structure. In two experiments, participants completed probe-tone ratings before and after a half-hour period of exposure to melodies in a novel musical scale with a predefined statistical structure. In Experiment 1, participants were randomly assigned to either a no-exposure control group, or to exposure groups who heard pure tone or complex tone sequences. In Experiment 2, participants were randomly assigned to exposure groups who heard complex tones constructed with odd harmonics or even harmonics. Learning outcome was assessed by correlating pre/post-exposure ratings and the statistical structure of tones within the exposure period. Spectral information significantly affected sensitivity to statistical structure: participants were able to learn after exposure to all tested timbres, but did best at learning with timbres with odd harmonics, which were congruent with scale structure. Results show that spectral amplitude distribution is a useful cue for statistical learning, and suggest that musical scale structure might be acquired through exposure to spectral distribution in sounds.


title: The habenula clock influences prediction of danger

abstract: The response of an animal to a sensory stimulus depends on the nature of the stimulus and on predictions mediated by spontaneous activity in neurons. Here, we ask how circadian variation in the prediction of danger, and thus the response to a potential threat, is controlled. We focus on the habenula, a mediator of threat response that functions by regulating neuromodulator release, and use zebrafish as the experimental system. Single cell transcriptomics indicates that multiple clock genes are expressed throughout the habenula, while quantitative in situ hybridization confirms that the clock oscillates. Two-photon calcium imaging indicates a circadian change in spontaneous activity of habenula neurons. To assess the role of this clock, a truncated clocka gene was specifically expressed in the habenula. This partially inhibited the clock, as shown by changes in per3 expression as well as altered day-night variation in dopamine, serotonin and acetylcholine levels. Behaviourally, anxiety-like responses evoked by an alarm pheromone were reduced. Circadian effects of the pheromone were disrupted, such that responses in the day resembled those at night. Behaviours that are regulated by the pineal clock and not triggered by stressors were unaffected. These findings establish that the habenula clock regulates the expectation of danger, thus identifying one mechanism for circadian change in the response to a stressor.


title: Single-cell analysis reveals mechanisms of plasticity of leukemia initiating cells

abstract: Leukemia initiating cells (LICs) fuel leukemic growth and spark relapse. Previously thought to be primitive and rare, the LIC state may actually be heterogeneous and dynamic, enabling evasion of therapies. Here, we use single-cell transcriptomics to track LIC multipotency within the cellular ontogeny of MLL-rearranged B-lymphoblastic leukemia (MLL-r B-ALL). Although we identify rare transcriptionally and phenotypically primitive LICs, we also observe LICs emerging from more differentiated populations with the capability to replenish the full leukemic cellular diversity. We find that activation of MYC-driven oxidative phosphorylation controls this process of facultative state conversion in LICs.


title: Hugin+ neurons link the sleep homeostat to circadian clock neurons

abstract: Sleep is controlled by homeostatic mechanisms, which drive sleep after wakefulness, and a circadian clock, which confers the 24-hour rhythm of sleep. These processes interact with each other to control the timing of sleep in a daily cycle as well as following sleep deprivation. However, the mechanisms by which they interact are poorly understood. We show here that hugin+ neurons, previously identified as neurons that function downstream of the clock to regulate rhythms of locomotor activity, are also targets of the sleep homeostat. Sleep deprivation decreases activity of hugin+ neurons, likely to suppress circadian-driven activity during recovery sleep, and manipulations of hugin+ neurons affect sleep increases generated by activation of the homeostatic sleep locus, the dorsal fanshaped body (dFB). Also, mutations in peptides produced by the hugin+ locus increase recovery sleep following deprivation. Trans-synaptic mapping reveals that hugin+ neurons feed-back onto central clock neurons, which also show decreased activity upon sleep loss, in a Hugin-peptide dependent fashion. We propose that hugin+ neurons integrate circadian and sleep signals to modulate circadian circuitry and regulate the timing of sleep.


title: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

abstract: Low-pass sequencing (sequencing a genome to an average depth less than 1 coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5x and 1x) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave-one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ~ 0.5x and higher compared to the Illumina GSA.


title: A Behavioral Association Between Prediction Errors and Risk-Seeking: Theory and Evidence

abstract:
Reward prediction errors (RPEs) and risk preferences have two things in common: both can shape decision making behavior, and both are commonly associated with dopamine. RPEs drive value learning and are thought to be represented in the phasic release of striatal dopamine. Risk preferences bias choices towards or away from uncertainty; they can be manipulated with drugs that target the dopaminergic system. The common neural substrate suggests that RPEs and risk preferences might be linked on the level of behavior as well, but this has never been tested. Here, we aim to close this gap. First, we apply a recent theory of learning in the basal ganglia to predict how exactly RPEs might influence risk preferences. We then test our behavioral predictions using a novel bandit task in which value and risk vary independently across options. Critically, conditions are included where options vary in risk but are matched for value. We find that subjects become more risk seeking if choices are preceded by positive RPEs, and more risk averse if choices are preceded by negative RPEs. These findings cannot be explained by other known effects, such as nonlinear utility curves or dynamic learning rates. Finally, we show that RPE-induced risk-seeking is indexed by pupil dilation: participants with stronger pupillary correlates of RPE also show more pronounced behavioral effects.

