title: Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types

abstract: Resistance to piperacillin/tazobactam (TZP) in Escherichia coli has predominantly been associated with mechanisms that confer resistance to third generation cephalosporins. Recent reports have identified E. coli strains with phenotypic resistance to piperacillin/tazobactam but susceptibility to third generation cephalosporins (TZP-R/3GC-S). In this study we sought to determine the genetic diversity of this phenotype in E. coli (n = 58) isolated between 2014-2017 at a single tertiary hospital in Liverpool, UK, as well as the associated resistance mechanisms. We compare our findings to a UK-wide collection of invasive E. coli isolates (n = 1509) with publicly available phenotypic and genotypic data. These data sets included the TZP-R/3GC-S phenotype (n = 68), a piperacillin/tazobactam and third generation cephalosporin-susceptible (TZP-S/3GC-S, n = 1271) phenotypes. The TZP-R/3GC-S phenotype was displayed in a broad range of sequence types which was mirrored in the same phenotype from the UK-wide collection, and the overall diversity of invasive E. coli isolates. The TZP-R/3GC-S isolates contained a diverse range of plasmids, indicating multiple acquisition events of TZP resistance mechanisms rather than clonal expansion of a particular plasmid or sequence type. The putative resistance mechanisms were equally diverse, including hyperproduction of TEM-1, either via strong promoters or gene amplification, carriage of inhibitor resistant {beta}-lactamases, and an S133G b/aCTX-M-15 mutation detected for the first time in clinical isolates. Several of these mechanisms were present at a lower abundance in the TZP-S/3GC-S isolates from the UK-wide collection, but without the associated phenotypic resistance to TZP. Our findings highlight the complexity of this cryptic phenotype and the need for continued phenotypic monitoring, as well as further investigation to improve detection and prediction of the TZP-R/3GC-S phenotype from genomic data.


title: Non-additive biotic interactions improve predictions of tropical tree growth and impact community size structure

abstract: Growth in individual size or biomass is a key demographic component in population models, with wide-ranging applications from quantifying species performance across abiotic or biotic conditions to assessing landscape-level dynamics under global change. In forest ecology, the responses of tree growth to biotic interactions are widely held to be crucial for understanding forest diversity, function, and structure. To date, most studies on plant-plant interactions only examine the additive competitive or facilitative interactions between species pairs; however, there is increasing evidence of non-additive, higher-order interactions (HOIs) impacting species demographic rates. When HOIs are present, the dynamics of a multi-species community cannot be fully understood or accurately predicted solely from pairwise outcomes because of how additional species  interfere with the direct, pairwise interactions. Such HOIs should be particularly prevalent where species show nonlinear functional responses to resource availability and resource-acquisition traits themselves are density dependent. With this in mind, we used data from a tropical secondary forest--a system that fulfills both of these conditions--to build a ontogenetic diameter-growth model for individuals across ten woody-plant species. We allowed both direct and indirect interactions within communities to influence the species-specific growth parameters in a generalized Lotka-Volterra model. Specifically, indirect interactions entered the model as higher-order quadratic terms, i.e. non-additive effects of conspecific and heterospecific neighbour size on the focal individuals growth. For the whole community and for four out of ten focal species, the model that included HOIs had more statistical support than the model that included only direct interactions, despite the former containing a far greater number of parameters. HOIs had comparable effect sizes to direct interactions, and tended to further reduce the diameter growth rates of most species beyond what direct interactions had already reduced. In a simulation of successional stand dynamics, the inclusion of HOIs lead to rank swaps in species diameter hierarchies, even when community-level size distributions remained qualitatively similar. Our study highlights the implications, and discusses possible mechanisms, of non-additive density dependence in highly diverse and light-competitive tropical forests.

category: ecology


title: Population genomic evidence for a repeated introduction and rapidexpansion in Europe of a maize fungal pathogen

abstract:
Modern agricultural practices and the climate change foster the rapid spread of plant pathogens like the maize fungal pathogen Setosphaeria turcica, which causes Northern corn leaf blight and expanded into Central Europe since the 1980s. To investigate the rapid expansion of S. turcica we sequenced 121 isolates from Europe and Kenya. Population genomic inference revealed a single genetically diverse cluster in Kenya and three clonal lineages with low diversity and one cluster of multiple clonal sublineages in Europe. Phylogenetic dating suggests that all European lineages originated by sexual reproduction outside Europe and subsequently were subsequently introgressed multiple times. In contrast to Kenyan isolates, European isolates did not show sexual recombination despite the presence of both MAT1-1 and MAT1-2 mating types. Coalescent analysis of the geographically most widespread European lineage supported a neutral, strongly exponential population growth model over models with natural selection caused by host defence resistance or environmental adaptation. Within clonal lineages, we observed phenotypic variation in virulence to different monogenic resistances that may originate from repeated mutations in virulence genes. Association mapping between genetic clusters did not identify genomic regions associated with pathogen races but uncovered strongly differentiated genomic regions between clonal lineages that harbor putative effector genes. In conclusion, the expansion and population growth of S. turcica in Europe was mainly driven by the expansion of maize cultivation area and not by rapid adaptation.

Significance statementThe geographic expansion and plant pathogens caused by modern agricultural practices and climate change is a major problem in modern agriculture. We investigated the rapid spread of the maize fungal pathogen Setosphaeria turcica by whole genome sequencing of isolates from Kenya and Europe and demonstrated that the rapid expansion in Central Europe since the 1980s mainly reflects the rapid growth of the maize cultivation area in this region and not a rapid adaptation to resistant maize varieties. Our analyses show that by monitoring whole genome sequence diversity of plant pathogens and their invasion history, agricultural management and breeding strategies can be developed to control the evolution and future spread of plant pathogens.

category: evolutionary biology


title: Extended kinship analysis of historical remains using SNP capture

abstract: DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target ~25,000 (25K) and ~95,000 (95K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem, with captured DNA having mean insert sizes ranging from 32-170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction in 17 of the 21 pairwise comparisons. The 95K panel increased the average SNPs to 42,000 and resulted in two additional pairwise comparisons (19 of 21). This study provides the groundwork for the expansion of research involving compromised samples to include SNP hybridization capture.

category: genomics


title: Contrasting recruitment of skin-associated adipose depots during cold challenge of mouse and human

abstract:
Mammalian skin impacts metabolic efficiency system-wide, controlling the rate of heat loss and consequent heat production. Here we compare the unique fat depots associated with mouse and human skin, to determine whether they have corresponding function and regulation. For human, we assay a skin-associated fat (SAF) body-wide depot to distinguish it from the subcutaneous fat pads characteristic of abdomen and upper limbs. We show that the thickness of SAF is not related to general adiposity; it is much thicker (1.6-fold) in women than men, and highly subject-specific. We used molecular and cellular assays of {beta}-adrenergic induced lipolysis and found that dermal white adipose tissue (dWAT) in mice is resistant to lipolysis; in contrast, the body-wide human SAF depot becomes lipolytic, generating heat in response to {beta}-adrenergic stimulation. In mice challenged to make more heat to maintain body temperature (either environmentally or genetically), there is a compensatory increase in thickness of dWAT: A corresponding {beta}-adrenergic stimulation of human skin adipose (in vivo or in explant) depletes adipocyte lipid content. We summarize the regulation of skin-associated adipocytes by age, sex, and adiposity, for both species. We conclude that the body-wide dWAT depot of mice shows unique regulation that enables it to be deployed for heat preservation; combined with the actively lipolytic subcutaneous mammary fat pads they enable thermal defense. The adipose tissue that covers human subjects produces heat directly, providing an alternative to the brown adipose tissues.

KEY POINTS SUMMARYO_LISeveral distinct strategies produce and conserve heat to maintain body temperature of mammals, each associated with unique physiologies, with consequence for wellness and disease susceptibility
C_LIO_LIHighly regulated properties of skin offset the total requirement for heat production
C_LIO_LIWe hypothesize that the adipose component of skin is primarily responsible for modulating heat flux; here we evaluate the relative regulation of adipose depots in mouse and human, to test their recruitment to heat production and conservation
C_LIO_LIWe found that insulating mouse dermal white adipose tissue accumulates in response to environmentally- and genetically-induced cool stress; this layer is one of two adipose depots closely apposed to mouse skin, where the subcutaneous mammary gland fat pads are actively recruited to heat production
C_LIO_LIIn contrast, the body-wide adipose depot associated with human skin produces heat directly, potentially creating an alternative to the centrally regulated brown adipose tissue
C_LI

category: physiology


title: Joint language production: an electrophysiological investigation of simulated lexical access on behalf of task partner

abstract: This study investigates in a joint action setting a well-established effect in speech production, cumulative semantic interference, an increase in naming latencies when naming a series of semantically related pictures. In a joint action setting, two task partners take turns naming pictures. Previous work in this setting demonstrated that naming latencies increase not only with each semantically related picture speakers named themselves, but also with each picture named by the partner (Hoedemaker, Ernst, Meyer, & Belke, 2017; Kuhlen & Abdel Rahman, 2017). This suggests that speakers pursue lexical access on behalf of their partner. In two electrophysiological experiments (N=30 each) we investigated the neuro-cognitive signatures of such simulated lexical access. As expected, in both experiments speakers naming latency increased with successive naming instances within a given semantic category. Correspondingly, speakers EEG showed an increasing posterior positivity between 250-400ms, an ERP modulation typically associated with lexical access. However, unlike previous experiments, speakers were not influenced by their partners picture naming. Accordingly, we found no electrophysiological evidence of lexical access. To reconcile these findings we pooled behavioral data from five experiments (N=144). Within this large sample we find empirical evidence for partner-elicited interference. Furthermore, our data suggests that speakers may be less affected by their partners naming response in settings with remotely located task partners (as in present experiments). We conclude that speakers do not always represent their partners naming response and that our experimental setting may have limited the participants evaluation of the task as a joint action.

