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Biophysical basis of cellular multi-specificity encoded in a model molecular switch Molecular switches are central to signal transduction in protein interaction networks. One switch protein can independently regulate distinct cellular processes, but the molecular mechanisms enabling this functional multi-specificity remain unclear. Here we integrate system-scale cellular and biophysical measurements to study how a paradigm switch, the small GTPase Ran/Gsp1, achieves its functional multi-specificity. We make 55 targeted point mutations to individual interactions of Ran/Gsp1 and show through quantitative, systematic genetic and physical interaction mapping that Ran/Gsp1 interface perturbations have widespread cellular consequences that cluster by biological processes but, unexpectedly, not by the targeted interactions. Instead, the cellular consequences of the interface mutations group by their biophysical effects on kinetic parameters of the GTPase switch cycle, and cycle kinetics are allosterically tuned by distal interface mutations. We propose that the functional multi-specificity of Ran/Gsp1 is encoded by a differential sensitivity of biological processes to different kinetic parameters of the Gsp1 switch cycle, and that Gsp1 partners binding to the sites of distal mutations act as allosteric regulators of the switch. Similar mechanisms may underlie biological regulation by other GTPases and biological switches. Finally, our integrative platform to determine the quantitative consequences of cellular perturbations may help explain the effects of disease mutations targeting central switches.
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systems biology
|
The mechanisms of in vivo commensal control of Clostridioides difficile virulence We define multiple mechanisms by which commensals protect against or worsen Clostridioides difficile infection. Leveraging new systems-level models we show how metabolically distinct species of Clostridia modulate the pathogens colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Paraclostridium bifermentans survived infection while mice colonized with the butyrate- producer, Clostridium sardiniense, more rapidly succumbed. Systematic in vivo analyses revealed how each commensal altered the gut nutrient environment, modulating the pathogens metabolism, regulatory networks, and toxin production. Oral administration of P. bifermentans rescued conventional mice from lethal C. difficile infection via mechanisms identified in specifically colonized mice. Our findings lay the foundation for mechanistically informed therapies to counter C. difficile infections using systems biologic approaches to define host-commensal-pathogen interactions in vivo.
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[email protected]@b4290borg.highwire.dtl.DTLVardef@1f2af49org.highwire.dtl.DTLVardef@1d1e6b9_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG
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microbiology
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Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes While DNA sequence evolution has been well studied, the expression of genes is also subject to evolution, yet the evolution of gene expression is currently not well understood. Recently, new tissue/organ-specific gene expression datasets spanning several organisms across the tree of life, have become available, providing the opportunity to study gene expression evolution in more detail. While a theoretical model to study the evolution of continuous traits exists, in practice computational methods often cannot confidently distinguish between alternative evolutionary scenarios. This lack of power has been attributed to modest numbers of species considered in these studies.
We hypothesised that biological replicates can be used to increase predictive power of these models. With this in mind, we introduce EvoGeneX, a computationally efficient method to uncover the mode of gene expression evolution based on the Ornstein-Uhlenbeck process. Importantly, in addition to modelling expression variations between species, EvoGeneX models within-species variation.
Furthermore, to facilitate comparative analysis of gene expression evolution, we introduce a formal approach, based on Michaelis-Menten equation, to measure the dynamics of evolutionary divergence of a group of genes in terms of groups asymptotic divergence level and rate.
Finally, we used these tools to preform the first analysis the evolution of gene expression across different body parts, species, and sexes of the Drosophila genus. Our analysis revealed that neutral expression evolution can be confidently rejected in favor of purifying selection in nearly half of the genes. In addition, we quantified differences in the evolutionary dynamics of male and female gonads and uncovered interesting examples of adaptive gene expression evolution.
|
evolutionary biology
|
Different forms of variability could explain a difference between human and rat decision making When observers make rapid, difficult perceptual decisions, their response time is highly variable from trial to trial. In a visual motion discrimination task, it has been reported that human accuracy declines with increasing response time, whereas rat accuracy increases with response time. This is of interest because different mathematical theories of decision-making differ in their predictions regarding the correlation of accuracy with response time. On the premise that perceptual decision-making mechanisms are likely to be conserved among mammals, we seek to unify the rodent and primate results in a common theoretical framework. We show that a bounded drift diffusion model (DDM) can explain both effects with variable parameters: trial-to-trial variability in the starting point of the diffusion process produces the pattern typically observed in rats, whereas variability in the drift rate produces the pattern typically observed in humans. We further show that the same effects can be produced by deterministic biases, even in the absence of parameter stochasticity or parameter change within a trial.
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neuroscience
|
Mechanical control of morphogenetic robustness in an inherently challenging environment Epithelial sheets undergo highly reproducible remodeling to shape organs. This stereotyped morphogenesis depends on a well-defined sequence of events leading to the regionalized expression of developmental patterning genes that finally triggers downstream mechanical forces to drive tissue remodeling at a pre-defined position. However, how tissue mechanics controls morphogenetic robustness when challenged by intrinsic perturbations in close proximity has never been addressed.
Here, we show that a bias in force propagation ensures stereotyped morphogenesis despite the presence of mechanical noise in the environment. We found that knockdown of the Arp2/3 complex member Arpc5 specifically affects fold directionality without altering neither the developmental nor the force generation patterns. By combining in silico modeling, biophysical and ad hoc genetic tools, our data reveal that junctional Myosin II planar polarity favors long-range force channeling and ensures folding robustness, avoiding force scattering and thus isolating the fold domain from surrounding mechanical perturbations.
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developmental biology
|
Scanning electron microscopy preparation of the cellular actin cortex: a quantitative comparison between critical point drying and hexamethyldisilazane drying The cellular cortex is an approximately 200-nm-thick actin network that lies just beneath the cell membrane. It is responsible for the mechanical properties of cells, and as such, it is involved in many cellular processes, including cell migration and cellular interactions with the environment. To develop a clear view of this dense structure, high-resolution imaging is essential. As one such technique, electron microscopy, involves complex sample preparation procedures. The final drying of these samples has significant influence on potential artifacts, like cell shrinkage and the formation of artifactual holes in the actin cortex. In this study, we compared the three most used final sample drying procedures: critical-point drying (CPD), CPD with lens tissue (CPD-LT), and hexamethyldisilazane drying. We show that both hexamethyldisilazane and CPD-LT lead to fewer artifactual mesh holes within the actin cortex than CPD. Moreover, CPD-LT leads to significant reduction in cell height compared to hexamethyldisilazane and CPD. We conclude that the final drying procedure should be chosen according to the reduction in cell height, and so CPD-LT, or according to the spatial separation of the single layers of the actin cortex, and so hexamethyldisilazane.
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biophysics
|
Protein sequence design with a learned potential AO_SCPLOWBSTRACTC_SCPLOWThe task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. We investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with the in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.