Authors summaryMany of our decisions are based on expectations. Sometimes, however, surprises happen: outcomes are not as expected. Such discrepancies between expectations and actual outcomes are called prediction errors. Our brain recognises and uses such prediction errors to modify our expectations and make them more realistic--a process known as reinforcement learning. In particular, neurons that release the neurotransmitter dopamine show activity patterns that strongly resemble prediction errors. Interestingly, the same neurotransmitter is also known to regulate risk preferences: dopamine levels control our willingness to take risks. We theorised that, since learning signals cause dopamine release, they might change risk preferences as well. In this study, we test this hypothesis. We find that participants are more likely to make a risky choice just after they experienced an outcome that was better than expected, which is precisely what out theory predicts. This suggests that dopamine signalling can be ambiguous--a learning signal can be mistaken for an impulse to take a risk.


title: α-Synuclein facilitates clathrin assembly in synaptic vesicle endocytosis

abstract: -Synuclein and family members {beta}-, and {gamma}-synuclein, are presynaptic proteins that sense and generate membrane curvature, properties important for synaptic vesicle (SV) cycling. {beta}{gamma}-synuclein triple knockout (KO) neurons exhibit SV endocytosis (SVE) deficits. Here, we investigate how SVE is regulated by -synuclein. Immuno-electron microscopy (EM) of synaptosomes reveals that -synuclein relocalizes from SVs to the synaptic membrane upon stimulation, allowing -synuclein to function on presynaptic membranes during or after stimulation. On cell membranes, we observe that -synuclein is colocalized with clathrin and its adaptor AP180. Clathrin patches that contain both -synuclein and AP180 were significantly larger than clathrin patches containing either protein alone. We also find that recruitment of clathrin and AP180 recruitment to membranes are altered in the absence of synucleins. Visualizing clathrin assembly on membranes using an in vitro endocytosis reconstitution system reveals that -synuclein increases clathrin patch size and enhances clathrin lattice curvature, facilitating normal clathrin coated pit maturation. Thus, -synuclein is an endocytic accessory protein that acts at early stages of SVE to controls the size and curvature of clathrin structures on the membrane.


title: Removing the Gβγ-SNAP25 brake on exocytosis enhances insulin action, promotes adipocyte browning, and protects against diet-induced obesity

abstract:
Negative regulation of exocytosis from secretory cells throughout the body is accomplished through inhibitory signals from Gi/o G protein-coupled receptors by G{beta}{gamma} subunit inhibition of two common mechanisms: (i) decreased calcium entry and (ii) direct interaction of G{beta}{gamma} with the Soluble N-ethylmaleimide-sensitive factor Attachment Protein (SNAP) Receptor (SNARE) plasma membrane fusion machinery. We have previously shown that disabling the second mechanism with a truncation of SNAP25 (SNAP25{Delta}3/{Delta}3) decreases the affinity of G{beta}{gamma} for the SNARE complex, leaving exocytotic fusion as well as modulation of calcium entry intact. Here we report significant beneficial metabolic remodeling in mice carrying this mutation. Chow-fed SNAP25{Delta}3/{Delta}3 mice exhibit enhanced insulin sensitivity and increased beiging of white fat. In response to a high fat diet, the metabolic protection was amplified in SNAP25{Delta}3/{Delta}3 mice. Glucose homeostasis, whole body insulin action, and insulin-mediated glucose uptake into white adipose tissue were improved along with resistance to diet-induced obesity. This metabolic protection in SNAP25{Delta}3/{Delta}3 mice occurred without compromising the physiological response to fasting or cold. All metabolic phenotypes were reversed at thermoneutrality, suggesting basal autonomic tone is required. Thus, the G{beta}{gamma}-SNARE interaction represents a cellular mechanism that deserves further exploration as a new avenue for combatting metabolic disease.

GRAPHICAL ABSTRACT

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category: physiology


title: Suicidal thoughts, behaviors, and event-related potentials: A systematic review and meta-analysis

abstract:
BackgroundSuicidal thoughts and behaviors (STBs) are thought to result from, at least in part, abnormalities in various neural systems. Event-related potentials (ERPs) are a useful method for studying neural activity and can be leveraged to study neural deficits related to STBs; however, it is unknown how effective ERPs are at differentiating various STB groups. The present meta-analysis examined how well ERPs can differentiate (a) those with and without suicidal ideation, (b) those with and without suicide attempts, (c) those with different levels of suicide risk, and (d) differences between those with suicide attempts versus those with suicidal ideation only.

MethodThis meta-analysis included 208 effect sizes from 2,517 participants from 27 studies. We used a random-effects meta-analysis using a restricted maximum likelihood estimator with robust variance estimation. We meta-analyzed ERP-STB combinations that had at least three effect sizes across two or more studies.

ResultsA qualitative review found that for each ERP and STB combination, the literature is highly mixed. Our meta-analyses largely did not find significant relationships between STBs and ERPs. We also found that the literature is likely severely underpowered, with most studies only being sufficiently powered to detect unrealistically large effect sizes.

ConclusionsOur results provided little-to-no support for a reliable relationship between the ERPs assessed and STBs. However, the current literature is severely underpowered, and there are many methodological weaknesses that must be resolved before making this determination. We recommend large-scale collaboration and improvements in measurement practices to combat the issues in this literature.


title: OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

abstract:
Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. For example, a hemoglobin which branched out prior to the hemoglobin alpha/beta duplication could be closest to a hemoglobin alpha or beta sequence, whereas it is neither. To overcome this problem, phylogeny-driven tools have emerged but rely on gene trees, whose inference is computationally expensive.

Here, we first show that in multiple animal and plant datasets, 18 to 62% of assignments by closest sequence are misassigned, typically to an over-specific subfamily. Then, we introduce OMAmer, a novel alignment-free protein subfamily assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. OMAmer is based on an innovative method using evolutionarily-informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, we show that OMAmer provides better and quicker subfamily-level assignments than approaches relying on the closest sequence, whether inferred exactly by Smith-Waterman or by the fast heuristic DIAMOND.

OMAmer is available from the Python Package Index (as omamer), with the source code and a precomputed database available at https://github.com/DessimozLab/omamer.

category: bioinformatics


title: Characterizing the body morphology of the first metacarpal in the Homininae using 3D geometric morphometrics

abstract:
ObjectivesThe morphological characteristics of the thumb are of particular interest due to its fundamental role in enhanced manipulation. Despite its possible importance regarding this issue, the body of the first metacarcapal (MC1) has not been fully characterized using morphometrics. This could provide further insights into its anatomy, as well as its relationship with manipulative capabilities. Hence, this study quantifies the shape of the MC1s body in the extant Homininae and some fossil hominins to provide a better characterization of its morphology.