category: neuroscience


title: Thalamus and claustrum control parallel layer 1 circuits in retrosplenial cortex

abstract: The granular retrosplenial cortex (RSG) is critical for both spatial and non-spatial behaviors, but the underlying neural codes remain poorly understood. Here, we use optogenetic circuit mapping in mice to reveal a double dissociation that allows parallel circuits in superficial RSG to process disparate inputs. The anterior thalamus and dorsal subiculum, sources of spatial information, strongly and selectively recruit small low-rheobase (LR) pyramidal cells in RSG. In contrast, neighboring regular-spiking (RS) cells are preferentially controlled by claustral and anterior cingulate inputs, sources of mostly non-spatial information. Precise sublaminar axonal and dendritic arborization within RSG layer 1, in particular, permits this parallel processing. Observed thalamocortical synaptic dynamics enable computational models of LR neurons to compute the speed of head rotation, despite receiving head direction inputs that do not explicitly encode speed. Thus, parallel input streams identify a distinct principal neuronal subtype ideally positioned to support spatial orientation computations in the RSG.


title: Scribble mutation disrupts convergent extension and apical constriction during mammalian neural tube closure

abstract:
Morphogenesis of the vertebrate neural tube occurs by elongation and bending of the neural plate, tissue shape changes that are driven at the cellular level by polarized cell intercalation and cell shape changes, notably apical constriction and cell wedging. Coordinated cell intercalation, apical constriction, and wedging undoubtedly require complex underlying cytoskeletal dynamics and remodeling of adhesions. Mutations of the gene encoding Scribble result in neural tube defects in mice, however the cellular and molecular mechanisms by which Scrib regulates neural cell behavior remain unknown. Analysis of Scribble mutants revealed defects in neural tissue shape changes, and live cell imaging of mouse embryos showed that the Scrib mutation results in defects in polarized cell intercalation, particularly in rosette resolution, and failure of both cell apical constriction and cell wedging. Scrib mutant embryos displayed aberrant expression of the junctional proteins ZO-1, Par3, Par6, E- and N-cadherins, and the cytoskeletal proteins actin and myosin. These findings show that Scribble has a central role in organizing the molecular complexes regulating the morphomechanical neural cell behaviors underlying vertebrate neurulation, and they advance our understanding of the molecular mechanisms involved in mammalian neural tube closure.

HighlightsO_LIPolarized cell intercalation is lost in Scrib mutant embryos
C_LIO_LIScrib mutation has specific effects on rosette formation and resolution
C_LIO_LIScrib mutation disrupts apical constriction and cell shape changes necessary for neural tube closure
C_LIO_LIAdherens and tight junction composition is altered in the neural epithelial cells of Scrib mutants
C_LI

category: developmental biology


title: A global timing mechanism regulates cell-type specific wiring programs

abstract: The assembly of neural circuits is dependent upon precise spatiotemporal expression of cell recognition molecules1-6. Factors controlling cell-type specificity have been identified7-9, but how timing is determined remains unknown. Here we describe the induction of a cascade of transcription factors by a steroid hormone (Ecdysone) in all fly visual system neurons spanning target recognition and synaptogenesis. We demonstrate through single cell sequencing that the Ecdysone pathway regulates the expression of a common set of targets required for synaptic maturation and cell-type specific targets enriched for cell surface proteins regulating wiring specificity. Transcription factors in the cascade regulate the expression of the same wiring genes in complex ways, including activation in one cell-type and repression in another. We show that disruption of the Ecdysone-pathway generates specific defects in dendritic and axonal processes and synaptic connectivity, with the order of transcription factor expression correlating with sequential steps in wiring. We also identify shared targets of a cell-type specific transcription factor and the Ecdysone pathway which regulate specificity. We propose neurons integrate a global temporal transcriptional module with cell-type specific transcription factors to generate different cell-type specific patterns of cell recognition molecules regulating wiring.


title: Graded spikes differentially signal neurotransmitter input in cerebrospinal fluid contacting neurons of the mouse spinal cord

abstract: The action potential and its all-or-none nature is fundamental to neural communication. Canonically the action potential is initiated once voltage-gated Na+ channels are activated, and their rapid kinetics of activation and inactivation give rise to the action potentials all-or-none nature. Here we show that cerebrospinal fluid contacting neurons (CSFcNs) surrounding the central canal of the mouse spinal cord employ a different strategy. Rather than using voltage-gated Na+ channels to generate binary spikes, CSFcNs use two different types of voltage-gated Ca2+ channel, enabling spikes of different amplitude. T-type Ca2+ channels generate small amplitude spikes, whereas large amplitude spikes require high voltage-activated Cd2+ sensitive Ca2+ channels. We show that these different amplitude spikes signal input from different transmitter systems; purinergic inputs evoke smaller T-type dependent spikes while cholinergic inputs evoke large T-type independent spikes. Different synaptic inputs to CSFcNs can therefore be signalled by the spike amplitude.


title: A neural and behavioral tradeoff underlies exploratory decisions in normative anxiety

abstract: Exploration reduces uncertainty about the environment and improves the quality of future decisions, but at the cost of provisional uncertain and suboptimal outcomes. Although anxiety promotes intolerance to uncertainty, it remains unclear whether and by which mechanisms anxiety modulates exploratory decision-making. We use a dynamic three-armed-bandit task and find that higher trait-anxiety increases exploration, which in turn harms overall performance. We identify two distinct behavioral sources: first, decisions made by anxious individuals were guided towards reduction of uncertainty; and second, decisions were less guided by immediate value gains. Imaging (fMRI) revealed that anxiety correlated negatively with the representation of expected-value in the dorsal-anterior-cingulate-cortex, and in contrast, positively with the representation of uncertainty in the anterior-insula. Moreover, the findings were similar in both loss and gain domains, and demonstrated that affective trait modulates exploration and results in an inverse-U-shaped relationship between anxiety and overall performance. We conclude that a shift in balance towards representation of uncertainty in the insula prevails over reduced value representation in the dACC, and entails maladaptive decision-making in individuals with higher normal-range anxiety.


title: Value, confidence and deliberation: a functional partition of the medial prefrontal cortex across preference tasks

abstract: Deciding about courses of action involves minimizing costs and maximizing benefits. Decision neuroscience studies have implicated both the ventral and dorsal medial prefrontal cortex (vmPFC and dmPFC) in signaling goal value and action cost, but the precise functional role of these regions is still a matter of debate. Here, we suggest a more general functional partition that applies not only to decisions but also to judgments about goal value (expected reward) and action cost (expected effort). In this conceptual framework, cognitive representations related to options (reward value and effort cost) are dissociated from metacognitive representations (confidence and deliberation) related to solving the task (providing a judgment or making a choice). Thus, we used an original approach with the goal of identifying consistencies across several preference tasks, from likeability ratings to binary decisions involving both attribute integration and option comparison. FMRI results confirmed the vmPFC as a generic valuation system, its activity increasing with reward value and decreasing with effort cost. In contrast, more dorsal regions were not concerned with the valuation of options but with metacognitive variables, confidence level being reflected in mPFC activity and deliberation time in dmPFC activity. Thus, there was a dissociation between the effort attached to choice options (represented in the vmPFC) and the effort invested in deliberation (represented in the dmPFC), the latter being expressed in pupil dilation. More generally, assessing commonalities across preference tasks might help reaching a unified view of the neural mechanisms underlying the cost/benefit tradeoffs that drive human behavior.


title: Value, confidence, deliberation: a functional partition of the medial prefrontal cortex demonstrated across valuation and choice tasks


title: Value, confidence, deliberation: a functional partition of the medial prefrontal cortex demonstrated across rating and choice tasks


title: Expression of a modified astrocytic glutamate transporter alleviates Huntington hypokinesia, promotes synaptic glutamate clearance and counteracts potentially adverse EAAT2 interactions

abstract: Rapid removal of glutamate from the sites of glutamate release is an essential step in excitatory synaptic transmission. Despite many years of research, the molecular mechanisms underlying the intracellular regulation of glutamate transport at tripartite synapses have remained unclear. This limits the options for pharmacological treatment of motor disorders associated with glutamate excitotoxicity. Therefore, using the Q175 mouse model of Huntingtons disease (HD), we explored the effects of structural changes in the astrocytic excitatory amino acid transporter type 2 (EAAT2). We report that expression of a C-terminal-modified variant of EAAT2 can alleviate the symptoms of hypokinesia in mice with already advanced HD. At a cellular level, this beneficial outcome correlated with faster synaptic glutamate clearance, higher astrocytic glutamate uptake and larger amounts of native EAAT2 protein. Proteomics data indicate a partial reversal of HD-induced changes in the EAAT2 interactor spectrum. Thus, astrocytic glutamate transport remains a target for therapeutic intervention.