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bioinformatics
|
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson's disease at Chr16q11.2 and on the MAPT H1 allele Parkinsons disease (PD) is a common incurable neurodegenerative disease. The identification of genetic variants via genome-wide association studies (GWAS) has considerably advanced our understanding of the PD genetic risk. Understanding the functional significance of the risk loci is now a critical step towards translating these genetic advances into an enhanced biological understanding of the disease. Impaired mitophagy is a key causative pathway in familial PD, but its relevance to idiopathic PD is unclear. We used a mitophagy screening assay to evaluate the functional significance of risk genes identified through GWAS. We identified two new regulators of PINK1-mitophagy, KAT8 and KANSL1, previously shown to modulate lysine acetylation. We show that KAT8 and KANSL1 modulate PINK1 gene expression and subsequent PINK1-mitophagy. These findings suggest PINK1-mitophagy is a contributing factor to idiopathic PD. KANSL1 is located on chromosome 17q21 where the risk associated gene has long been considered to be MAPT. While our data does not exclude a possible association between the MAPT gene and PD, it provides strong evidence that KANSL1 plays a crucial role in the disease. Finally, these results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.
|
neuroscience
|
Lumbar corticospinal tract in rodents modulates sensory inputs but does not convey motor command It is generally assumed that the main function of the corticospinal tract (CST) is to convey motor commands to bulbar or spinal motoneurons. Yet the CST has also been shown to modulate sensory signals at their entry point in the spinal cord, through presynaptic inhibition. By sequentially investigating different routes of corticofugal pathways through electrophysiological recordings and an intersectional viral strategy, we here demonstrate that motor and sensory modulation commands in mice belong to segregated paths within the CST. Sensory modulation is excuted exclusively by the CST via a population of lumbar interneurons located in the deep dorsal horn. In contrast, the cortex conveys the motor command via a relay in the upper spinal cord or supraspinal motor centers. At lumbar level, the main role of the CST is thus the modulation of sensory inputs, which is an essential component of the selective tuning of sensory feedback, to ensure well-coordinated and skilled movement.
Impact statementWhile the corticospinal tract is often considered exclusively as a motor path, this study demonstrates that, in the mouse lumbar cord, its main role is the modulation of sensory inputs.
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neuroscience
|
Subliminal perception can be predicted from prestimulus activity Individuals are able to discriminate visual stimuli they report not consciously seeing. This phenomenon is known as "subliminal perception." Such capacity is often assumed to be relatively automatic in nature, and rely on stimulus-driven activity in low-level cortical areas. Instead, here we asked to what extent neural activity before stimulus presentation influences subliminal perception. We asked participants to discriminate the location of a briefly presented low-contrast visual stimulus, and then rate how well they saw the stimulus. Consistent with previous studies, participants correctly discriminated with slightly above chance-level accuracy the location of a stimulus they reported not seeing. Signal detection analyses indicated that while subjects categorized their percepts as "unconscious", their capacity to discriminate these stimuli lay on the same continuum as conscious vision. We show that the accuracy of discriminating the location of a subliminal stimulus could be predicted with relatively high accuracy (AUC = .70) based on lateralized electroencephalographic (EEG) activity before the stimulus, the hemifield where the stimulus was presented, and accuracy of previous trials discrimination response. Altogether, our results suggest that rather than being a separate unconscious capacity, subliminal perception is based on similar processes as conscious vison.
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neuroscience
|
Predictive feedback, early sensory representations and fast responses to predicted stimuli depend on NMDA receptors Learned associations between stimuli allow us to model the world and make predictions, crucial for efficient behavior; e.g., hearing a siren, we expect to see an ambulance and quickly make way. While there are theoretical and computational frameworks for prediction, the circuit and receptor-level mechanisms are unclear. Using high-density EEG, Bayesian modeling and machine learning, we show that inferred "causal" relationships between stimuli and frontal alpha activity account for reaction times (a proxy for predictions) on a trial-by-trial basis in an audio-visual delayed match-to-sample task which elicited predictions. Predictive beta feedback activated sensory representations in advance of predicted stimuli. Low-dose ketamine, a NMDA receptor blocker - but not the control drug dexmedetomidine - perturbed behavioral indices of predictions, their representation in higher-order cortex, feedback to posterior cortex and pre-activation of sensory templates in higher-order sensory cortex. This study suggests predictions depend on alpha activity in higher-order cortex, beta feedback and NMDA receptors, and ketamine blocks access to learned predictive information.
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neuroscience
|
Computed tomography reveals hip dysplasiain the extinct Pleistocene saber-tooth cat Smilodon Reconstructing the behavior of extinct species is challenging, particularly for those with no living analogues. However, damage preserved as paleopathologies on bone can record how an animal moved in life, potentially reflecting behavioral patterns. Here, we assess hypothesized etiologies of pathology in a pelvis and associated right femur of a Smilodon fatalis saber-toothed cat, one of the best-studied species from the Pleistocene-age Rancho La Brea asphalt seeps, California, USA, using visualization by computed tomography (CT). The pelvis exhibits massive destruction of the right hip socket that was interpreted, for nearly a century, to have developed from trauma and infection. CT imaging reveals instead that the pathological distortions characterize chronic remodeling that began at birth and led to degeneration of the joint over the animals life. These results suggest that this individual suffered from hip dysplasia, a congenital condition common in domestic dogs and cats. This individual reached adulthood but could not have hunted properly nor defended territory on its own, likely relying on a social group for feeding and protection. While extant social felids are rare, these fossils and others with similar pathologies are consistent with a spectrum of social strategies in Smilodon supported by a predominance of previous studies.
|
paleontology
|
Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons Type I interferons (IFNs) are essential for anti-viral immunity, but often impair protective immune responses during bacterial infections. An important question is how type I IFNs are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. The Super susceptibility to tuberculosis 1 (Sst1) locus in mice confers resistance to diverse bacterial infections. Here we provide evidence that Sp140 is a gene encoded within the Sst1 locus that represses type I IFN transcription during bacterial infections. We generated Sp140-/- mice and find they are susceptible to infection by Legionella pneumophila and Mycobacterium tuberculosis. Susceptibility of Sp140-/- mice to bacterial infection was rescued by crosses to mice lacking the type I IFN receptor (Ifnar-/-). Our results implicate Sp140 as an important negative regulator of type I IFNs that is essential for resistance to bacterial infections.
Impact StatementRepression of type I interferons by SP140 is essential for resistance to Legionella pneumophila and Mycobacterium tuberculosis.
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immunology
|
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9-99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.
|
bioinformatics
|
Bayesian cell-type deconvolution and gene expression inference reveals tumor-microenvironment interactions Understanding the interactions between cells in their environment is a major challenge in genomics. Here we developed BayesPrism, a Bayesian method to jointly predict cellular composition and gene expression in each cell type, including heterogeneous malignant cells, from bulk RNA-seq using scRNA-seq as prior information. We conducted an integrative analysis of 1,412 bulk RNA-seq samples in primary glioblastoma, head and neck squamous cell carcinoma, and melanoma using single-cell datasets of 85 patients. We identified cell types correlated with clinical outcomes and explored spatial heterogeneity in malignant cell states and non-malignant cell type composition. We refined subtypes using gene expression in malignant cells, after excluding confounding non-malignant cell types. Finally, we identified genes whose expression in malignant cells correlated with infiltration of macrophages, T cells, fibroblasts, and endothelial cells across multiple tumor types. Our work introduces a new lens that uses scRNA-seq to accurately infer cellular composition and expression in large cohorts of bulk data.
|
genomics
|
RNA-binding protein Syncrip regulates Starvation-Induced Hyperactivity in adult Drosophila How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 23 significant loci, corresponding to 14 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of syp in regulating SIH. syp encodes Syncrip (Syp), an RBP. While ubiquitous knockdown of syp led to semi-lethality in adult flies, adult flies with neuron-specific syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. To determine how syp is regulated by starvation, we performed RNA-seq using the heads of flies maintained under either food or starvation conditions. RNA-seq analyses revealed that syp was alternatively spliced under starvation while its expression level was unchanged. We further generated an alternatively-spliced-exon-specific knockout (KO) line and found that KO flies showed reduced SIH. Together, this study demonstrates a significant genetic contribution to SIH as a behavioral trait, identifies syp as a SIH gene, and highlights the significance of RBPs and post-transcriptional processes in the brain in regulating behavioral responses to starvation.