Materials and methodsThe sample includes MC1s of modern humans (n=42), gorillas (n=27) and chimpanzees (n=30), as well as Homo neanderthalensis, Homo naledi and Australopithecus sediba. 3D geometric morphometrics were used to quantify the shape of MC1s body.

ResultsThe results show a clear distinction among the three extant genera. H. neanderthalensis mostly falls within the modern human range of variation. H. naledi varies slightly from modern humans, although also showing some unique trait combination, whereas A. sediba varies to an even greater extent. When classified using a discriminant analysis, the three fossils are categorized within the Homo group. Conclusion: The modern human MC1 is characterized by a distinct suite of traits, not present to the same extent in the great apes, that are consistent with an ability to use forceful precision grip. This morphology was also found to align very closely with that of H. neanderthalensis. H. naledi shows a number of human-like adaptations, whilst A. sediba presents a mix of both derived and more primitive traits.

category: paleontology


title: Specificity of Gβ and γ subunits to the SNARE complex both at rest and after α2aadrenergic receptor stimulation

abstract:
Though much is known about the various physiological functions of each GPCR and the specificity of G subunits, the specificity of G{beta}{gamma} activated by a given GPCR and activating each effector in vivo is not known. Previously, we identified different G{beta} and G{gamma} subunits interacting specifically with 2a-adrenergic receptors (2aAR). In this study, we examined its in vivo specificity to the soluble NSF attachment proteins (SNARE) complex in adrenergic (auto-2aAR) and non-adrenergic (hetero-2aAR) neurons. We applied a quantitative targeted multiple reaction monitoring proteomic analysis of G{beta} and G{gamma} subunits bound to the SNARE complex, and found only a subset of G{beta} and G{gamma} bound. Without stimulation of auto-2aAR, G{beta}1 and G{gamma}3 interacted with the SNARE complex. When auto-2aAR were activated, G{beta}1, G{beta}2, and G{gamma}3 were found. Further understanding of in vivo G{beta}{gamma} specificity to its effectors provides new insights into the multiplicity of genes for G{beta} and G{gamma}.

SummarySpecific G{beta}{gamma} dimers interact with the SNARE complex following presynaptic 2aAR activation in both adrenergic and non-adrenergic neurons.


title: Personality, Subjective Well-Being, and the Serotonin 1a Receptor Gene in Common Marmosets (Callithrix jacchus)

abstract: Studies of personality traits in common marmosets (Callithrix jacchus) indicate that there are five or six constructs--sociability, dominance, neuroticism, openness, and two related to conscientiousness--that define personality in common marmosets. The present study attempted to determine whether our earlier study of laboratory-housed individuals only yielded three domains--Dominance, Sociability, and Neuroticism--because of a low amount of between-subjects variance. We therefore increased our sample size from 77 to 128. In addition, we ascertained the reliability and validity of ratings and whether polymorphisms related to the serotonin 1a receptor were associated with personality. We found Sociability, Dominance, and Negative Affect factors that resembled three domains found in previous studies, including ours. We also found an Openness and Impulsiveness factor, the latter of which bore some resemblance to Conscientiousness, and two higher-order factors, Pro-sociality and Boldness. Further analyses could not exclude the possibility that Pro-sociality and Boldness represented a higher-level of personality organization. Correlations between personality factors and well-being were consistent with the definitions of the factors. There were no significant associations between personality and genotype. These results are consistent with the possibility that common marmoset personality structure varies as a function of rearing or housing variables that have not yet been investigated systematically.


title: Downregulation of Perilipin1 by IMD leads to LD reconfiguration and adaptation to bacterial infection in Drosophila

abstract: Lipid droplets (LDs) are dynamic intracellular organelles critical for lipid metabolism. Dynamic alterations in the configurations and functions of LDs during innate immune response to bacterial infections and the underlying mechanisms however, remain largely unknown. Herein, we trace the time-course morphology of LDs in fat bodies of Drosophila after transient bacterial infection. Detailed analysis shows that perilipin1 (plin1), a core gene regulating lipid metabolism of LDs is suppressed by IMD/Relish, an innate immune signaling. During immune activation, downregulated plin1 promotes the enlargement of LDs, which in turn alleviates immune reaction-associated reactive oxygen species (ROS) stress. Thus, the growth of LDs is likely an active adaptation to maintain redox homeostasis in response to IMD activation. Therefore, our study provides evidence that plin1 serves as a modulator on LDs reconfiguration in regulating infection-induced pathogenesis, and Plin1 might be a potential therapeutic target for coordinating inflammation resolution and lipid metabolism.


title: A novel DNA binding mode, conformational change and intramolecular signaling in MutS upon mismatch recognition in replication DNA structures

abstract: MutS initiates mismatch repair by recognizing mismatches in newly replicated DNA. Specific interactions between MutS and mismatches within double-stranded DNA promote ADP-ATP exchange and a conformational change into a sliding clamp. Here, we demonstrated that MutS from Pseudomonas aeruginosa associates with primed DNA replication substrates. The predicted structure of this MutS-DNA complex revealed a new DNA binding site, in which Asn 279 and Arg 272 appeared to directly interact with the 3-OH terminus of primed DNA. Mutation of these residues resulted in a noticeable defect in the interaction of MutS with replication DNA substrates. Remarkably, MutS interaction with a mismatch within primed DNA induced a compaction of the protein structure and impaired the formation of an ATP-bound sliding clamp. Our findings reveal a novel DNA binding mode, conformational change and intramolecular signaling for MutS recognition of mismatches within DNA replication structures.


title: Developmental co-emergence of cardiac and gut tissues modeled by human iPSC-derived organoids

abstract: During embryogenesis, paracrine signaling between tissues in close proximity contributes to the determination of their respective cell fate(s) and development into functional organs. Organoids are in vitro models that mimic organ formation and cellular heterogeneity, but lack the paracrine input of surrounding tissues. Here, we describe a human multilineage iPSC-derived organoid that recapitulates cooperative cardiac and gut development and displays extensive cellular and structural complexity of both tissues. We demonstrate that the presence of endoderm tissue (gut/intestine) in multilineage organoids contributed to the development of the cardiac tissue, specifically cardiomyocyte expansion, compartmentalization, enrichment of atrial/nodal cells, myocardial compaction and functional fetal-like maturation. Overall, this study demonstrates the ability to generate specific cooperative tissues originating from different germ lineages within a single organoid model, an advance that will further the examination of multi-tissue interactions during development and disease.