title: Dual strategies in human confidence judgments

abstract: Although confidence is commonly believed to be an essential element in decision making, it remains unclear what gives rise to ones sense of confidence. Recent Bayesian theories propose that confidence is computed, in part, from the degree of uncertainty in sensory evidence. Alternatively, observers can use physical properties of the stimulus as a heuristic to confidence. In the current study, we developed ideal observer models for either hypothesis and compared their predictions against human data obtained from psychophysical experiments. Participants reported the orientation of a stimulus, and their confidence in this estimate, under varying levels of internal and external noise. As predicted by the Bayesian model, we found a consistent link between confidence and behavioral variability for a given stimulus orientation. Confidence was higher when orientation estimates were more precise, for both internal and external sources of noise. However, we observed the inverse pattern when comparing between stimulus orientations: although observers gave more precise orientation estimates for cardinal orientations (a phenomenon known as the oblique effect), they were more confident about oblique orientations. We show that these results are well explained by a strategy to confidence that is based on the perceived amount of noise in the stimulus. Altogether, our results suggest that confidence is not always computed from the degree of uncertainty in ones perceptual evidence, but can instead be based on visual cues that function as simple heuristics to confidence.


title: Neural encoding of reliability of directional information during the preparation of targeted movements

abstract: Visual information about the location of an upcoming target can be used to prepare an appropriate motor response and reduce its reaction time. Here, we investigated the brain mechanisms associated with the reliability of directional information used for motor preparation. We recorded brain activity using magnetoencephalography (MEG) during a delayed reaching task in which a visual cue provided valid information about the location of the upcoming target with 50, 75 or 100% reliability. We found that reaction time increased as cue reliability decreased and that trials with invalid cues had longer reaction times than trials with valid cues. MEG channel analysis showed that during the late cue period the power of the beta-band from left mid-anterior channels, contralateral to the responding hand, correlated with the reliability of the cue. This effect was source localized over a large motor-related cortical and subcortical network. In addition, during invalid-cue trials there was a phasic increase of theta-band power following target onset from left posterior channels, localized to the left occipito-parietal cortex. Furthermore, the theta-beta cross-frequency coupling between left mid-occipital and motor cortex transiently increased before responses to invalid-cue trials. In conclusion, beta-band power in motor-related areas reflected the reliability of directional information used during motor preparation, whereas phasic theta-band activity may have signaled whether the target was at the expected location or not. These results elucidate mechanisms of interaction between attentional and motor processes.


title: Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulationembryos

abstract: In recent years, allele-specific single-cell RNA-seq (scRNA-seq) analysis has demonstrated wide-spread dynamic random monoallelic expression of autosomal genes (aRME) in different cell types. However, the prevalence of dynamic aRME during pre-gastrulation development remains unknown. Here, we show that dynamic aRME is wide-spread in different lineages of pre-gastrulation embryos. Additionally, the origin of dynamic aRME remains poorly understood. Theoretically, it is believed that independent transcriptional bursting from each allele leads to the dynamic aRME. However, based on analysis of allele-specific burst kinetics of autosomal genes, we found that allelic burst is not perfectly independent, rather it happens in semi-coordinated fashion. Importantly, we show that semi-coordinated allelic bursting of the genes; particularly with low burst frequency, leads to frequent asynchronous allelic bursting, thereby shaping the landscape of dynamic aRME in pre-gastrulation embryos. Altogether, our study provides significant insight into the prevalence and origin of dynamic aRME and cell to cell expression heterogeneity during early mammalian development. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

category: genetics


title: Consistent ultra-long DNA sequencing with automated slow pipetting

abstract:
BackgroundOxford Nanopore Technologies instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules through library preparation by pipetting reagents as slowly as possible to minimize shearing. This process is time-consuming and inconsistent at preserving read length as even small changes in volumetric flow rate can result in template shearing.

ResultsWe have designed SNAILS (Slow Nucleic Acid Instrument for Long Sequences), a 3D-printable instrument that automates slow pipetting of reagents used in long read library preparation for Oxford Nanopore sequencing. Across six sequencing libraries, SNAILS preserved more reads exceeding one hundred kilobases in length and increased its libraries average read length over manual slow pipetting.

ConclusionsSNAILS is a low-cost, easily deployable solution for improving sequencing projects that require reads of significant length. By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing.


title: Processing variables of direct-write, near-field electrospinning impact size and morphology of gelatin fibers

abstract: Several biofabrication methods are being investigated to produce scaffolds that can replicate the structure of the extracellular matrix. Direct-write, near-field electrospinning of polymer solutions and melts is one such method which combines fine fiber formation with computer-guided control. Research with such systems has focused primarily on synthetic polymers. To better understand the behavior of biopolymers used for direct-writing, this project investigated changes in fiber morphology, size, and variability caused by varying gelatin and acetic acid concentration, as well as process parameters such as needle gauge and height, stage speed, and interfiber spacing. Increasing gelatin concentration at a constant acetic acid concentration improved fiber morphology from large, planar structures to small, linear fibers with a median of 2.3 m. Further varying the acetic acid concentration at a constant gelatin concentration did not alter fiber morphology and diameter throughout the range tested. Varying needle gauge and height further improved the median fiber diameter to below 2 m and variability of the first and third quartiles to within +/-1 m of the median for the optimal solution combination of gelatin and acetic acid concentrations. Additional adjustment of stage speed did not impact the fiber morphology or diameter. Repeatable interfiber spacings down to 250 m were shown to be capable with the system. In summary, this study illustrates the optimization of processing parameters for direct-writing of gelatin to produce fibers on the scale of collagen fibers. This system is thus capable of replicating the fibrous structure of musculoskeletal tissues with biologically relevant materials which will provide a durable platform for the analysis of single cell-fiber interactions to help better understand the impact scaffold materials and dimensions have on cell behavior.

category: bioengineering


title: GREEN-DB: A framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data

abstract: Non-coding variants have emerged as important contributors to the pathogenesis of human diseases, not only as common susceptibility alleles but also as rare high-impact variants. Despite recent advances in the study of regulatory elements and the availability of specialized data collections, the systematic annotation of non-coding variants from genome sequencing remains challenging. Here, we propose a new framework for the prioritization of non-coding regulatory variants that integrates information about regulatory regions with prediction scores and HPO-based prioritization. Firstly, we created a comprehensive collection of annotations for regulatory regions including a curated database of 2.4 million regulatory elements (GREEN-DB) annotated with controlled gene(s), tissue(s) and associated phenotype(s) where available. Secondly, we calculated a variation constraint metric and showed that constrained regulatory regions associate with disease-associated genes and essential genes from mouse knock-out screens. Thirdly, we compared 19 non-coding impact prediction scores providing suggestions for variant prioritization. Finally, we developed a VCF annotation tool (GREEN-VARAN) that can integrate all these elements to annotate variants for their potential regulatory impact. In our evaluation, we show that GREEN-DB can capture previously published disease-associated non-coding variants as well as identify additional candidate disease genes in WGS trio analyses.

category: bioinformatics


title: Potent activation of SARM1 by NMN analogue VMN underlies vacor neurotoxicity

abstract: Axon loss underlies symptom onset and progression in many neurodegenerative disorders. Axon degeneration in injury and disease is promoted by activation of the nicotinamide adenine dinucleotide (NAD)-consuming enzyme SARM1 (sterile alpha and TIR motif-containing protein 1). Here, we report vacor mononucleotide (VMN), a metabolite of the pesticide and neurotoxin vacor, as the most potent yet SARM1 activator. Removal of SARM1 shows complete rescue from vacor-induced neuron and axon death in vitro and in vivo. We present the crystal structure of VMN bound to the Drosophila SARM1 regulatory armadillo-repeat domain, thus facilitating drug development to prevent SARM1 activation in human disease. This study indicates the likely mechanism of action of vacor as a pesticide and lethal neurotoxin in humans, provides important new tools for drug discovery, and further demonstrates that SARM1 removal can permanently block programmed axon death specifically induced by toxicity as well as genetic mutation.


title: The stem loop 2 motif is a site of vulnerability for SARS-CoV-2

abstract: RNA structural elements occur in numerous single stranded (+)-sense RNA viruses. The stemloop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 3 UTR in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including SARS-CoV and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts implicates a key role of s2m in the viral infection cycle. Our findings indicate that the element, while stably folded, can nonetheless be invaded and remodelled spontaneously by antisense oligonucleotides (ASOs) that initiate pairing in exposed loops and trigger efficient sequence-specific RNA cleavage in reporter assays. ASOs also act to inhibit replication in an astrovirus replicon model system in a sequence-specific, dose-dependent manner and inhibit SARS-CoV-2 infection in cell culture. Our results thus permit us to suggest that the s2m element is a site of vulnerability readily targeted by ASOs, which show promise as anti-viral agents.