Author summaryAnimals living in the wild often face periods of starvation. How to physiologically and behaviorally respond to starvation is essential for survival. One behavioral response is Starvation-Induced Hyperactivity (SIH). We used the Drosophila melanogaster Genetic Reference Panel, derived from a wild population, to study the genetic basis of SIH. Our results show that there is a significant genetic contribution to SIH in this population, and that genes encoding RNA binding proteins (RBPs) are especially important. Using RNA interference and the TARGET system, we confirmed the role of an RBP Syp in adult neurons in SIH. Using RNA-seq and Western blotting, we found that syp was alternatively spliced under starvation while its expression level was unchanged. Further studies from syp exon-specific knockout flies showed that alternative splicing involving two exons in syp was important for SIH. Together, this study identifies syp as a SIH gene and highlights an essential role of post-transcriptional modification in regulating this behavior.
|
genomics
|
4DNvestigator: Time Series Genomic Data Analysis Toolbox Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the "4DNvestigator", a user-friendly network based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.
Availabilityhttps://github.com/lindsly/4DNvestigator
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bioinformatics
|
A silent disco: Persistent entrainment of low-frequency neural oscillations underlies beat-based, but not pattern-based temporal expectations The brain uses temporal structure in the environment, like rhythm in music and speech, to predict the timing of events, thereby optimizing their processing and perception. Temporal expectations can be grounded in different aspects of the input structure, such as a regular beat or a predictable pattern. One influential account posits that a generic mechanism underlies beat-based and pattern-based expectations, namely entrainment of low frequency neural oscillations to rhythmic input, while other accounts assume different underlying neural mechanisms. Here, we addressed this outstanding issue by examining EEG activity and behavioral responses during silent periods following rhythmic auditory sequences. We measured responses outlasting the rhythms both to avoid confounding the EEG analyses with evoked responses, and to directly test whether beat-based and pattern-based expectations persist beyond stimulation, as predicted by entrainment theories. To properly disentangle beat-based and pattern-based expectations, which often occur simultaneously, we used non-isochronous rhythms with a beat, a predictable pattern, or random timing. In Experiment 1 (N = 32), beat-based expectations affected behavioral ratings of probe events for two beat-cycles after the end of the rhythm, while the effects of pattern-based expectations subsided almost instantly. In Experiment 2 (N = 27), using EEG, we found enhanced spectral power at the beat frequency for beat-based sequences both during listening and the silence, but for pattern-based sequences, enhanced power at a pattern-specific frequency was only present during listening, not silence. Moreover, we found a negative deflection in the evoked signal following pattern-based, but not beat-based sequences. Finally, we show how multivariate pattern decoding and multi scale entropy - measures sensitive to non-oscillatory components of the signal - can be used to probe temporal expectations. Together, our results suggest that different mechanisms implement temporal expectations, depending on the input structure. We suggest climbing activity may reflect pattern-based, and persistent low frequency oscillations beat-based expectations specifically.
Highlights- Temporal expectations can be based on both regular beats and predictable patterns
- Behavioral effects persist longer for beat-based than pattern-based expectations
- EEG power tracks the beat, but not the pattern, outlasting rhythmic stimuli
- Pattern-based, but not beat-based expectations elicit a CNV-like ERP component
- Decoding and entropy may index temporal expectations in a time-resolved way
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neuroscience
|
The formation of microbial exoskeletons is driven by a controlled calcium-concentrating subcellular niche In nature, bacteria reside in biofilms - multicellular differentiated communities held together by extracellular matrix. In this work, we identified a novel subpopulation essential for biofilm formation - mineral-forming cells. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community.
The molecular mechanisms promoting calcite scaffold formation were conserved between three distant phyla - the Gram-positive Bacillus subtilis, Gram-negative Pseudomonas aeruginosa and the actinobacterium Mycobacterium abscessus. Biofilm development of all three species was similarly impaired by inhibition of calcium uptake and carbonate accumulation. Moreover, chemical inhibition and mutations targeting mineralization both significantly reduced the attachment of P. aeruginosa to the lung, as well as the subsequent damage inflicted by biofilms to lung tissues, and restored their sensitivity to antibiotics.
The evolutionary conserved cellular pathway controlling the fundamental feature of biofilm development uncovered in this work offers novel druggable targets for antibiotics to combat otherwise untreatable biofilm infections.
|
microbiology
|
Geographical and environmental contributions to genomic divergence in mangrove forests Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent-ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
|
evolutionary biology
|
A semi-empirical model of the aerodynamics of manoeuvring insect flight Blade element modelling provides a quick analytical method for estimating the aerodynamic forces produced during insect flight, but such models have yet to be tested rigorously using kinematic data recorded from free-flying insects. This is largely because of the paucity of detailed free-flight kinematic data, but also because analytical limitations in existing blade element models mean that they cannot incorporate the complex three-dimensional movements of the wings and body that occur during insect flight. Here, we present a blade element model with empirically-fitted aerodynamic force coefficients that incorporates the full three-dimensional wing kinematics of manoeuvring Eristalis hoverflies, including torsional deformation of their wings. The two free parameters were fitted to a large free-flight dataset comprising N = 26, 541 wingbeats, and the fitted model captured approximately 80% of the variation in the stroke-averaged forces in the sagittal plane. We tested the robustness of the model by subsampling the data, and found little variation in the parameter estimates across subsamples comprising 10% of the flight sequences. The simplicity and generality of the model that we present is such that it can be readily applied to kinematic datasets from other insects, and also used for the study of insect flight dynamics.
|
biophysics
|
Trial-by-trial predictions of subjective time from human brain activity Human experience of time exhibits systematic, context-dependent deviations from veridical clock time; for example, time is experienced differently at work than on holiday. Here we test the proposal that differences from clock time in subjective experience of time arise because time estimates are constructed by accumulating the same quantity that guides perception: salient events. Healthy human participants watched naturalistic, silent videos of up to [~]1 minute in duration and estimated their duration while fMRI was acquired. We were able to reconstruct trial-by-trial biases in participants duration reports, which reflect subjective experience of time (rather than veridical clock time), purely from salient events in their visual cortex BOLD activity. This was not the case for control regions in auditory and somatosensory cortex, despite being able to predict clock time from all three brain areas. Our results reveal that the information arising during sensory processing of our dynamic environment provides a sufficient basis for reconstructing human subjective time estimates.
|
neuroscience
|
Fundamental resource specialization of herbivorous butterflies decreases toward lower latitudes AimIt is generally assumed that the degree of resource specialization in herbivorous insects increases towards lower latitudes. However, latitudinal patterns in herbivore diet breadth at large spatial scales remain poorly understood. In this work, we investigated drivers of latitudinal variation in lepidopteran "fundamental" resource specialization, which we defined as the host breadth when not limited by interspecific interactions at the same trophic level.
LocationThe Japanese archipelago (22{degrees}N-45{degrees}N), including hemiboreal, temperate, and subtropical zones.
TaxonHerbivorous butterflies.
MethodsSpecies-specific fundamental host breadth was calculated based on pooled geographical occurrence and host-use records. We investigated the latitudinal pattern and significant drivers of the degree of specialization in regional species pools at a 10-km grid level. As potential drivers, we focused on geography, current climate, and diversity and body size of butterflies. Through Bayesian structural equation modeling, we investigated the complicated relationships between these variables and community-level resource specialization represented by three different indices of host breadth.