category: developmental biology


title: Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency

abstract: Heterozygous de novo loss-of-function mutations in the gene expression regulator HNRNPU cause an early-onset developmental and epileptic encephalopathy. To gain insight into pathological mechanisms and lay the potential groundwork for developing targeted therapies, we characterized the neurophysiologic and cell-type-specific transcriptomic consequences of a mouse model of HNRNPU haploinsufficiency. Heterozygous mutants demonstrated neuroanatomical abnormalities, global developmental delay, impaired ultrasonic vocalizations and increased seizure susceptibility, thus modeling aspects of the human disease. Single-cell RNA-sequencing of hippocampal and neocortical cells revealed widespread, yet modest, dysregulation of gene expression across mutant neuronal subtypes. We observed an increased burden of differentially-expressed genes in mutant excitatory neurons of the subiculum--a region of the hippocampus implicated in temporal lobe epilepsy. Evaluation of transcriptomic signature reversal as a therapeutic strategy highlights the potential importance of generating cell-type-specific signatures. Overall, this work provides insight into HNRNPU-mediated disease mechanisms, and provides a framework for using single-cell RNA-sequencing to study transcriptional regulators implicated in disease.


title: Representative diatom and coccolithophore species exhibit divergent responses throughout simulated upwelling cycles

abstract: Wind-driven upwelling followed by relaxation results in cycles of cold nutrient-rich water fueling intense phytoplankton blooms followed by nutrient-depletion, bloom decline, and sinking of cells. Surviving cells at depth can then be vertically transported back to the surface with upwelled waters to seed another bloom. As a result of these cycles, phytoplankton communities in upwelling regions are transported through a wide range of light and nutrient conditions. Diatoms appear to be well-suited for these cycles, but their responses to them remain understudied. To investigate the bases for diatoms ecological success in upwelling environments, we employed laboratory simulations of a complete upwelling cycle with a common diatom, Chaetoceros decipiens, and coccolithophore, Emiliania huxleyi. We show that while both organisms exhibited physiological and transcriptomic plasticity, the diatom displayed a distinct response enabling it to rapidly shift-up growth rates and nitrate assimilation when returned to light and available nutrients following dark, nutrient-deplete conditions. As observed in natural diatom communities, C. decipiens highly expresses before upwelling, or frontloads, key transcriptional and nitrate assimilation genes coordinating its rapid response to upwelling conditions. Low iron simulations showed that C. decipiens is capable of maintaining this response when iron is limiting to growth, whereas E. huxleyi is not. Differential expression between iron treatments further revealed specific genes used by each organism under low iron availability. Overall, these results highlight the responses of two dominant phytoplankton groups to upwelling cycles, providing insight into the mechanisms fueling diatom blooms during upwelling events.


title: Reproductive biology of wild and domesticated Ensete ventricosum: Further evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop

abstract:
O_LILoss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop.
C_LIO_LIWe examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterise optimum germination requirements.
C_LIO_LIWe report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution.
C_LIO_LIOur findings provide evidence that sexual reproductive capacity has been maintained despite long-term near-exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology, may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding.
C_LI


title: Trait-based responses to forestry and reindeer husbandry modify long-term changes in forest understories

abstract:
AimLand use is the foremost cause of global biodiversity decline, but species do not respond equally to land-use practices. Instead, it is suggested that responses vary with species traits, but long-term data on the trait-mediated effects of land-use on communities is scarce. Here we study how forest understory communities have been affected by two land-use practices during 4-5 decades, and whether changes in plant diversity are related to changes in functional composition.

LocationFinland

Time period1968-2019

Major taxa studiedVascular plants

MethodsWe resurveyed 245 vegetation plots in boreal herb-rich forest understories, and used hierarchical Bayesian linear models to relate changes in diversity, species composition, average plant size, and leaf economic traits to reindeer abundance, forest management intensity, and changes in climate, canopy cover and composition.

ResultsIntensively managed forests decreased in species richness and had increased turnover, but management did not affect functional composition. Increased reindeer densities corresponded with increased leaf dry matter content, evenness and diversity, and decreased height and specific leaf area. Successional development in the canopy was associated with increased specific leaf area and decreased leaf dry matter content and height in the understory over the study period. Effects of reindeer abundance and canopy density on diversity were partially mediated by vegetation height, which had a negative relationship with evenness. Observed changes in climate had no discernible effect on any variable.

Main conclusionsFunctional traits are useful in connecting vegetation changes to the mechanisms that drive them, and provide unique information compared to turnover and diversity metrics. These trait-dependent selection effects could inform whether species benefit or suffer from land use changes and explain observed biodiversity changes under global change.


title: Trait-based responses to land use and canopy dynamics modify long-term diversity changes in forest understories


title: Auditory cue combination in perceptual externalization of static sound sources: a model-based meta analysis

abstract: Under natural conditions, listeners perceptually attribute sounds to external objects in their environment. This core function of perceptual inference is often distorted when sounds are produced via hearing devices such as headphones or hearing aids, resulting in sources being perceived unrealistically close or even inside the head. Psychoacoustic studies suggest a mixed role of various monaural and interaural cues contributing to the externalization process. We developed a model framework for perceptual externalization able to probe the contribution of cue-specific expectation errors and to contrast dynamic versus static strategies for combining those errors within static listening environments. Effects of reverberation and visual information were not considered. The model was applied to various acoustic distortions as tested under various spatially static conditions in five previous experiments. Most accurate predictions were obtained for the combination of monaural and interaural spectral cues with a fixed relative weighting (approximately 60% of monaural and 40% of interaural). That model version was able to reproduce the externalization rating of the five experiments with an average error of 12% (relative to the full rating scale). Further, our results suggest that auditory externalization in spatially static listening situations underlie a fixed weighting of monaural and interaural spectral cues, rather than a dynamic selection of those auditory cues.