category: molecular biology


title: LiftPose3D, a deep learning-based approach for transforming 2D to 3D pose in laboratory animals

abstract: Markerless 3D pose estimation has become an indispensable tool for kinematic studies of laboratory animals. Most current methods recover 3D pose by multi-view triangulation of deep network-based 2D pose estimates. However, triangulation requires multiple, synchronized cameras and elaborate calibration protocols that hinder its widespread adoption in laboratory studies. Here, we describe LiftPose3D, a deep network-based method that overcomes these barriers by reconstructing 3D poses from a single 2D camera view. We illustrate LiftPose3Ds versatility by applying it to multiple experimental systems using flies, mice, rats, and macaque monkeys and in circumstances where 3D triangulation is impractical or impossible. Our framework achieves accurate lifting for stereotyped and non-stereotyped behaviors from different camera angles. Thus, LiftPose3D permits high-quality 3D pose estimation in the absence of complex camera arrays, tedious calibration procedures, and despite occluded body parts in freely behaving animals.

category: animal behavior and cognition


title: Multiscale model of heart growth during pregnancy: Integrating mechanical and hormonal signaling

abstract: Pregnancy stands at the interface of mechanics and biology. The growing fetus continuously loads the maternal organs as circulating hormone levels surge, leading to significant changes in mechanical and hormonal cues during pregnancy. In response, maternal soft tissues undergo remarkable growth and remodeling to support the mother and baby for a healthy pregnancy. We focus on the maternal left ventricle, which increases its cardiac output and mass during pregnancy. This study develops a multiscale cardiac growth model for pregnancy to understand how mechanical and hormonal cues interact to drive this growth process. We coupled a cell signaling network model that predicts cell-level hypertrophy in response to hormones and stretch to a compartmental model of the rat heart and circulation that predicts organ-level growth in response to hemodynamic changes. We calibrated this multiscale model to data from experimental volume overload (VO) and hormonal infusions of angiotensin 2 (AngII), estrogen (E2), and progesterone (P4). We then validated the models ability to capture interactions between inputs by comparing model predictions against published observations for the combinations of VO+E2 and AngII+E2. Finally, we simulated pregnancy-induced changes in hormones and hemodynamics to predict heart growth during pregnancy. Our model produced growth consistent with experimental data. Overall, our analysis suggests that the rise in P4 during the first half of gestation is an important contributor to heart growth during pregnancy. We conclude with suggestions for future experimental studies that will provide a better understanding of how hormonal and mechanical cues interact to drive pregnancy-induced heart growth.


title: MetaFusion: A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates.

abstract:
MotivationCurrent fusion detection tools use diverse calling approaches and provide varying results, making selection of the appropriate tool challenging. Ensemble fusion calling techniques appear promising; however, current options have limited accessibility and function.

ResultsMetaFusion is a flexible meta-calling tool that amalgamates outputs from any number of fusion callers. Individual caller results are standardized by conversion into the new file type Common Fusion Format (CFF). Calls are annotated, merged using graph clustering, filtered, and ranked to provide a final output of high confidence candidates. MetaFusion consistently achieves higher precision and recall than individual callers on real and simulated datasets, and reaches up to 100% precision, indicating that ensemble calling is imperative for high confidence results. MetaFusion uses FusionAnnotator to annotate calls with information from cancer fusion databases, and is provided with a benchmarking toolkit to calibrate new callers.

AvailabilityMetaFusion is freely available at https://github.com/ccmbioinfo/MetaFusion

Contactarun.ramani@sickkids.ca

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides

abstract:
AimA  leaky gut barrier has been implicated in the initiation and progression of a multitude of diseases, e.g., inflammatory bowel disease, irritable bowel syndrome, celiac disease, and colorectal cancers. Here we show how pro-hormone Chromogranin A (CgA), produced by the enteroendocrine cells, and Catestatin (CST: hCgA352-372), the most abundant CgA-derived proteolytic peptide, affect the gut barrier.

MethodsColon tissues from region-specific CST-knockout (CST-KO) mice, CgA-knockout (CgA-KO) and WT mice were analyzed by immunohistochemistry, ultrastructural and flowcytometry studies. FITC-dextran assays were used to measure intestinal barrier function. Mice were supplemented with CST or CgA fragment pancreastatin (PST: CgA250-301). The microbial composition of cecum was determined. CgA and CST levels were measured in blood of IBD patients.

ResultsCST-KO mice displayed (i) elongated tight, adherens junctions and desmosomes similar to IBD patients, and (ii) gut inflammation. Consistently, plasma FITC-dextran measurements showed increased intestinal paracellular permeability in the CST-knockout mice. This correlated with a higher ratio of Firmicutes to Bacteroidetes, a dysbiotic pattern commonly encountered in various diseases. Supplementation of CST-knockout mice with recombinant CST restored paracellular permeability and reversed inflammation, whereas CgA-knockout mice supplementation with CST and/or PST in CgA-KO mice showed that intestinal paracellular permeability is regulated by the antagonistic roles of these two peptides: CST reduces and PST increases permeability.

ConclusionThe pro-hormone CgA regulates the intestinal paracellular permeability. CST is both necessary and sufficient to reduce permeability and primarily acts via antagonizing the effects of PST.


title: Seed morphological traits as a tool to quantify variation maintained in ex situ collections: a case study in Pinus torreyana (Parry)

abstract:
BackgroundUnderstanding the within- and among-population distribution of trait variation within seed collections may provide a means to approximate standing genetic variation and inform plant conservation.

AimsThis study aimed to estimate population- and family-level seed trait variability for existing seed collections of Torrey pine (Pinus torreyana), and to use these data to guide sampling of future collections.

MethodsWe quantified variation in 14 seed morphological traits and seedling emergence within and among Torrey pine populations. Using a simulation-based approach, we used estimates of within-population variance to assess the number of maternal families required to capture 95% of trait variation within each existing seed collection.

ResultsSubstantial structure was observed both within and among Torrey pine populations, with island and mainland seeds varying in seed size and seed coat thickness. Despite morphological differences, seedling emergence was similar across populations. Simulations revealed that 83% and 71% of all maternal families within island and mainland seed collections respectively needed to be resampled to capture 95% of seed trait variation within existing collections.

ConclusionsFrom a conservation perspective, our results indicate that to optimize genetic diversity captured in Torrey pine seed collections, maximizing the number of maternal families sampled within each population will be necessary.

category: plant biology


title: Orbitofrontal cortex and learning predictions of state transitions

abstract:
Learning the transition structure of the environment - the probabilities of transitioning from one environmental state to another - is a key prerequisite for goal-directed planning and model-based decision making. To investigate the role of the orbitofrontal cortex (OFC) in goal-directed planning and decision making, we used fMRI to assess univariate and multivariate activity in the OFC while humans experienced state transitions that varied in degree of surprise. Converging with recent evidence, we found that OFC activity was related to greater learning about transition structure. However, the observed relationship was inconsistent with a straightforward interpretation of OFC activity as representing a state prediction error that would facilitate learning of transitions via error-correcting mechanisms. The state prediction error hypothesis predicts that OFC activity at the time of observing an outcome should increase expectation of that same observed outcome on subsequent trials. Instead, our results showed that OFC activity was associated with increased expectation of the more probable outcome; that is, with more optimal predictions. These results suggest that the OFC is involved in updating or reinforcing a learned transition model on a trial-by-trial basis, specifically for the currently observed cue-outcome associations. Our findings add to the evidence of OFC involvement in learning state-to-state transition structure, while providing new constraints for algorithmic hypotheses regarding how these transitions are learned.

Significance StatementThe orbitofrontal cortex (OFC) has been implicated in model-based decision making--the kind of decisions that result from planning using an "environment model" of how current actions affect our future states. However, the widely suggested role of the OFC in representing expected values of future states is not sufficient to explain why the OFC would be critical for planning in particular. A new line of evidence implicates the OFC in learning about transition structure of the environment - a key component of the "environment model" used for planning. We investigate this function, adding to the growing literature on the role of the OFC in learning and decision making, while unveiling new questions about the algorithmic role of OFC in goal-directed planning.


title: Comparison of multiple tractography methods for reconstruction of the retinogeniculate visual pathway using diffusion MRI

abstract: The retinogeniculate visual pathway (RGVP) conveys visual information from the retina to the lateral geniculate nucleus. The RGVP has four subdivisions, including two decussating and two non-decussating pathways that cannot be identified on conventional structural magnetic resonance imaging (MRI). Diffusion MRI tractography has the potential to trace these subdivisions and is increasingly used to study the RGVP. However, it is not yet known which fiber tracking strategy is most suitable for RGVP reconstruction. In this study, four tractography methods are compared, including constrained spherical deconvolution (CSD) based probabilistic (iFOD1) and deterministic (SD-Stream) methods, and multi-fiber (UKF-2T) and single-fiber (UKF-1T) unscented Kalman filter (UKF) methods. Experiments use diffusion MRI data from 57 subjects in the Human Connectome Project. The RGVP is identified using regions of interest created by two clinical experts. Quantitative anatomical measurements and expert anatomical judgment are used to assess the advantages and limitations of the four tractography methods. Overall, we conclude that UKF-2T and iFOD1 produce the best RGVP reconstruction results. The iFOD1 method can better quantitatively estimate the percentage of decussating fibers, while the UKF-2T method produces reconstructed RGVPs that are judged to better correspond to the known anatomy and have the highest spatial overlap across subjects. Overall, we find that it is challenging for current tractography methods to both accurately track RGVP fibers that correspond to known anatomy and produce an approximately correct percentage of decussating fibers. We suggest that future algorithm development for RGVP tractography should take consideration of both of these two points.