ResultsWe found that fundamental resource specialization of butterfly communities increases toward higher latitudes. This pattern is contrary to the presumed general trend found in studies based on realized resource specialization within local communities. We found that the observed pattern is driven mainly by factors related to climate, butterfly diversity, and body size in each community. Above all, annual mean temperature most strongly drove community-level fundamental host breadth of butterflies.
Main conclusionsOur findings suggest that fundamental resource specialization may show different latitudinal patterns from the conventional prediction based on knowledge of realized resource specialization. Our results emphasize the importance of the current climate as a major factor regulating butterfly morphology and fundamental host breadth, regardless of whether the impact is direct or indirect.
|
ecology
|
Succination of Dihydrolipoyllysine Succinyltransferase by Fumarate Exacerbates Defective Mitochondrial ATP Production during Complex I Deficiency The NDUFS4 knockout (KO) mouse phenotype resembles the human Complex I deficiency Leigh Syndrome. The irreversible succination of protein thiols by fumarate is increased in select regions of the NDUFS4 KO brain affected by neurodegeneration, suggesting a mechanistic role in neurodegenerative decline. We report that dihydrolipoyllysine-residue succinyltransferase (DLST), a component of the -ketoglutarate dehydrogenase complex (KGDHC) of the tricarboxylic acid (TCA) cycle, is succinated in the NDUFS4 KO brain. Succination of DLST reduced KGDHC activity in the brainstem (BS) and olfactory bulb (OB) of KO mice. The defective production of KGDHC derived succinyl-CoA resulted in decreased mitochondrial substrate level phosphorylation, further aggravating the OXPHOS ATP deficit. Protein succinylation, an acylation modification that requires succinyl-CoA, was reduced in the KO mice. Our data demonstrate that the biochemical deficit extends beyond impaired Complex I assembly and OXPHOS deficiency, functionally impairing select components of the TCA cycle to drive metabolic perturbations in affected neurons.
HighlightsO_LICysteine succination by fumarate is increased in model of Complex I deficiency
C_LIO_LISuccination of DLST impairs KGDHC activity, limits SLP, and reduces lysine succinylation
C_LIO_LIIrreversible succination drives neuropathology independent of the bioenergetic defect
C_LI
|
biochemistry
|
Propranolol promotes bone formation and limits resorption through novel mechanisms during anabolic parathyroid hormone treatment in female C57BL/6J mice Although the non-selective {beta}-blocker, propranolol, improves bone density with PTH treatment in mice, the mechanism of this effect is unclear. To address this, we used a combination of in vitro and in vivo approaches to address how propranolol influences bone remodeling in the context of PTH treatment. In female C57BL/6J mice, intermittent PTH and propranolol had complementary effects in the trabecular bone of the distal femur and L5 vertebra, with combination treatment achieving micro-architectural parameters beyond that of PTH alone. Combined treatment improved the serum bone formation marker, P1NP, but did not impact other histomorphometric parameters relating to osteoblast function at the L5. In vitro, propranolol amplified the acute, PTH-induced, intracellular calcium signal in osteoblast-like cells. The most striking finding, however, was suppression of PTH-induced bone resorption. Despite this, PTH-induced receptor activator of nuclear factor kappa-B ligand (RANKL) mRNA and protein levels were unaltered by propranolol, which led us to hypothesize that propranolol could act directly on osteoclasts. Using in situ methods, we found Adrb2 expression in osteoclasts in vivo, suggesting {beta}-blockers may directly impact osteoclasts. Taken together, this work suggests a strong anti-osteoclastic effect of non-selective {beta}-blockers in vivo, indicating that combining propranolol with PTH could be beneficial to patients with extremely low bone density.
|
physiology
|
Changes in partner traits drive variation in plant-nectar robber interactions across habitats The frequency and outcome of biotic interactions commonly vary with environmental conditions, even without changes to community composition. Yet the drivers of such environmentally-mediated change in biotic interactions are poorly understood, limiting our ability to predict how environmental change will impact communities. Studying nectar robbery by stingless bees of Odontonema cuspidatum (Acanthaceae) in a coffee agroecosystem, we documented a temporally consistent difference in nectar robbing intensity between anthropogenic and seminatural habitats. Plants growing in coffee fields (anthropogenic habitat) experienced significantly more nectar robbery than plants growing in forest fragments (seminatural habitat). Using a combination of field surveys and manipulative experiments, we found that nectar robbery was higher in coffee fields primarily due to environmental effects on a) neighborhood floral context and b) O. cuspidatum floral traits. This led to both preferential foraging by nectar robbers in coffee fields, and to changes in foraging behavior on O. cuspidatum that increased robbery. Nectar robbery significantly reduced fruit set in O. cuspidatum. These results suggest that the effects of anthropogenic environmental change on species traits may be more important than its effect on species density in determining how interaction frequency and outcome are affected by such environmental change.
|
ecology
|
DLG2 knockout reveals neurogenic transcriptional programs underlying neuropsychiatric disorders and cognition Brain development requires a complex choreography of cell proliferation, specialisation, migration and network formation, guided by the activation and repression of gene expression programs. It remains unclear how this process is disrupted in neuropsychiatric disorders. Here we integrate human genetics with transcriptomic data from the differentiation of human embryonic stem cells into cortical excitatory neurons. This reveals a cascade of transcriptional programs, activated during early corticoneurogenesis in vitro and in vivo, in which genetic variation is robustly associated with neuropsychiatric disorders and cognitive function. Within these early neurogenic programs, genetic risk is concentrated in loss-of-function intolerant (LoFi) genes, capturing virtually all LoFi disease association. Down-regulation of these programs in DLG2 knockout lines delays expression of cell-type identity alongside marked deficits in neuronal migration, morphology and action potential generation, validating computational predictions. These data implicate specific cellular pathways and neurodevelopmental processes in the aetiology of multiple neuropsychiatric disorders and cognition.
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developmental biology
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Design and demonstration in vitro of mouse-specific Transcranial Magnetic Stimulation coil BackgroundTranscranial Magnetic Stimulation (TMS) is a technique used to treat different neurological disorders non-invasively. A pulsed current to a coil generates a magnetic field (B-field) which induces an electric field (E-field). Underlying biophysical effects of TMS are unclear. Therefore, animal experiments are needed; however, making small TMS coils suitable for mice is difficult and their field strengths are typically much lower than for human sized coils.
Objectives/HypothesisWe aimed to design and demonstrate a mouse-specific coil that can generate high and focused E-field.
MethodsWe designed a tapered TMS coil of 50 turns of 0.2 mm diameter copper wire around a 5 mm diameter tapered powdered iron core and discharged a 220 F capacitor at 50 V through it. We measured B-field with a Hall probe and induced E-field with a wire loop. We measured temperature rise with a thermocouple. We applied 1200 pulses of continuous theta burst stimulation (cTBS) and intermittent theta burst stimulation (iTBS) to mouse brain slices and analysed how spontaneous electrical activity changed.
ResultsThe coil gave maximum B-field of 685 mT at the base of the coil and 340 mT at 2 mm below the coil, and maximum E-field 2 mm below the coil of approximately 10 V/m, at 50 V power supply, with a temperature increase of 20 degrees after 1200 pulses of cTBS. We observed no changes in B-field with heating. cTBS reduced frequency of spontaneous population events in mouse brain slices up to 20 minutes after stimulation and iTBS increased frequency up to 20 minutes after stimulation. No frequency changes occurred after 20 minutes. No changes in amplitude of spontaneous events were found.