title: Decision making in auditory externalization perception:model predictions for static conditions


title: Detecting neural state transitions underlying event segmentation

abstract:
Segmenting perceptual experience into meaningful events is a key cognitive process that helps us make sense of what is happening around us in the moment, as well as helping us recall past events. Nevertheless, little is known about the underlying neural mechanisms of the event segmentation process. Recent work has suggested that event segmentation can be linked to regional changes in neural activity patterns. Accurate methods for identifying such activity changes are important to allow further investigation of the neural basis of event segmentation and its link to the temporal processing hierarchy of the brain. In this study, we introduce a new set of elegant and simple methods to study these mechanisms. We introduce a method for identifying the boundaries between neural states in a brain area and a complementary one for identifying the number of neural states. Furthermore, we present the results of a comprehensive set of simulations and analyses of empirical fMRI data to provide guidelines for reliable estimation of neural states and show that our proposed methods outperform the current state-of-the-art in the literature. This methodological innovation will allow researchers to make headway in investigating the neural basis of event segmentation and information processing during naturalistic stimulation.

HighlightsO_LIBoundaries between meaningful events are related to neural state transitions.
C_LIO_LINeural states are temporarily stable regional brain activity patterns.
C_LIO_LIWe introduce novel methods for data-driven detection of neural state boundaries.
C_LIO_LIThese methods can identify the location and the number of neural state boundaries.
C_LIO_LISimulations and empirical data support the reliability and validity of our methods.
C_LI


title: Child specific activation in left auditory cortex predicts behavioral performance in inhibition tasks.

abstract: Sensory processing during development is important for the emerging cognitive skills underlying goal-directed behavior. Yet, it is not known how auditory processing in children is related to their cognitive functions. Here, we utilized combined magneto- and electroencephalographic (M/EEG) measurements to show that child-unique auditory cortical activity at [~]250 ms after auditory stimulation predicts the performance in inhibition tasks. While unaffected by task demands, the amplitude of the left-hemisphere activation pattern was significantly correlated with the variability of behavioral response time. Since this activation pattern is not present in adults, our results suggest divergent brain mechanisms in adults and children for consistent performance in auditory-based cognitive tasks. This difference can be explained as a shift in cortical resources for cognitive control from sensorimotor associations in the auditory cortex of children to top-down regulated control processes involving (pre)frontal and cingulate areas in adults.


title: tRNA Biogenesis and Specific Aminoacyl-tRNA Synthetases Regulate Senescence Stability Under the Control of mTOR

abstract:
Oncogenes or chemotherapy treatments trigger the induction of suppressive pathways such as apoptosis or senescence. Senescence was initially defined as a definitive arrest of cell proliferation but recent results have shown that this mechanism is also associated with cancer progression and chemotherapy resistance. Senescence is therefore much more heterogeneous than initially thought. How this response varies is not really understood, it has been proposed that its outcome relies on the secretome of senescent cells and on the maintenance of their epigenetic marks.

Using experimental models of senescence escape, we now described that the stability of this suppression relies on specific tRNAs and aminoacyl-tRNA synthetases. Following chemotherapy treatment, the DNA binding of the type III RNA polymerase was reduced to prevent tRNA transcription and induce a complete cell cycle arrest. By contrast, during senescence escape, specific tRNAs such as tRNA-Leu-CAA and tRNA-Tyr-GTA were up-regulated. Reducing tRNA transcription appears necessary to control the strength of senescence since RNA pol III inhibition through BRF1 depletion maintained senescence and blocked cell persistence. mTOR inhibition also prevented CIS escape in association with a reduction of tRNA-Leu-CAA and tRNA-Tyr-GTA expression. Further confirming the role of the tRNA-Leu-CAA and tRNA-Tyr-GTA, their corresponding tRNA ligases, YARS and LARS, were necessary for senescence escape. This effect was specific since the CARS ligase had no effect on persistence. YARS and LARS inactivation reduced cell emergence and proteomic analysis indicated that this effect was associated with the down-regulation of E2F1 target genes.

Overall, these findings highlight a new regulation of tRNA biology during senescence and suggest that specific tRNAs and ligases contribute to the strength and heterogeneity of this suppression.


title: Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

abstract: Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Here we reveal, in the plant model Arabidopsis thaliana, that the PIN7 gene, which encodes a polarly localized transporter for the phytohormone auxin, produces two evolutionary-conserved transcripts. These isoforms PIN7a and PIN7b, differing in a 4 amino acid motif, are present at nearly equal levels in most cells. Although both variants do not differ in the subcellular localization and transport auxin with similar capacity, they closely associate and mutually influence their stability within the plasma membrane. Phenotypic complementation tests reveal that the functional contribution of PIN7b per se is minor but it markedly attenuates the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. These results establish alternative splicing of the PIN family as a conserved, functionally-relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.


title: Infanticide by females is a leading source of juvenile mortality in a large social carnivore

abstract: Social animals benefit from their groupmates, so why do they sometimes kill each others offspring? Using 30 years of data from multiple groups of wild spotted hyenas, we address three critical aims for understanding infanticide in any species: (1) quantify the contribution of infanticide to overall mortality (2) describe the circumstances under which infanticide occurs and (3) evaluate hypotheses about the evolution of infanticide. We find that, although observed only rarely, infanticide is in fact a leading source of juvenile mortality. Infanticide accounted for 24% of juvenile mortality, and 1 in 10 hyenas born in our population perished due to infanticide. In all observed cases of infanticide, killers were adult females, but victims could be of both sexes. Of four hypotheses regarding the evolution of infanticide, we found the most support for the hypothesis that infanticide in spotted hyenas reflects competition over social status among matrilines.


title: Steric blockage of lysenin toxin by crowding

abstract: bioRxiv has withdrawn this manuscript in response to an institutional investigation by INSERM.