title: Dimerization mechanism and structural features of human LI-cadherin

abstract: LI-cadherin is a member of the cadherin superfamily, which encompasses a group of Ca2+-dependent cell adhesion proteins. The expression of LI-cadherin is observed on various types of cells in the human body, such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gastric cancer imaging. However, since the cell adhesion mechanism of LI-cadherin has remained unknown, rational design of therapeutic molecules targeting this cadherin has been hampered. Here, we have studied the homodimerization mechanism of LI-cadherin. We report the crystal structure of the LI-cadherin EC1-4 homodimer. The EC1-4 homodimer exhibited a unique architecture different from that of other cadherins reported so far. The crystal structure also revealed that LI-cadherin possesses a noncanonical calcium ion-free linker between EC2 and EC3. Various biochemical techniques and molecular dynamics (MD) simulations were employed to elucidate the mechanism of homodimerization. We also showed that the formation of the homodimer observed by the crystal structure is necessary for LI-cadherin-dependent cell adhesion by performing cell aggregation assay.

category: biochemistry


title: Orchestrating and sharing large multimodal data for transparent and reproducible research

abstract: Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA (orcestra.ca), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.


title: Measuring competitive exclusion in non-small cell lung cancer

abstract: Therapeutic strategies for tumor control have traditionally assumed that maximizing reduction in tumor volume correlates with clinical efficacy. Unfortunately, this rapid decrease in tumor burden is almost invariably followed by the emergence of therapeutic resistance. Evolutionary based treatment strategies attempt to delay resistance via judicious treatments that maintain a significant treatable subpopulation. While these strategies have shown promise in recent clinical trials, they often rely on biological conjecture and intuition to derive parameters. In this study we experimentally measure the frequency-dependent interactions between a gefitinib resistant non-small cell lung cancer (NSCLC) population and its sensitive ancestor via the evolutionary game assay. We show that cost of resistance is insufficient to accurately predict competitive exclusion and that frequency-dependent growth rate measurements are required. In addition, we show that frequency-dependent growth rate changes may ultimately result in a safe harbor for resistant populations to safely accumulate, even those with significant cost of resistance. Using frequency-dependent growth rate data we then show that gefitinib treatment results in competitive exclusion of the ancestor, while absence of treatment results in a likely, but not guaranteed exclusion of the resistant strain. Finally, using our empirically derived growth rates to constrain simulations, we demonstrate that incorporating ecological growth effects can dramatically change the predicted time to sensitive strain extinction. In addition, we show that higher drug concentrations may not lead to the optimal reduction in tumor burden. Taken together, these results highlight the potential importance of frequency-dependent growth rate data for understanding competing populations, both in the laboratory and the clinic.

category: cancer biology


title: Age and Sex Effects on Advanced White Matter Microstructure Measures in 15,628 UKBiobank Participants

abstract: A comprehensive characterization of the brains white matter is critical for improving our understanding of healthy and diseased aging. Here we used diffusion-weighted magnetic resonance imaging (dMRI) to estimate age and sex effects on white matter microstructure in a cross-sectional sample of 15,628 adults aged 45-80 years old (47.6% male, 52.4% female). Microstructure was assessed using the following four models: a conventional single-shell model, diffusion tensor imaging (DTI); a more advanced single-shell model, the tensor distribution function (TDF); an advanced multi-shell model, neurite orientation dispersion and density imaging (NODDI); and another advanced multi-shell model, mean apparent propagator MRI (MAPMRI). Age was modeled using a data-driven statistical approach, and normative centile curves were created to provide sex-stratified white matter reference charts. Participant age and sex substantially impacted many aspects of white matter microstructure across the brain, with the advanced dMRI models TDF and NODDI detecting such effects the most sensitively. These findings and the normative reference curves provide an important foundation for the study of healthy and diseased brain aging.


title: Age and Sex Effects on Advanced White Matter Microstructure Measures in 15,628 Older Adults: A UK Biobank Study


title: Cryo-EM of a viral RNA and RNA-protein complex reveals how structural dynamics and novel tRNA mimicry combine to hijack host machinery

abstract: Viruses require multifunctional structured RNAs to hijack their hosts biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo-EM, we visualized the structure of the mysterious viral tRNA-like structure (TLS) from brome mosaic virus (BMV), which affects replication, translation, and genome encapsidation. Structures in isolation and bound to tyrosyl-tRNA synthetase (TyrRS) show that this [~]55 kDa purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs dramatically from tRNA. Our studies reveal how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions and highlights the utility of cryo-EM for visualizing small conformationally dynamic structured RNAs.

category: biophysics


title: Force generation by protein-DNA co-condensation

abstract: Interactions between liquids and surfaces generate forces1,2 that are crucial for many processes in biology, physics, and engineering, including the motion of insects on the surface of water3, modulation of the material properties of spider silk4, and self-assembly of microstructures5. Recent studies have shown that cells assemble biomolecular condensates via phase separation6. In the nucleus, these condensates are thought to drive transcription7, heterochromatin formation8, nucleolus assembly9, and DNA repair10. Here, we show that the interaction between liquid-like condensates and DNA generates forces that might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, optical tweezers, and theory to show that the transcription factor FoxA1 mediates the condensation of a DNA-protein phase via a mesoscopic first- order phase transition. After nucleation, co-condensation forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA in close proximity, suggesting that this physical mechanism is a possible general regulatory principle for chromatin organization that may be relevant in vivo.


title: Auditory Target Detection Enhances Visual Processing and Hippocampal Functional Connectivity

abstract: Though dividing ones attention between two input streams typically impairs performance, detecting a behaviorally relevant stimulus can sometimes enhance the encoding of unrelated information presented at the same time. Previous research has shown that selection of this kind boosts visual cortical activity and memory for concurrent items. An important unanswered question is whether such effects are reflected in processing quality and functional connectivity in visual regions and in the hippocampus. In this fMRI study, participants were asked to memorize a stream of naturalistic images and press a button only when they heard a predefined target tone (400 or 1200 Hz, counterbalanced). Images could be presented with a target tone, with a distractor tone, or without a tone. Auditory target detection increased activity throughout the ventral visual cortex but lowered it in the hippocampus. Enhancements in functional connectivity between the ventral visual cortex and the hippocampus were also observed following auditory targets. Multi-voxel pattern classification of image category was more accurate on target tone trials than on distractor and no tone trials in the fusiform gyrus and parahippocampal gyrus. This effect was stronger in visual cortical clusters whose activity was more correlated with the hippocampus on target tone than on distractor tone trials. In agreement with accounts suggesting that subcortical noradrenergic influences play a role in the attentional boost effect, auditory target detection also caused an increase in locus coeruleus activity and phasic pupil responses. These findings outline a network of cortical and subcortical regions that are involved in the selection and processing of information presented at behaviorally relevant moments.


title: SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads

abstract: The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (SHIMS). In recent years, improvements to SHIMS have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we describe SHIMS 3.0, an extension of our SHIMS sequencing strategy, using ultra-long nanopore reads to augment the Illumina data from SHIMS 2.0 assemblies and resolve internally repetitive structures. This greatly minimizes the need for manual finishing of Illumina-based draft assemblies, allowing a small team with no prior finishing experience to sequence challenging targets with high accuracy. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about 80 dollars per clone. We recently used this protocol to produce reference sequence of structurally complex palindromes on chimpanzee and rhesus macaque X chromosomes; as a further demonstration of the capabilities of SHIMS 3.0, we finish the TSPY array on the human Y chromosome, which could not be resolved by previous sequencing methods. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.


title: Evolutionary and Structural Constraints Influencing Apolipoprotein A-I Amyloid Behavior

abstract: Apolipoprotein A-I (apoA-I) has a key function in the reverse cholesterol transport mediated by the high density lipoprotein (HDL) particles. However, aggregation of apoA-I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural impacts introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA-I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation-prone regions (APRs) present in apoA-I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA-I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA-I. Structural properties of the full-length apoA-I model suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Following we set up to study the effect of natural mutations on protein conformation and stability. Compared to natural silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of apoA-I amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha-helix bundle with the concomitant exposure of APR1 to the solvent and the formation of beta-sheet segments at the C-terminus of apoA-I, giving a possible hint about the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA-I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region. This information contributes to our understanding of how apoA-I, with its high degree of structural flexibility, maintains a delicate equilibrium between its monomeric native structure and intrinsic tendency to form amyloid aggregates. In addition, our stability measurements could be used as a proxy to interpret the structural impact of new mutations.


title: HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks

abstract:
Signaling networks mediate many aspects of cellular function. The conventional, mechanistically motivated approach to modeling such networks is through mass-action chemistry, which maps directly to biological entities and facilitates experimental tests and predictions. However such models are complex, need many parameters, and are computationally costly. Here we introduce the HillTau form for signaling models. HillTau retains the direct mapping to biological observables, but it uses far fewer parameters, and is 100 to over 1000 times faster than ODE-based methods. In the HillTau formalism, the steady-state concentration of signaling molecules is approximated by the Hill equation, and the dynamics by a time-course tau. We demonstrate its use in implementing several biochemical motifs, including association, inhibition, feedforward and feedback inhibition, bistability, oscillations, and a synaptic switch obeying the BCM rule. The major use-cases for HillTau are system abstraction, model reduction, scaffolds for data-driven optimization, and fast approximations to complex cellular signaling.