ConclusionThe design generated fields strong enough to modulate brain activity in vitro.
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neuroscience
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Choice can be predicted from populations of bursting neurons in superficial layers of monkey V1 Primary visual cortex (V1) is absolutely necessary for normal visual processing, but whether V1 encodes upcoming behavioral decisions based on visual information is an unresolved issue, with conflicting evidence. Further, no study so far has been able to predict choice from time-resolved spiking activity in V1. Here, macaque monkeys are tested in a decision-making task with a categorical variable: match versus non-match of two consecutive stimuli. Our aim is to predict the binary choice "same" versus "different" on trials that only differ in choice, but not in stimuli. Classical decoding schemes fail to predict the choice in such a setting, however, the choice can be predicted by learning the structure of population responses in trials with correct behavior. The learned structure of population responses transfers to the representation of the choice, even when the choice is incorrect. With such generalized learning scheme, the choice can be successfully predicted from spiking activity of neural ensembles in V1 in single trials. We show that the choice signal is primarily carried by bursting neurons in the superficial layer of the cortex. Results suggest that bursting of single neurons and noise correlations between neurons with similar decoding selectivity are dynamical mechanisms that help the formation of time-resolved choice signals.
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neuroscience
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Radius-Optimized Efficient Template Matching for Lesion Detection from Brain Images Computer-aided detection of brain lesions from volumetric magnetic resonance imaging (MRI) is in demand for fast and automatic diagnosis of neural diseases. The template-matching technique can provide satisfactory outcome for automatic localization of brain lesions; however, finding the optimal template size that maximizes similarity of the template and the lesion remains challenging. This increases the complexity of the algorithm and the requirement for computational resources, while processing large MRI volumes with three-dimensional (3D) templates. Hence, reducing the computational complexity of template matching is needed. In this paper, we first propose a mathematical framework for computing the normalized cross-correlation coefficient (NCCC) as the similarity measure between the MRI volume and approximated 3D Gaussian template with linear time complexity, [Formula], as opposed to the conventional fast Fourier transform (FFT) based approach with the complexity [Formula], where N is the number of voxels in the image and amax is the number of tried template radii. We then propose a mathematical formulation to analytically estimate the optimal template radius for each voxel in the image and compute the NCCC with the location-dependent optimal radius, reducing the complexity to [Formula]. We test our methods on one synthetic and two real multiple-sclerosis databases, and compare their performances in lesion detection with FFT and a state-of-the-art lesion prediction algorithm. We demonstrate through our experiments the efficiency of the proposed methods for brain lesion detection and their comparable performance with existing techniques.
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neuroscience
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Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define colorectal cancer cell types and signals controlling their development. More than 30,000 epithelial single cell transcriptomes of tumors and matched non-cancerous tissues of twelve colorectal cancer patients were clustered into six patient-overarching groups defined by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories, providing a basis for non-genetic resistance to targeted therapies.
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cancer biology
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Highly Multiplexed Single-Cell Full-Length cDNA Sequencing of human immune cells with 10X Genomics and R2C2 Single cell transcriptome analysis elucidates facets of cell biology that have been previously out of reach. However, the high-throughput analysis of thousands of single cell transcriptomes has been limited by sample preparation and sequencing technology. High-throughput single cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5 or 3 end. These cDNA pools are most often analyzed by short read Illumina sequencing which can identify the cellular origin of a transcript and what gene it was transcribed from. However, these methods fail to retrieve isoform information. In principle, cDNA pools prepared using these approaches can be analyzed with Pacific Biosciences and Oxford Nanopore long-read sequencers to retrieve isoform information but current implementations rely heavily on Illumina short-reads for analysis in addition to long reads. Here, we used R2C2 to sequence and demultiplex 12 million full-length cDNA molecules generated by the 10X Chromium platform from [~]3000 peripheral blood mononuclear cells (PBMCs). We used these reads to - independent from Illumina data - cluster cells into B cells, T cells, and Monocytes and generate isoform-level transcriptomes for these cell types. We also generated isoform-level transcriptomes for all single cells and used this information to identify a wide range of isoform diversity between genes. Finally, we also designed a computational workflow to extract paired adaptive immune receptors - T cell receptor and B cell receptor (TCR and BCR) - sequences unique to each T and B cell. This work represents a new, simple, and powerful approach that - using a single sequencing method - can extract an unprecedented amount of information from thousands of single cells.
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genomics
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Music-selective neural populations arise without musical training Recent work has shown that human auditory cortex contains neural populations anterior and posterior to primary auditory cortex that respond selectively to music. However, it is unknown how this selectivity for music arises. To test whether musical training is necessary, we measured fMRI responses to 192 natural sounds in 10 people with almost no musical training. When voxel responses were decomposed into underlying components, this group exhibited a music-selective component that was very similar in response profile and anatomical distribution to that previously seen in individuals with moderate musical training. We also found that musical genres that were less familiar to our participants (e.g., Balinese gamelan) produced strong responses within the music component, as did drum clips with rhythm but little melody, suggesting that these neural populations are broadly responsive to music as a whole. Our findings demonstrate that the signature properties of neural music selectivity do not require musical training to develop, showing that the music-selective neural populations are a fundamental and widespread property of the human brain.
NEW & NOTEWORTHYWe show that music-selective neural populations are clearly present in people without musical training, demonstrating that they are a fundamental and widespread property of the human brain. Additionally, we show music-selective neural populations respond strongly to music from unfamiliar genres as well as music with rhythm but little pitch information, suggesting that they are broadly responsive to music as a whole.
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neuroscience
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Differential contributions of synaptic and intrinsic inhibitory currents to speech segmentation via flexible phase-locking in neural oscillators Current hypotheses suggest that speech segmentation - the initial division and grouping of the speech stream into candidate phrases, syllables, and phonemes for further linguistic processing - is executed by a hierarchy of oscillators in auditory cortex. Theta (~3-12 Hz) rhythms play a key role by phase-locking to recurring acoustic features marking syllable boundaries. Reliable synchronization to quasi-rhythmic inputs, whose variable frequency can dip below cortical theta frequencies (down to ~1 Hz), requires "flexible" theta oscillators whose underlying neuronal mechanisms remain unknown. Using biophysical computational models, we found that the flexibility of phase-locking in neural oscillators depended on the types of hyperpolarizing currents that paced them. Simulated cortical theta oscillators flexibly phase-locked to slow inputs when these inputs caused both (i) spiking and (ii) the subsequent buildup of outward current sufficient to delay further spiking until the next input. The greatest flexibility in phase-locking arose from a synergistic interaction between intrinsic currents that was not replicated by synaptic currents at similar timescales. Flexibility in phase-locking enabled improved entrainment to speech input, optimal at mid-vocalic channels, which in turn supported syllabic-timescale segmentation through identification of vocalic nuclei. Our results suggest that synaptic and intrinsic inhibition contribute to frequency-restricted and -flexible phase-locking in neural oscillators, respectively. Their differential deployment may enable neural oscillators to play diverse roles, from reliable internal clocking to adaptive segmentation of quasi-regular sensory inputs like speech.
Author summaryOscillatory activity in auditory cortex is believed to play an important role in auditory and speech processing. One suggested function of these rhythms is to divide the speech stream into candidate phonemes, syllables, words, and phrases, to be matched with learned linguistic templates. This requires brain rhythms to flexibly synchronize with regular acoustic features of the speech stream. How neuronal circuits implement this task remains unknown. In this study, we explored the contribution of inhibitory currents to flexible phase-locking in neuronal theta oscillators, believed to perform initial syllabic segmentation. We found that a combination of specific intrinsic inhibitory currents at multiple timescales, present in a large class of cortical neurons, enabled exceptionally flexible phase-locking, which could be used to precisely segment speech by identifying vowels at mid-syllable. This suggests that the cells exhibiting these currents are a key component in the brains auditory and speech processing architecture.