title: Social play is critical for the development of prefrontal inhibitory synapses and cognitive flexibility in rats

abstract: Sensory driven activity during early life is critical for setting up the proper connectivity of the sensory cortices. Here we ask if social play behavior, a particular form of social interaction that is highly abundant during post-weaning development, is equally important for setting up connections in the developing prefrontal cortex (PFC). Young rats were deprived from social play with peers for 3 weeks during the period in life when social play behavior normally peaks (P21-42; SPD rats), followed by resocialization until adulthood. We recorded synaptic currents in L5 cells in slices from medial PFC of adult SPD and control rats and observed that inhibitory synaptic currents were reduced in SPD slices, while excitatory synaptic currents were unaffected. This was associated with a decrease in perisomatic inhibitory synapses from parvalbumin-positive GABAergic cells. In parallel experiments, adult SPD rats achieved more reversals in a probabilistic reversal learning task (PRL), which depends on the integrity of the PFC. They appeared to use a different cognitive strategy than controls. One hour of intense play during SPD did not prevent the decrease in inhibitory synaptic inputs and had only a limited effect on behavioral outcomes in the PRL. Our data demonstrate the importance of unrestricted social play for the development of inhibitory synapses in the PFC and cognitive skills in adulthood.


title: Serotonergic psychedelic drugs LSD and psilocybin reduce the hierarchical differentiation of unimodal and transmodal cortex

abstract: LSD and psilocybin are serotonergic psychedelic compounds with potential in the treatment of mental health disorders. Past neuroimaging investigations have revealed that both compounds can elicit significant changes to whole-brain functional organization and dynamics. A recent proposal linked past findings into a unified model and hypothesized reduced whole-brain hierarchical organization as a key mechanism underlying the psychedelic state, but this has yet to be directly tested. We applied a non-linear dimensionality reduction technique previously used to map hierarchical connectivity gradients to pharmacological resting-state fMRI data to assess cortical organization in the LSD and psilocybin state. Results supported our primary hypothesis: The principal gradient of cortical connectivity, describing a hierarchy from unimodal to transmodal cortex, was significantly flattened under both drugs relative to their respective placebo conditions. Between-condition contrasts revealed that this was driven by a reduction of functional differentiation at both hierarchical extremes - default and frontoparietal networks at the upper end, and somatomotor at the lower. Gradient-based connectivity mapping confirmed that this was underpinned by increased unimodal-transmodal crosstalk. In addition, LSD-dependent principal gradient changes tracked changes in self-reported ego-dissolution. Results involving the second and third gradient, which respectively represent axes of sensory and executive differentiation, also showed significant alterations across both drugs. These findings provide support for a recent mechanistic model of the psychedelic state relevant to therapeutic applications of psychedelics. More fundamentally, we provide the first evidence that macroscale connectivity gradients are sensitive to a pharmacological manipulation, specifically highlighting an important relationship between cortical organization and serotonergic modulation.


title: Virtual Mouse Brain Histology from Multi-contrast MRI via Deep Learning

abstract: 1H MRI maps brain structure and function non-invasively through versatile contrasts that exploit inhomogeneity in tissue micro-environments. Inferring histopathological information from MRI findings, however, remains challenging due to absence of direct links between MRI signals and cellular structures. Here, we show that deep convolutional neural networks, developed using co-registered multi-contrast MRI and histological data of the mouse brain, can estimate histological staining intensity directly from MRI signals at each pixel. The results provide three-dimensional maps of axons and myelin with tissue contrasts that closely mimics target histology and enhanced sensitivity and specificity compared to conventional MRI markers. Furthermore, the relative contribution of each MRI contrast within the networks can be used to optimize multi-contrast MRI acquisition. We anticipate our method to be a starting point for translation of MRI results into easy-to-understand virtual histology for neurobiologists and provide resources for validating novel MRI techniques.

category: bioengineering


title: Network analysis reveals different strategies of Trichoderma spp. associated with XYR1 and CRE1 during cellulose degradation

abstract: Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.


title: Network Analysis Reveals Different Cellulose Degradation Strategies across Trichoderma harzianum Strains Associated with XYR1 and CRE1


title: Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer's disease

abstract:
BackgroundIron trafficking and accumulation is associated with Alzheimers disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterized, making it difficult to explore these in existing datasets.

ObjectiveTo identify sets of genes predicted to contain Iron Responsive Elements (IREs) and use these to explore possible iron dyshomeostasis-associated gene expression responses in AD.

MethodsComprehensive sets of genes containing predicted IRE or IRE-like motifs in their 3 or 5 untranslated regions (UTRs) were identified in human, mouse, and zebrafish reference transcriptomes. Further analyses focusing on these genes were applied to a range of cultured cell, human, mouse, and zebrafish gene expression datasets.

ResultsIRE gene sets are sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, changes in IRE transcript abundance are amongst the earliest observable changes in zebrafish familial AD (fAD)-like brains, preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some IREs in the 3 untranslated regions of transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead display decreased stability, indicating that this is not a generalizable paradigm.

ConclusionOur results reveal IRE gene expression changes as early markers of the pathogenic process in fAD and are consistent with iron dyshomeostasis as an important driver of this disease. Our work demonstrates how differences in the stability of IRE- containing transcripts can be used to explore and compare iron dyshomeostasis-associated gene expression responses across different species, tissues, and conditions.


title: Gliding motility of Plasmodium merozoites

abstract:
Plasmodium malaria parasites are obligate intracellular protozoans that use a unique form of locomotion, termed gliding motility, to move through host tissues and invade cells. The process is substrate-dependent and powered by an actomyosin motor that drives the posterior translocation of extracellular adhesins which in turn propel the parasite forward. Gliding motility is essential for tissue translocation in the sporozoite and ookinete stages; however, the short-lived erythrocyte-invading merozoite stage has never been observed to undergo gliding movement. Here we show Plasmodium merozoites possess the ability to undergo gliding motility and that this mechanism is likely an important precursor step for successful parasite invasion. We demonstrate that two human infective species, P. falciparum and P. knowlesi, have distinct merozoite motility profiles which may reflect distinct invasion strategies. Additionally, we develop and validate a higher throughput assay to evaluate the effects of genetic and pharmacological perturbations on both the molecular motor and complex signaling cascade that regulates motility in merozoites. The discovery of merozoite motility provides a new model to study the glideosome and may facilitate the pursuit of new targets for malaria treatment.