Author summaryChemical signals mediate many computations in cells, from housekeeping functions in all cells to memory and pattern selectivity in neurons. These signals form complex networks of interactions. Computer models are a powerful way to study how such networks behave, but it is hard to get all the chemical details for typical models, and it is slow to run them with standard numerical approaches to chemical kinetics. We introduce HillTau as a simplified way to model complex chemical networks. HillTau models condense multiple reaction steps into single steps defined by a small number of parameters for activation and settling time. As a result the models are simple, easy to find values for, and they run quickly. Remarkably, they fit the full chemical formulations rather well. We illustrate the utility of HillTau for modeling several signaling network functions, and for fitting complicated signaling networks.

category: systems biology


title: Dorsal Anterior Cingulate Cortex Encodes the Integrated Incentive Motivational Value of Cognitive Task Performance

abstract:
Humans can seamlessly combine value signals from diverse motivational incentives, yet it is not well-understood how these signals are "bundled" in the brain to modulate cognitive control. The dorsal anterior cingulate cortex (dACC) is theorized to integrate motivational value dimensions in the service of goal-directed action, though this hypothesis has yet to receive rigorous confirmation. In the present study, we examined the role of human dACC in motivational incentive integration. Healthy young adult men and women were scanned with fMRI while engaged in an experimental paradigm that quantifies the combined effects of liquid (e.g., juice, neutral, saltwater) and monetary incentives on cognitive task performance. Monetary incentives modulated trial-by-trial dACC activation, whereas block-related effects of liquid incentives on dACC activity were observed. When bundled together, incentive-related dACC modulation predicted fluctuations in both cognitive performance and self-report motivation ratings. Statistical mediation analyses suggest that dACC encoded the incentives in terms of their integrated subjective motivational value, and that this value signal was most proximally associated with task performance. Finally, we confirmed that these incentive integration effects were selectively present in dACC. Together, the results support an account in which dACC integrates motivational signals to compute the expected value of goal-directed cognitive control.

Significance StatementHow are primary and secondary incentives integrated in the brain to influence goal-directed behavior? Using an innovative experimental fMRI paradigm that combines motivational incentives that have historically been studied independently between species (e.g., monetary rewards for humans, food rewards for animals), we examine the relationship between incentive motivational value and cognitive control allocation. We find evidence that the integrated incentive motivational value of combined incentives is encoded in human dorsal anterior cingulate cortex (dACC). Further, self-reported motivational shifts mediated the effects of incentive-modulated dACC activity on task performance, revealing convergence in how self-reported and experimentally-induced motivation are encoded in the human brain. Our findings may inform future translational studies examining affective/motivational and cognitive impairments in psychopathology (e.g., anxiety, depression, addiction).


title: Oxytocin administration in neonates shapes the hippocampal circuitry and restores social behavior in a mouse model of autism.

abstract:
Oxytocin is a master regulator of the social brain. In some animal models of autism, notably in Magel2 tm1.1Mus-deficient mice, peripheral administration of oxytocin in infancy improves social behaviors until adulthood. However, neither the mechanisms responsible for social deficits nor the mechanisms by which such oxytocin administration has long-term effects are known. Here, we aimed to clarify these oxytocin-dependent mechanisms focusing on social memory performance.

We showed that Magel2tm1.1Mus-deficient mice present a deficit in social memory and studied the hippocampal circuits underlying this memory. We showed a co-expression of Magel2 and oxytocin-receptor in the dentate gyrus and CA2/CA3 hippocampal regions. Then, we demonstrated: an increase of the GABAergic activity of CA3-pyramidal cells associated with an increase in the quantity of oxytocin-receptors and of somatostatin interneurons. We also revealed a delay in the GABAergic development sequence in Magel2tm1.1Mus-deficient pups, linked to phosphorylation modifications of KCC2. Above all, we demonstrated the positive effects of subcutaneous administration of oxytocin in the mutant neonates, restoring neuronal alterations and social memory.

Although clinical trials are debated, this study highlights the mechanisms by which peripheral oxytocin-administration in neonates impacts the brain and demonstrates the therapeutic value of oxytocin to treat infants with autism spectrum disorders.


title: MYC uncouples HIF target gene expression from glycolytic flux in hypoxic proliferating primary cells

abstract: Hypoxia requires metabolic adaptations to sustain cellular functions that underlie numerous physiologic and pathologic processes. While many studies have explored the metabolic consequences of hypoxia in cancer models, comparatively little is known about the metabolic response of primary cells to hypoxia. Here, we performed metabolic flux analyses of proliferating human lung fibroblasts and pulmonary artery smooth muscle cells in hypoxia. Unexpectedly, glycolytic flux was decreased in hypoxic cells despite activation of the hypoxia-inducible factor (HIF) transcriptional program and increased expression of glycolytic enzymes. Pharmacologic activation of HIF with the prolyl hydroxylase (PHD) inhibitor molidustat in normoxia did increase glycolytic flux, but hypoxia abrogated this effect. Multi-omic profiling of cells treated with hypoxia or molidustat, separately or together, revealed distinct molecular responses to hypoxia and pharmacologic PHD inhibition and suggested a critical role for MYC in modulating the HIF response in hypoxia. MYC knockdown in hypoxia increased lactate efflux while MYC overexpression in normoxia blunted the effects of molidustat treatment. Together, these data suggest that other factors, notably MYC, supersede the anticipated effects of HIF-dependent up-regulation of glycolytic gene expression on glycolytic flux in hypoxic proliferating primary cells.

category: cell biology


title: Deciphering how interneuron specific 3 cells control oriens lacunosum-moleculare cells to contribute to circuit function

abstract:
The wide diversity of inhibitory cells across the brain makes them suitable to contribute to network dynamics in specialized fashions. However, the contributions of a particular inhibitory cell type in a behaving animal are challenging to untangle as one needs to both record cellular activities and identify the cell type being recorded. Thus, using computational modeling and theory to predict and hypothesize cell-specific contributions is desirable. Here, we examine potential contributions of interneuron-specific 3 (I-S3) cells - an inhibitory interneuron found in CA1 hippocampus that only targets other inhibitory interneurons - during simulated theta rhythms. We use previously developed multi-compartment models of oriens lacunosum-moleculare (OLM) cells, the main target of I-S3 cells, and explore how I-S3 cell inputs during in vitro and in vivo scenarios contribute to theta. We find that I-S3 cells suppress OLM cell spiking, rather than engender its spiking via post-inhibitory rebound mechanisms, and contribute to theta frequency spike resonance during simulated in vivo scenarios. To elicit recruitment similar to in vitro experiments, inclusion of disinhibited pyramidal cell inputs is necessary, implying that I-S3 cell firing broadens the window for pyramidal cell disinhibition. Using in vivo virtual networks, we show that I-S3 cells contribute to a sharpening of OLM cell recruitment at theta frequencies. Further, shifting the timing of I-S3 cell spiking due to external modulation shifts the timing of the OLM cell firing and thus disinhibitory windows. We propose a specialized contribution of I-S3 cells to create temporally precise coordination of modulation pathways.

New & NoteworthyHow information is processed across different brain structures is an important question that relates to the different functions that the brain performs. Using modelling and theoretical analyses, we show that an inhibitory cell type that only inhibits other inhibitory cells can broaden the window for disinhibition of excitatory cells, manage input pathway switching, and modulate inhibitory cell spiking. This work contributes to knowledge of how coordination between sensory and memory consolidation information can be attained.


title: Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects human cells upon binding of its spike (S) glycoproteins to ACE2 receptors and causes the coronavirus disease 2019 (COVID-19). Therapeutic approaches to prevent SARS-CoV-2 infection are mostly focused on blocking S-ACE2 binding, but critical residues that stabilize this interaction are not well understood. By performing all-atom molecular dynamics (MD) simulations, we identified an extended network of salt bridges, hydrophobic and electrostatic interactions, and hydrogen bonding between the receptor-binding domain (RBD) of the S protein and ACE2. Mutagenesis of these residues on the RBD was not sufficient to destabilize binding but reduced the average work to unbind the S protein from ACE2. In particular, the hydrophobic end of RBD serves as the main anchor site and unbinds last from ACE2 under force. We propose that blocking the hydrophobic surface of RBD via neutralizing antibodies could prove an effective strategy to inhibit S-ACE2 interactions.