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neuroscience
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Calcium-independent astrocytic lipid release modulates neuronal excitability Accumulating data point to a key role of Ca2+-dependent gliotransmitter release as a modulator of neuronal networks. Here, we tested the hypothesis that astrocytes in response to agonist exposure also release lipid modulators through activation of Ca2+-independent phospholipase A2 (iPLA2) activity. We found that cultured rat astrocytes treated with selective ATP and glutamatergic agonists released arachidonic acid (AA) and/or its derivatives, including the endogenous cannabinoid 2-arachidonoyl-sn-glycerol (2AG) and prostaglandin E2 (PGE2). Surprisingly, buffering of cytosolic Ca2+ resulted in a sharp increase in agonist-induced astrocytic lipid release. In addition, astrocytic release of PGE2 enhanced miniature excitatory post-synaptic potentials (mEPSPs) by inhibiting the opening of neuronal Kv channels in brain slices. This study provides the first evidence for the existence of a Ca2+-independent pathway regulating the release of PGE2 from astrocytes, and furthermore demonstrates a functional role for astrocytic lipid release in the modulation of synaptic activity.
Significance StatementUntil now, the majority of studies implicating astrocytes in modulating synaptic activity have focused on Ca2+-dependent release of traditional gliotransmitters such as D-serine, ATP, and glutamate. Mobilization of intracellular stores of Ca2+ occurs within a matter of seconds, but this novel Ca2+-independent lipid pathway in astrocytes could potentially occur on a still faster time scale and thus participate in the rapid signaling processes involved in synaptic potentiation, attention, and neurovascular coupling.
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neuroscience
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A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes BackgroundGiven the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs.
ResultsWe introduce a novel statistic, Hind/HE, that uses the probability that two reads sampled from a genotype will belong to different alleles, instead of observed heterozygosity. The expected value of Hind/HE is the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. In addition to filtering paralogs, it can be used to filter loci with null alleles or high overdispersion, and identify individuals with unexpected ploidy and hybrid status. We demonstrate that the statistic is useful at read depths as low as five to 10, well below the depth needed for accurate genotype calling in polyploid and outcrossing species.
ConclusionsOur methodology for estimating Hind/HE across loci and individuals, as well as determining reasonable thresholds for filtering loci, is implemented in polyRAD v1.6, available at https://github.com/lvclark/polyRAD. In large sequencing datasets, we anticipate that the ability to filter markers and identify problematic individuals prior to genotype calling will save researchers considerable computational time.
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bioinformatics
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Engram reactivation during memory retrieval predicts long-term memory performance in aged mice Age-related cognitive decline preferentially targets long-lasting episodic memories that require intact hippocampal function. Memory traces (or engrams) are believed to be encoded within the neurons activated during learning (neuronal ensembles), and recalled by reactivation of the same population. However, whether engram reactivation dictates memory performance late in life is not known. Here, we labelled neuronal ensembles formed during object location recognition learning in the dentate gyrus, and analyzed the reactivation of this population by long-term memory recall in young adult, cognitively impaired-and unimpaired-aged mice. We found that reactivation of memory-encoding neuronal ensembles at long-term memory recall was disrupted in impaired but not unimpaired-aged mice. Furthermore, we showed that the memory performance in the aged population correlated with the degree of engram reactivation at long-term memory recall. Overall, our data implicates recall-induced engram reactivation as a prediction factor of memory performance in aging. Moreover, our findings suggest impairments in neuronal ensemble stabilization and/or reactivation as an underlying mechanism in age-dependent cognitive decline.
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neuroscience
|
Structural analysis of Sulfolobus solfataricus TF55β chaperonin in open and filamentous states Chaperonins are biomolecular complexes that assist protein folding. Thermophilic Factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has , {beta} and {gamma} subunits. Using cryo-electron microscopy, we have determined the structure of the {beta}-only complex of S. solfataricus TF55 complexes to 3.6-4.2 [A] resolution and a filamentous form to 5.2 [A] resolution. The structures of the TF55{beta} complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle. The structure of the filamentous state indicates how helical protrusions facilitate end-on-end interactions.
SynopsisThe isolated complex and filamentous forms of TF55{beta} chaperonin from the thermophilic archaea Sulfolobus solfataricus are reported. Using cryo-EM, nucleotide-bound complexes of TF55{beta} at 3.6-4.2 [A] resolution reveal an open conformation, while a 5.2 [A] reconstruction of the filamentous chaperonin reveals contacts at the apical domain similar to crystal-packed structures.
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biophysics
|
Increased fronto-temporal connectivity by modified melody in real music In real music, the original melody may appear intact, with little elaboration only, or significantly modified. Since a melody is most easily perceived in music, hearing significantly modified melody may change a brain connectivity. Mozart KV 265 is comprised of a theme with an original melody of "Twinkle Twinkle Little Star" and its significant variations. We studied whether effective connectivity changes with significantly modified melody, between bilateral inferior frontal gyri (IFGs) and Heschls gyri (HGs) using magnetoencephalography (MEG). Among the 12 connectivities, the connectivity from the left IFG to the right HG was consistently increased with significantly modified melody compared to the original melody in 2 separate sets of the same rhythmic pattern with different melody (p = 0.005 and 0.034, Bonferroni corrected). Our findings show that the modification of an original melody in a real music changes the brain connectivity.
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neuroscience
|
Species coexistence in resource-limited patterned ecosystems is facilitated by the interplay of spatial self-organisation and intraspecific competition The exploration of mechanisms that enable species coexistence under competition for a sole limiting resource is widespread across ecology. Two examples of such facilitative processes are intraspecific competition and spatial self-organisation. These processes determine the outcome of competitive dynamics in many resource-limited patterned ecosystems, classical examples of which include dryland vegetation patterns, intertidal mussel beds and Sub-alpine ribbon forests. Previous theoretical investigations have explained coexistence within patterned ecosystems by making strong assumptions on the differences between species (e.g. contrasting dispersal behaviours or different functional responses to resource availability). In this paper, I show that the interplay between the detrimental effects of intraspecific competition and the facilitative nature of self-organisation forms a coexistence mechanism that does not rely on species-specific assumptions and captures coexistence across a wide range of the environmental stress gradient. I use a theoretical model that captures the interactions of two generic consumer species with an explicitly modelled resource to show that coexistence relies on a balance between species colonisation abilities and their local competitiveness, provided intraspecific competition is sufficiently strong. Crucially, the requirements on species self-limitation for coexistence to occur differ on opposite ends of the resource input spectrum. For low resource levels, coexistence is facilitated by strong intraspecific dynamics of the species superior in its colonisation abilities, but for larger volumes of resource input, strong intraspecific competition of the locally superior species enables coexistence. Results presented in this paper also highlight the importance of hysteresis in understanding tipping points, in particular extinction events. Finally, the theoretical framework provides insights into spatial species distributions within single patches, supporting verbal hypotheses on co-existence of herbaceous and woody species in dryland vegetation patterns and suggesting potential empirical tests in the context of other patterned ecosystems.
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ecology
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Evolutionary and ecological processes influencing chemical defense variation in an aposematic and mimetic Heliconius butterfly Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. Cyanogenic Heliconius butterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation in de novo biosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations of Heliconius erato along environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles of H. erato from geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems.