Significance statementPlasmodium malaria parasites use a unique substrate-dependent locomotion termed gliding motility to translocate through tissues and invade cells. Dogma has suggested that the small labile invasive stages that invade erythrocytes, merozoites, use this motility solely to penetrate target erythrocytes. Here we reveal that merozoites use gliding motility for translocation across host cells prior to invasion. This forms an important pre-invasion step that is powered by a conserved actomyosin motor and is regulated by a complex signaling pathway. This work fundamentally changes our understanding of the role of gliding motility and invasion in the blood and will have a significant impact on our understanding of blood stage host-pathogen interactions, parasite biology, and could have implications for vaccine development.


title: The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons

abstract: Host-associated microbiotas guide the trajectory of developmental programs, and microbial dysbiosis is linked to neurodevelopmental conditions such as autism spectrum disorder. Recent work suggests that microbiotas modulate behavioral phenotypes associated with these disorders. We discovered that the zebrafish microbiota is required for normal social behavior, and reveal a molecular pathway linking the microbiota, microglial remodeling of neural circuits, and social behavior in this experimentally tractable model vertebrate. Examining neuronal correlates of behavior, we found that the microbiota restrains neurite complexity and targeting of forebrain neurons required for normal social behavior and is necessary for localization of forebrain microglia, brain resident phagocytes that remodel neuronal arbors. The microbiota also influences microglial molecular functions, including promoting expression of the remodeling factor c1q, which we find is required for normal forebrain neurite complexity. Several distinct bacterial taxa are individually sufficient for normal microglial and neuronal phenotypes, suggesting that host neuroimmune development is sensitive to a feature common among many bacteria. Our results demonstrate that the microbiota influences zebrafish social behavior by stimulating microglial remodeling of forebrain circuits during early neurodevelopment, and suggest pathways for new interventions in multiple neurodevelopmental disorders.


title: Identification of synaptic PPT1 substrates highlight roles of depalmitoylation in disulfide bond formation and synaptic function

abstract:
Loss-of-function mutations in the depalmitoylating enzyme palmitoyl protein thioesterase 1 (PPT1) cause Neuronal Ceroid Lipofuscinosis type 1 (CLN1), a devastating neurodegenerative disease. Here, we provide a resource identifying PPT1 substrates. We utilized Acyl Resin-Assisted Capture and mass spectrometry to identify proteins with increased in vivo palmitoylation in PPT1 knockout mouse brains. We then validated putative substrates through direct depalmitoylation with recombinant PPT1. This stringent screen elucidated >100 novel PPT1 substrates at the synapse, including channels and transporters, G-protein-associated molecules, endo/exocytic components, synaptic adhesion molecules, and mitochondrial proteins. Cysteine depalmitoylation sites in transmembrane PPT1 substrates frequently participate in disulfide bonds in the mature protein. We confirmed that depalmitoylation regulates disulfide bond formation in a tertiary screen analyzing post-translational modifications. Collectively, the diverse PPT1 substrates highlight the role of PPT1 in mediating synapse functions, implicate molecular pathways in the etiology of CLN1, and advance our basic understanding of the purpose of depalmitoylation.

HighlightsO_LI[~]10% of palmitoylated proteins are palmitoyl protein thioesterase 1 (PPT1) substrates
C_LIO_LIUnbiased proteomic approaches identify 9 distinct classes of PPT1 substrates, including synaptic adhesion molecules and endocytic proteins
C_LIO_LIProtein degradation does not require depalmitoylation by PPT1
C_LIO_LIDepalmitoylation mediates disulfide bond formation in transmembrane PPT1 substrates
C_LI


title: Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment

abstract: Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measurements. Several computational methods to estimate RNA processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate RNA synthesis, processing and degradation rates from a single sample. Our method is computationally efficient and outputs rates that correlate well with previously published data sets. Using it on a single sample, we were able to reproduce the observation that dynamic biological processes tend to involve genes with higher metabolic rates, while stable processes involve genes with lower rates. This supports the hypothesis that cells control not only the mRNA steady-state abundance, but also its responsiveness, i.e., how fast steady-state is reached. In addition to saving experimental work and computational time, having a sample-based rate estimation has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and perform quality control. Finally the method and theoretical results described here are general enough to be useful in other contexts such as nucleotide conversion methods and single cell metabolic labeling experiments.


title: Precise optical control of gene expression in C. elegans using genetic code expansion and Cre recombinase

abstract: Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an efficient genetic code expansion system in C. elegans and use it to create a photo-activatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to the C. elegans touch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted.


title: Inside-out regulation of E-cadherin conformation and adhesion

abstract:
Cadherin cell-cell adhesion proteins play key roles in tissue morphogenesis and wound healing. Cadherin ectodomains bind in two conformations, X-dimers and strand-swap dimers, with different adhesive properties. However, the mechanisms by which cells regulate ectodomain conformation are unknown. Cadherin intracellular regions associate with several actin-binding proteins including vinculin, which are believed to tune cell-cell adhesion by remodeling the actin cytoskeleton. Here, we show at the single molecule level, that vinculin association with the cadherin cytoplasmic region allosterically converts weak X-dimers into strong strand-swap dimers, and that this process is mediated by myosin II dependent changes in cytoskeletal tension. We also show that in epithelial cells, [~]70% of apical cadherins exist as strand-swap dimers while the remaining form X-dimers, providing two cadherin pools with different adhesive properties. Our results demonstrate, for the first time, the inside-out regulation of cadherin conformation and establish a mechanistic role for vinculin in this process.