category: immunology


title: Antihypertensive effect of brain-targeted mechanical intervention with passive head motion

abstract: Physical exercise is known to be beneficial for various brain functions. However, the mechanisms behind the positive effects of exercise on the brain remain to be elucidated. Here we show that passive head motion in hypertensive rats, which reproduces the mechanical accelerations generated in their heads during moderate-velocity treadmill running, decreases the expression of angiotensin II type 1 receptor (AT1R) in astrocytes in the rostral ventrolateral medulla (RVLM), thereby lowering blood pressure. Passive head motion generates interstitial fluid movement that is estimated to exert shear stress with an average magnitude of <1 Pa on the cells in the rat medulla. Fluid shear stress of a sub-Pa magnitude decreases AT1R expression in cultured astrocytes. In hypertensive rats, inhibition of interstitial fluid movement following hydrogel introduction to the RVLM eliminates the antihypertensive effects of passive head motion and treadmill running. Furthermore, vertically oscillating chair riding by hypertensive adult humans, which reproduces the mechanical accelerations generated in their heads during light jogging or fast walking, lowers their blood pressure. Our findings indicate that moderate mechanical intervention can have antihypertensive effects by modulating the function of RVLM astrocytes through interstitial fluid shear stress. We anticipate that mechanical regulation is responsible for a variety of the positive effects of physical exercise on human health, particularly those related to brain functions.


title: Expansion of CD10neg neutrophils and CD14+HLA-DRneg/low monocytes driving proinflammatory responses in patients with acute myocardial infarction

abstract: Immature neutrophils and HLA-DRneg/low monocytes expand in cancer, autoimmune diseases and viral infections, but their appearance and functional characteristics after acute myocardial infarction (AMI) remain underexplored. We found an expansion of circulating immature CD16+CD66b+CD10neg neutrophils and CD14+HLA-DRneg/low monocytes in patients with AMI, correlating with cardiac damage, function and serum levels of immune-inflammation markers. Increased frequency of immature CD10neg neutrophils and elevated circulating levels of IFN-{gamma} were linked, mainly in cytomegalovirus (CMV)-seropositive patients with high anti-CMV antibody titers and expanded CD4+CD28null T-cells. At a mechanistic level, CD10neg neutrophils enhance IFN-{gamma} production by CD4+ T-cells through induction of interleukin-12. Moreover, we showed that HLA-DRneg/low monocytes are not immunosuppressive but secrete high levels of pro-inflammatory cytokines after differentiation to macrophages and IFN-{gamma} stimulation. Thus, the immunoregulatory functions of immature CD10neg neutrophils play a dynamic role in mechanisms linking myeloid cell compartment dysregulation, Th1-type immune responses and inflammation in patients with AMI.


title: Robust differentiation of human enteroendocrine cells from intestinal stem cells

abstract: Enteroendocrine (EE) cells are the most abundant hormone-producing cells in humans and are critical regulators of energy homeostasis and gastrointestinal function. Challenges in converting human intestinal stem cells (ISCs) into functional EE cells, ex vivo, have limited progress in elucidating their role in disease pathogenesis and in harnessing their therapeutic potential. To address this, we employed small molecule targeting of the endocannabinoid receptor signaling pathway, JNK and FOXO1, known to mediate endodermal development and/or hormone production, together with directed differentiation of human ISCs from the duodenum and rectum. We observed marked induction of EE cell differentiation and gut-derived expression and secretion of SST, 5HT, GIP, CCK, GLP-1 and PYY upon treatment with various combinations of three small molecules: rimonabant, SP600125 and AS1842856. Robust differentiation strategies capable of driving human EE cell differentiation is a critical step towards understanding these essential cells and the development of cell-based therapeutics.


title: The complex evolution of the metazoan HSP70 gene family

abstract: The metazoan 70-kDa heat shock protein (HSP70) family contains several members localized in different subcellular compartments. The cytosolic members have been classified into inducible HSP70s and constitutive heat shock cognates (HSC70s), but their distinction and evolutionary relationship remain unclear because of occasional reports of "constitutive HSP70s" and the lack of cross-phylum comparisons. Here we provide novel insights into the evolution of these important molecular chaperones. Phylogenetic analyses of [~]100 full-length HSP70s revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage (A) contains a relatively small number of Lophotrochozoan and Ecdysozoan genes, none of which have been shown to be constitutively expressed (i.e., either inducible or unknown). The other lineage (B) included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and Lineage B contains well-supported phylum-specific clades for Rotifera, Nematoda, and Chordata. Some genes in Lineage B have likely independently acquired inducibility, which may explain the sporadic distribution of "HSP70" or "HSC70" in previous analyses. Consistent with the diversification history within each group, inducible members show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family, encouraging us to propose a new nomenclature: "HSP70 + subcellular localization + linage + copy number in the organism + inducible or constitutive, if known." e.g., HSP70cA1i for cytosolic Lineage A, copy 1, inducible.

category: evolutionary biology


title: Identification of microRNAs that stabilize p53 in HPV-positive cancer cells

abstract:
Etiologically, 5% of all cancers worldwide are caused by the high-risk human papillomaviruses (hrHPVs). These viruses encode two oncoproteins (E6 and E7) whose expression is required for cancer initiation and maintenance. Among their cellular targets are the p53 and the retinoblastoma tumor suppressor proteins. Inhibition of the hrHPV E6-mediated ubiquitylation of p53 through the E6AP ubiquitin ligase results in the stabilization of p53, leading to cellular apoptosis. We utilized a live cell high throughput screen to determine whether exogenous microRNA (miRNA) transfection had the ability to stabilize p53 in hrHPV-positive cervical cancer cells expressing a p53-fluorescent protein as an in vivo reporter of p53 stability. Among the miRNAs whose transfection resulted in the greatest p53 stabilization was 375-3p that has previously been reported to stabilize p53 in HeLa cells, providing validation of the screen. The top 32 miRNAs in addition to 375-3p were further assessed using a second cell-based p53 stability reporter system as well as in non-reporter HeLa cells to examine their effects on endogenous p53 protein levels, resulting in the identification of 23 miRNAs whose transfection increased p53 levels in HeLa cells. While a few miRNAs that stabilized p53 led to decreases in E6AP protein levels, all targeted HPV oncoprotein expression. We further examined subsets of these miRNAs for their abilities to induce apoptosis and determined whether it was p53-mediated. The introduction of specific miRNAs revealed surprisingly heterogeneous responses in different cell lines. Nonetheless, some of the miRNAs described here have potential as therapeutics for treating HPV-positive cancers.

ImportanceHuman papillomaviruses cause approximately 5% of all cancers worldwide and encode genes that contribute to both the initiation and maintenance of these cancers. The viral oncoprotein E6 is expressed in all HPV-positive cancers and functions by targeting the degradation of p53 through the engagement of the cellular ubiquitin ligase E6AP. Inhibiting the degradation of p53 leads to apoptosis in HPV-positive cancer cells. Using a high throughput live cell assay we identified several miRNAs whose transfection stabilize p53 in HPV-positive cells. These miRNAs have the potential to be used in the treatment of HPV-positive cancers.


title: Optimized cultivar deployment improves the efficiency and stability of sunflower crop production at national scale

abstract:
Plant breeding programs design new crop cultivars which, while developed for distinct populations of environments, are nevertheless grown over large areas during their time in the market. Over its cultivation area, the crop is exposed to highly diverse stress patterns caused by climatic uncertainty and multiple management options, which often leads to decreased expected crop performance.

In this study, we aim is to assess how finer spatial management of genetic resources could reduce the yield variance explained by genotype x environment interactions in a set of cropping environments and ultimately improve the efficiency and stability of crop production. We used modeling and simulation to predict the crop performance resulting from the interaction between cultivar growth and development, climate and soil conditions, and management practices. We designed a computational experiment that evaluated the performance of a collection of commercial sunflower cultivars in a realistic population of cropping conditions in France, built from extensive agricultural surveys. Distinct farming locations sharing similar simulated abiotic stress patterns were clustered together to specify environment types. We then used optimization methods to search for cultivars x environments combinations leading to increased yield expectations.

Results showed that a single cultivar choice adapted to the most frequent environment-type in the population is a robust strategy. However, the relevance of cultivar recommendations to specific locations was gradually increasing with the knowledge of pedo-climatic conditions. We argue that this approach while being operational on current genetic material could act synergistically with plant breeding as more diverse material could enable access to cultivars with distinctive traits, more adapted to specific conditions.

Key messageCrop simulation helps to analyze environmental impacts on crops and provides year-independent context information. This information is of major importance when deciding which cultivar to choose at sowing time.


title: Coherent theta activity in the medial and orbital frontal cortices encodes reward value

abstract: This study examined how the medial frontal (MFC) and orbital frontal (OFC) cortices process reward information. We simultaneously recorded local field potentials in the two areas as rats consumed liquid sucrose rewards. Both areas exhibited a 4-8 Hz "theta" rhythm that was phase locked to the lick cycle. The rhythm tracked shifts in sucrose concentrations and fluid volumes, demonstrating that it is sensitive to differences in reward magnitude. The coupling between the rhythm and licking was stronger in MFC than OFC and varied with response vigor and absolute reward value in the MFC. Spectral analysis revealed zero-lag coherence between the cortical areas, and found evidence for a directionality of the rhythm, with MFC leading OFC. Our findings suggest that consummatory behavior generates simultaneous theta range activity in the MFC and OFC that encodes the value of consumed fluids, with the MFC having a top-down role in the control of consumption.


title: AI-guided discovery of the invariant host response to viral pandemics

abstract:
We sought to define the host immune response, a.k.a, the "cytokine storm" that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a  seed gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. Surprisingly, this 166-gene signature was conserved in all viral pandemics, including COVID-19, and a subset of 20-genes classified disease severity, inspiring the nomenclatures ViP and severe-ViP signatures, respectively. The ViP signatures pinpointed a paradoxical phenomenon wherein lung epithelial and myeloid cells mount an IL15 cytokine storm, and epithelial and NK cell senescence and apoptosis determines severity/fatality. Precise therapeutic goals were formulated and subsequently validated in high-dose SARS-CoV-2-challenged hamsters using neutralizing antibodies that abrogate SARS-CoV-2*ACE2 engagement or a directly acting antiviral agent, EIDD-2801. IL15/IL15RA were elevated in the lungs of patients with fatal disease, and plasma levels of the cytokine tracked with disease severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.