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evolutionary biology
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Phosphatidylinositol Acyl Chains Configure Priming and Activation of the NLRP3 Inflammasome Imbalance in lipid homeostasis is associated with discrepancies in immune signalling and is tightly linked to metabolic disorders. The diverse ways in which lipids impact immune signalling, however, remain ambiguous. The phospholipid phosphatidylinositol (PI), which is implicated in numerous immune disorders, is chiefly defined by its phosphorylation status. By contrast, the significance of the two fatty acid chains attached to the PI remains unknown. Here, by employing a mass-spectrometry-based assay, we demonstrate a role for PI acyl group chains in regulating both the priming and activation steps of the NLRP3 inflammasome in mouse macrophages. In response to NLRP3 stimuli, cells deficient in ABC transporter ABCB1, which effluxes lipid derivatives, revealed defective inflammasome activation. Mechanistically, Abcb1-deficiency shifted the total PI configuration exhibiting a reduced ratio of short-chain to long-chain PI-acyl lipids. Consequently, Abcb1-deficiency resulted in rapid degradation of TIRAP, the TLR adaptor protein which binds PI(4,5)-phosphate. Moreover, this accompanied increased NLRP3 phosphorylation at the Ser293 position and blunted inflammasome activation. Exogenously supplementing WT cells with linoleic acid, but not arachidonic acid, reconfigured PI acyl chains. Accordingly, linoleic acid supplementation increased TIRAP degradation, elevated NLRP3 phosphorylation, and abrogated inflammasome activation. Altogether, our study reveals a novel metabolic-inflammatory circuit which contributes to calibrating immune responses.
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immunology
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Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development Cell competition is emerging as a quality control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mouse, prior to gastrulation 35% of epiblast cells are eliminated. Here we have performed single cell transcriptional profiling of these cells and find that they show the hallmarks of cell competition and have mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function is sufficient to trigger competition. Importantly, we show that in the embryo cell competition eliminates cells with mitochondrial DNA mutations and that even non-pathological changes in mitochondrial DNA sequence can induce cell competition. Our results therefore suggest that cell competition is a purifying selection that optimises mitochondrial performance prior to gastrulation.
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developmental biology
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Conceptual knowledge affects early stages of visual mental imagery and object perception When we imagine an object and when we actually see that object, similar brain regions become active. Yet, the time course and mechanisms with which imagery engages perceptual networks remain to be better understood. An emerging view holds that imagery and perception follow distinct dynamics during early visual processing with similarities arising only during later, high-level visual processing. However, confounds of visual stimulation and paradigms favoring observation of high-level processes associated with subjective imagery strength may have precluded evidence of earlier shared mechanisms. We therefore manipulated prior knowledge that informs early-stage top-down predictions and tracked electrophysiological brain responses while fully controlling visual stimulation. Participants saw and imagined objects associated with varying amounts of semantic knowledge. Imagery and perception were equally influenced by knowledge at an early stage (P1 component), revealing shared mechanisms that support low-level visual processing. This finding complements previous research by showing that imagery is not merely perception in reverse. Instead, in line with the predictive processing framework, both, perception and imagery are active and constructive processes that share top-down mechanisms already in early phases of processing.
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neuroscience
|
Efficient Coding in the Economics of Human Brain Connectomics In systems neuroscience, most models posit that brain regions communicate information under constraints of efficiency. Yet, evidence for efficient communication in structural brain networks characterized by hierarchical organization and highly connected hubs remains sparse. The principle of efficient coding proposes that the brain transmits maximal information in a metabolically economical or compressed form to improve future behavior. To determine how structural connectivity supports efficient coding, we develop a theory specifying minimum rates of message transmission between brain regions to achieve an expected fidelity, and we test five predictions from the theory based on random walk communication dynamics. In doing so, we introduce the metric of compression efficiency, which quantifies the trade-off between lossy compression and transmission fidelity in structural networks. In a large sample of youth (n = 1,042; age 8-23 years), we analyze structural networks derived from diffusion weighted imaging and metabolic expenditure operationalized using cerebral blood flow. We show that structural networks strike compression efficiency trade-offs consistent with theoretical predictions. We find that compression efficiency prioritizes fidelity with development, heightens when metabolic resources and myelination guide communication, explains advantages of hierarchical organization, links higher input fidelity to disproportionate areal expansion, and shows that hubs integrate information by lossy compression. Lastly, compression efficiency is predictive of behavior--beyond the conventional network efficiency metric--for cognitive domains including executive function, memory, complex reasoning, and social cognition. Our findings elucidate how macroscale connectivity supports efficient coding, and serve to foreground communication processes that utilize random walk dynamics constrained by network connectivity.
Author SummaryMacroscale communication between interconnected brain regions underpins most aspects of brain function and incurs substantial metabolic cost. Understanding efficient and behaviorally meaningful information transmission dependent on structural connectivity has remained challenging. We validate a model of communication dynamics atop the macroscale human structural connectome, finding that structural networks support dynamics that strike a balance between information transmission fidelity and lossy compression. Notably, this balance is predictive of behavior and explanatory of biology. In addition to challenging and reformulating the currently held view that communication occurs by routing dynamics along metabolically efficient direct anatomical pathways, our results suggest that connectome architecture and behavioral demands yield communication dynamics that accord to neurobiological and information theoretical principles of efficient coding and lossy compression.
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neuroscience
|
A Connectivity-based Psychometric Prediction Framework for Brain-behavior Relationship Studies The recent availability of population-based studies with neuroimaging and behavioral measurements opens promising perspectives to investigate the relationships between interindividual variability in brain regions connectivity and behavioral phenotypes. However, the multivariate nature of connectivity-based prediction model severely limits the insight into brain-behavior patterns for neuroscience. To address this issue, we propose a connectivity-based psychometric prediction framework based on individual regions connectivity profiles. We first illustrate two main applications: 1) single brain regions predictive power for a range of psychometric variables, and 2) single psychometric variables predictive power variation across brain region. We compare the patterns of brain-behavior provided by these approaches to the brain-behavior relationships from activation approaches. Then, capitalizing on the increased transparency of our approach, we demonstrate how the influence of various data processing and analyses can directly influence the patterns of brain-behavior relationships, as well as the unique insight into brain-behavior relationships offered by this approach.
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neuroscience
|
Modular and distinct PlexinA4/Farp2/Rac1 signaling controls dendrite morphogenesis Diverse neuronal populations with distinct cellular morphologies coordinate the complex function of the nervous system. Establishment of distinct neuronal morphologies critically depends on signaling pathways that control axonal and dendritic development. The Sema3A-Nrp1/PlxnA4 signaling pathway promotes cortical neuron basal dendrite arborization but also repels axons. However, the downstream signaling components underlying these disparate functions of Sema3A signaling are unclear. Using the novel PlxnA4KRK-AAA knock-in male and female mice, generated by CRISPR/cas9, we show here that the KRK motif in the PlxnA4 cytoplasmic domain is required for Sema3A-mediated cortical neuron dendritic elaboration but is dispensable for inhibitory axon guidance. The RhoGEF FARP2, which binds to the KRK motif, shows identical functional specificity as the KRK motif in the PlxnA4 receptor. We find that Sema3A activates the small GTPase Rac1, and that Rac1 activity is required for dendrite elaboration but not axon growth cone collapse. This work identifies a novel Sema3A-Nrp1/PlxnA4/FARP2/Rac1 signaling pathway that specifically controls dendritic morphogenesis but is dispensable for repulsive guidance events. Overall, our results demonstrate that the divergent signaling output from multifunctional receptor complexes critically depends on distinct signaling motifs, highlighting the modular nature of guidance cue receptors and its potential to regulate diverse cellular responses.