SIGNIFICANCE STATEMENTCadherin cell-cell adhesion proteins play key roles in the formation and maintenance of tissues. Their adhesion is carefully regulated to orchestrate complex movement of cells. While cadherin ectodomains bind in two conformations with different adhesive properties, the mechanisms by which cells regulate the conformation (and consequently adhesion) of individual cadherins are unknown. Here, we demonstrate that the association of intracellular vinculin to the cadherin cytoplasmic region, regulates cadherin adhesion by switching ectodomains from a weak binding to the strongly adhesive conformation. In contrast with the prevailing view which suggests that vinculin regulates adhesion solely by remodeling the cytoskeleton, we show that vinculin can directly modulate single cadherin ectodomain conformation and that this process is mediated by changes in cytoskeletal tension.


title: Sequestration of the exocytic SNARE Psy1 into multiprotein nodes reinforces polarized morphogenesis in fission yeast

abstract: Polarized morphogenesis is achieved by targeting or inhibiting growth at distinct regions. Rod-shaped fission yeast cells grow exclusively at their ends by restricting exocytosis and secretion to these sites. This growth pattern implies the existence of mechanisms that prevent exocytosis and growth along non-growing cell sides. We previously identified a set of 50-100 megadalton-sized node structures along the sides of fission yeast cells that contain the interacting proteins Skb1 and Slf1. Here, we show that Skb1-Slf1 nodes contain the syntaxin-like SNARE Psy1, which mediates exocytosis in fission yeast. Psy1 localizes in a diffuse pattern at cell tips where it likely promotes exocytosis and growth, but Psy1 is sequestered in Skb1-Slf1 nodes at cell sides where growth does not occur. Mutations that prevent node assembly or inhibit Psy1 localization to nodes lead to aberrant exocytosis at cell sides and increased cell width. Genetic results indicate that this Psy1 node mechanism acts in parallel to actin cables and Cdc42 regulation. Our work suggests that sequestration of syntaxin-like Psy1 at non-growing regions of the cell cortex reinforces cell morphology by restricting exocytosis to proper sites of polarized growth.

category: cell biology


title: Closed-loop sacral neuromodulation for bladder function using dorsal root ganglia sensory feedback in an acute feline model

abstract: Overactive bladder patients suffer from a frequent, uncontrollable urge to urinate, which can lead to a poor quality of life. We aim to improve open-loop sacral neuromodulation therapy by developing a conditional stimulation paradigm using neural recordings from dorsal root ganglia (DRG) as sensory feedback. Experiments were performed in 5 anesthetized felines. We implemented a Kalman filter-based algorithm to estimate the bladder pressure in real-time using sacral-level DRG neural recordings and initiated sacral root electrical stimulation when the algorithm detected an increase in bladder pressure. Closed-loop neuromodulation was performed during continuous cystometry and compared to bladder fills with continuous and no stimulation. Overall, closed-loop stimulation increased bladder capacity by 13.8% over no stimulation (p < 0.001) and reduced stimulation time versus continuous stimulation by 57.7%. High-confidence bladder single units had a reduced sensitivity during stimulation, with lower linear trendline fits and higher pressure thresholds for firing observed during stimulation trials. This study demonstrates the utility of decoding bladder pressure from neural activity for closed-loop control of sacral neuromodulation. An underlying mechanism for sacral neuromodulation may be a reduction in bladder sensory neuron activity during stimulation. Real-time validation during behavioral studies is necessary prior to clinical translation of closed-loop sacral neuromodulation.


title: Obesity-induced astrocyte dysfunction impairs heterosynaptic plasticity in the orbitofrontal cortex.

abstract:
SO_SCPLOWUMMARYC_SCPLOWOverconsumption of highly palatable, energy dense food is considered a key driver of the obesity pandemic. The orbitofrontal cortex (OFC) is critical for reward valuation of gustatory signals, yet how the OFC adapts to obesogenic diets is poorly understood. Here we show that extended access to a cafeteria diet impairs astrocyte glutamate clearance, which leads to a heterosynaptic depression of GABA transmission onto pyramidal neurons of the OFC. This decrease in GABA tone is due to an increase in extrasynaptic glutamate, which acts via metabotropic glutamate receptors to liberate endocannabinoids. This impaired the induction of endocannabinoid-mediated long-term plasticity. In obese rats, this cascade of synaptic impairments was rescued by restoring astrocyte glutamate transport with the nutritional supplement, N-acetylcysteine. Together, our findings indicate that obesity targets astrocytes to disrupt the delicate balance between excitatory and inhibitory transmission in the OFC.

HO_SCPLOWIGHLIGHTSC_SCPLOWO_LIDiet-induced obesity induces hypertrophy of astrocytes and impairs their ability to transport glutamate.
C_LIO_LIFailure of astrocytes to clear extrasynaptic glutamate drives endocannabinoid-mediated inhibitory long-term depression of principal output neurons in the OFC.
C_LIO_LIAstrocytic glutamate transporter function is restored with NAC, which rescues the synaptic deficits.
C_LI


title: Principal component analysis revealed multiple consistent responses to naturalistic stimuli in children and adults

abstract: Functional MRI (fMRI) study of naturalistic conditions, e.g. movie watching, usually focuses on shared responses across subjects. However, individual differences have been attracting increasing attention in search of group differences or associations with behavioral outcomes. Individual differences are typically studied by directly modeling the pair-wise intersubject correlation matrix or projecting the relations onto a single dimension. We contend that it is critical to examine whether there are one or more consistent responses underlying the whole sample, because multiple components, if exist, may undermine the intersubject relations using the previous methods. We propose to use principal component analysis (PCA) to examine the heterogeneity of brain responses across subjects and project the individual variability into higher dimensions. By analyzing an fMRI dataset of children and adults watching a cartoon movie, we showed evidence of two consistent responses in the supramarginal gyrus and other regions. While the first components in many regions represented a response pattern mostly in older children and adults, the second components mainly represented the younger children. The second components in the supramarginal network resembled a delayed version of the first PCs for 4 seconds (2 TR), indicating slower responses in the younger children than the older children and adults. The analyses highlight the importance of identifying multiple consistent responses in responses to naturalistic stimuli. This PCA-based approach could be complementary to the commonly used intersubject correlation to analyze movie watching data.