One Sentence SummaryThe host immune response in COVID-19.

PANEL: RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe SARS-CoV-2 pandemic has inspired many groups to find innovative methodologies that can help us understand the host immune response to the virus; unchecked proportions of such immune response have been implicated in fatality. We searched GEO and ArrayExpress that provided many publicly available gene expression data that objectively measure the host immune response in diverse conditions. However, challenges remain in identifying a set of host response events that are common to every condition. There are no studies that provide a reproducible assessment of prognosticators of disease severity, the host response, and therapeutic goals. Consequently, therapeutic trials for COVID-19 have seen many more  misses than  hits. This work used multiple (> 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them.

Added value of this studyThis work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the  cytokine storm mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs.

Implications of all the available evidenceThe ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.


title: Rapid, dose-dependent and efficient inactivation of surface dried SARS-CoV-2 by 254 nm UV-C irradiation

abstract:
BackgroundThe SARS-CoV-2 pandemic urges for cheap, reliable, and rapid technologies for disinfection and decontamination. One frequently proposed method is UV-C irradiation. However, UV-C doses necessary to achieve inactivation of high-titer SARS-CoV-2 are poorly defined.

MethodsUsing a box and two handheld systems designed to decontaminate objects and surfaces we evaluated the efficacy of 254 nm UV-C treatment to inactivate surface dried SARS-CoV-2.

ResultsDrying for two hours did not have a major impact on the infectivity of SARS-CoV-2, indicating that exhaled virus in droplets or aerosols stays infectious on surfaces at least for a certain amount of time. Short exposure of high titer surface dried virus (3-5*10^6 IU/ml) with UV-C light (16 mJ/cm2) resulted in a total inactivation of SARS-CoV-2. Dose-dependency experiments revealed that 3.5 mJ/cm2 were still effective to achieve a > 6-log reduction in viral titers whereas 1.75 mJ/cm2 lowered infectivity only by one order of magnitude.

ConclusionsOur results demonstrate that SARS-CoV-2 is rapidly inactivated by relatively low doses of UV-C irradiation. Furthermore, the data reveal that the relationship between UV-C dose and log-viral titer reduction of surface residing SARS-CoV-2 is non-linear. In the context of UV-C-based technologies used to disinfect surfaces, our findings emphasize the necessity to assure sufficient and complete exposure of all relevant areas by integrated UV-C doses of at least 3.5 mJ/cm2 at 254 nm. Altogether, UV-C treatment is an effective non-chemical possibility to decontaminate surfaces from high-titer infectious SARS-CoV-2.

category: microbiology


title: The environment modulates the effects of the microbiome on host adaptive potential

abstract: Can the microbiome serve as a reservoir of adaptive potential for hosts? To address this question, we leveraged [~]150 generations of experimental evolution in Drosophila melanogaster in a stressful high sugar (HS) diet. We performed a fully reciprocal transplant experiment using the dominant control and HS bacteria and measured life-history and metabolic traits. If the microbiome can indeed confer benefits to hosts, then transplant recipients should gain fitness benefits compared to controls. Interestingly, we found that these benefits do exist, but are non-linear. The benefits depend on specific interactions between host genotype and the microbiome, and these interactions are modulated by the environment. Mismatches between fly evolution and microbiome exerted fitness costs by slowing development and reducing fecundity, especially in the stressful HS diet. The dominant HS bacteria (Acetobacter pasteurianus) uniquely encoded several genes to enable uric acid degradation, mediated the toxic effects of uric acid accumulation due to the HS diet for flies. Our study demonstrates that host genotype x microbiome x environment interactions have substantial effects on host phenotype, highlighting how host evolution and ecological context together shape the adaptive potential of the microbiome.


title: Host evolutionary history and ecological context modulate the adaptive potential of the microbiome


title: Probing Causality of the Brainstem-Hypothalamic Murine Models of Sleep-Wake Regulation

abstract: Sleep-wake regulation is thought to be governed by interactions among several nuclei in midbrain, pons, and hypothalamic regions. Determination of the causal role of these nuclei in state transitions requires simultaneous measurements from the nuclei with sufficient spatial and temporal resolution. We obtained long-term experimental single- and multi-unit measurements simultaneously from multiple nuclei of the putative hypothalamic and brainstem sleep-wake regulatory network in freely behaving rats. Cortical and hippocampal activity, along with head acceleration were also acquired to assess behavioral state. Here, we confirm that the general activity profile of the recorded sleep-wake regulatory nuclei is similar to the patterns presented previously in brief recordings of individual nuclei in head-fixed animals. However, we found that these activity profiles when studied with respect to cortical and behavioral signs of state transitions differ significantly from previous reports. Our findings pose fundamental questions about the neural mechanisms that maintain specific states and the neural interactions that lead to the emergence of sleep-wake states.


title: The N300: An Index For Predictive Coding Of Complex Visual Objects and Scenes

abstract: Predictive coding models can simulate known perceptual or neuronal phenomena, but there have been fewer attempts to identify a reliable neural signature of predictive coding for complex stimuli. In a pair of studies, we test whether the N300 component of the event-related potential, occurring 250-350 ms post-stimulus-onset, has the response properties expected for such a signature of perceptual hypothesis testing at the level of whole objects and scenes. We show that N300 amplitudes are smaller to representative ("good exemplars") compared to less representative ("bad exemplars") items from natural scene categories. Integrating these results with patterns observed for objects, we establish that, across a variety of visual stimuli, the N300 is responsive to statistical regularity, or the degree to which the input is "expected" (either explicitly or implicitly) based on prior knowledge, with statistically regular images evoking a reduced response. Moreover, we show that the measure exhibits context-dependency; that is, we find the N300 sensitivity to category representativeness when stimuli are congruent with, but not when they are incongruent with, a category pre-cue. Thus, we argue that the N300 is the best candidate to date for an index of perceptual hypotheses testing for complex visual objects and scenes.


title: EPISPOT: an epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies

abstract: We present EPISPOT, a fully joint framework which exploits large panels of epigenetic annotations as variant-level information to enhance molecular quantitative trait locus (QTL) mapping. Thanks to a purpose-built Bayesian inferential algorithm, EPISPOT accommodates functional information for both cis and trans actions, including QTL hotspot effects. It effectively couples simultaneous QTL analysis of thousands of genetic variants and molecular traits, and hypothesis-free selection of biologically interpretable annotations which directly contribute to the QTL effects. This unified, epigenome-aided learning boosts statistical power and sheds light on the regulatory basis of the uncovered hits; EPISPOT therefore marks an essential step towards improving the challenging detection and functional interpretation of trans-acting genetic variants and hotspots. We illustrate the advantages of EPISPOT in simulations emulating real-data conditions and in a monocyte expression QTL study, which confirms known hotspots and finds other signals, as well as plausible mechanisms of action. In particular, by highlighting the role of monocyte DNase-I sensitivity sites from > 150 epigenetic annotations, we clarify the mediation effects and cell-type specificity of major hotspots close to the lysozyme gene. Our approach forgoes the daunting and underpowered task of one-annotation-at-a-time enrichment analyses for prioritising cis and trans QTL hits and is tailored to any transcriptomic, proteomic or metabolomic QTL problem. By enabling principled epigenome-driven QTL mapping transcriptome-wide, EPISPOT helps progress towards a better functional understanding of genetic regulation.


title: SingleChannelNet: A Model for Automatic Sleep Stage Classification with Raw Single-Channel EEG

abstract: In diagnosing sleep disorders, sleep stage classification is a very essential yet time-consuming process. Most of the existing state-of-the-art approaches rely on hand-crafted features and multi-modality polysomnography (PSG) data, where prior knowledge is compulsory and high computation cost can be expected. Besides, few studies are able to obtain high accuracy sleep staging using raw single-channel electroencephalogram (EEG). To overcome these shortcomings, this paper proposes an end-to-end framework with a deep neural network, namely SingleChannelNet, for automatic sleep stage classification based on raw single-channel EEG. The proposed model utilizes a 90s epoch as the textual input and employs two multi-convolution blocks and several max-average pooling layers to learn different scales of feature representations. To demonstrate the efficiency of the proposed model, we evaluate our model using different raw single-channel EEGs (C4/A1 and Fpz-Cz) on two different datasets (CC-SHS and Sleep-EDF datasets). Experimental results show that the proposed architecture can achieve better over-all accuracy and Cohens kappa (CCSHS: 90.2%-86.5%, Sleep-EDF: 86.1%-80.5%) compared with state-of-the-art approaches. Additionally, the proposed model can learn features automatically for sleep stage classification using different single-channel EEGs with distinct sampling rates from different datasets without using any hand-engineered features.