Significance StatementThe proper formation of axonal and dendritic morphologies is crucial for the precise wiring of the nervous system that ultimately leads to the generation of complex functions in an organism. The Semaphorin3A-Neuropilin1/Plexin-A4 signaling pathway has been shown to have multiple key roles in neurodevelopment, from axon repulsion to dendrite elaboration. This study demonstrates that three specific amino acids, the KRK motif within the Plexin-A4 receptor cytoplasmic domain, are required to coordinate the downstream signaling molecules to promote Sema3A-mediated cortical neuron dendritic elaboration, but not inhibitory axon guidance. Our results unravel a novel Semaphorin3A-Plexin-A4 downstream signaling pathway and shed light on how the disparate functions of axon guidance and dendritic morphogenesis are accomplished by the same extracellular ligand in vivo.
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neuroscience
|
De novo learning versus adaptation of continuous control in a manual tracking task How do people learn to perform tasks that require continuous adjustments of motor output, like riding a bicycle? People rely heavily on cognitive strategies when learning discrete movement tasks, but such time-consuming strategies are infeasible in continuous control tasks that demand rapid responses to ongoing sensory feedback. To understand how people can learn to perform such tasks without the benefit of cognitive strategies, we imposed a rotation/mirror reversal of visual feedback while participants performed a continuous tracking task. We analyzed behavior using a system identification approach which revealed two qualitatively different components of learning: adaptation of a baseline controller and formation of a new, task-specific continuous controller. These components exhibited different signatures in the frequency domain and were differentially engaged under the rotation/mirror reversal. Our results demonstrate that people can rapidly build a new continuous controller de novo and can simultaneously deploy this process with adaptation of an existing controller.
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neuroscience
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Positive selection and gene duplications in tumour suppressor genes reveal clues abouthow cetaceans resist cancer Cetaceans are the longest-living species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases such cancer, although the underlying molecular bases of these remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of 1077 tumour suppressor genes (TSGs) in cetaceans. We used a comparative genomic approach to analyse two sources of molecular variation in the form of dN/dS rates and gene copy number variation. We found a signal of positive selection in the ancestor of cetaceans within the CXCR2 gene, an important regulator of DNA-damage, tumour dissemination, and immune system. Further, in the ancestor of baleen whales, we found six genes exhibiting positive selection relating to such diseases as breast carcinoma, lung neoplasm (ADAMTS8) and leukaemia (ANXA1). The TSG turnover rate (gene gain and loss) was almost 2.4-fold higher in cetaceans as compared to other mammals, and noticeably even faster in baleen whales. The molecular variants in TSGs found in baleen whales, combined with the faster gene turnover rate, could have favoured the evolution of their particular traits of anti-cancer resistance, gigantism and longevity. Additionally, we report 71 genes with duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and SIK1) and are important regulators of senescence, cell proliferation and metabolism. Overall, these results provide evolutionary evidence that natural selection in tumour suppressor genes could act on species with large body sizes and extended life span, providing novel insights into the genetic basis of disease resistance.
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evolutionary biology
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Regeneration in adult Drosophila brain Neurodegenerative diseases such as Alzheimers and Parkinsons currently affect [~]25 million people worldwide (EO_SCPLOWRKKINENC_SCPLOW et al. 2018). The global incidence of traumatic brain injury (TBI) is estimated at [~]70 million/year (DO_SCPLOWEWANC_SCPLOW et al. 2018). Both neurodegenerative diseases and TBI remain without effective treatments. We are utilizing adult Drosophila melanogaster to investigate the mechanisms of brain regeneration with the long term goal of identifying targets for neural regenerative therapies. Like mammals, Drosophila have few proliferating cells in the adult brain. Nonetheless, within 24 hours of a Penetrating Traumatic Brain Injury (PTBI) to the central brain, there is a significant increase in the number of proliferating cells. We subsequently detect both new glia and new neurons and the formation of new axon tracts that target appropriate brain regions. Glial cells divide rapidly upon injury to give rise to new glial cells. Other cells near the injury site upregulate neural progenitor genes including asense and deadpan and later give rise to the new neurons. Locomotor abnormalities observed after PTBI are reversed within two weeks of injury, supporting the idea that there is functional recovery. Together, these data indicate that adult Drosophila brains are capable of neuronal repair. We anticipate that this paradigm will facilitate the dissection of the mechanisms of neural regeneration and that these processes will be relevant to human brain repair.
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neuroscience
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The hippocampal formation as a hierarchical generative model supporting generative replay and continual learning We advance a novel computational theory of the hippocampal formation as a hierarchical generative model that organizes sequential experiences, such as rodent trajectories during spatial navigation, into coherent spatiotemporal contexts. We propose that the hippocampal generative model is endowed with inductive biases to pattern-separate individual items of experience (first hierarchical layer), organize them into sequences (second layer) and cluster them into maps (third layer). This theory entails a novel characterization of hippocampal reactivations as generative replay: the offline resampling of fictive sequences from the generative model, which supports the continual learning of multiple sequential experiences. We show that the model learns and efficiently retains multiple spatial navigation trajectories, by organizing them into spatial maps. Furthermore, the hierarchical model reproduces flexible and prospective aspects of hippocampal dynamics that are challenging to explain within existing frameworks. This theory reconciles multiple roles of the hippocampal formation in map-based navigation, episodic memory and imagination.
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neuroscience
|
Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation Among the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and the hand-wing index) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found evidence that species that fly less have greater wing loading and this is associated with accelerated rates of mutation. An elongated wing morphology is associated with greater flight activity and with molecular signatures of positive selection or reduced population sizes. Meanwhile, environmental temperature and UV radiation interact to explain molecular rates at sites affected by selection and population size, contrary to the expectation of their impact on mutation rates. Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size.
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evolutionary biology
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Genetic population structure constrains local adaptation in sticklebacks Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2x stronger population structuring among freshwater populations and >10x stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.
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evolutionary biology
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Chronic Staphylococcus aureus infection is cured by theory-driven therapy Staphylococcus aureus is considered a dangerous pathogen due to its ability to evade the immune system and resist multiple antibiotics. These evasive strategies lead to difficult-to-treat chronic infections and abscesses in internal organs including kidneys, which are associated with the expansion of myeloid-derived suppressor cells (MDSCs) and their suppressive effect on T cells. Here, we developed a mathematical model of chronic S. aureus infection that incorporates the T-cell suppression by MDSCs and suggests therapeutic strategies to eradicate S. aureus. We quantified in silico a therapeutic protocol with heat-killed S. aureus (HKSA), which we tested in vivo. Contrary to conventional administration of heat-killed bacteria as vaccination prior to infection, we administered HKSA as treatment, when the hosts were already chronically infected. Our treatment cured all chronically S. aureus-infected mice, reduced MDSCs, and reversed T-cell dysfunction by inducing acute inflammation during ongoing, chronic infection without any use of standard treatments that involve antibiotics, MDSC-targeting drugs (chemotherapy), or procedures such as abscess drainage. This study is a proof-of-principle for a treatment protocol against chronic S. aureus infection and renal abscesses by repurposing heat-killed treatments, guided and quantified by mathematical modelling. Our mathematical model further explains why previous treatment with inactivated S. aureus administered to long-term infected human patients has not led to cure. Overall, our results can have direct relevance to the design of human therapeutics against chronic S. aureus infections.
In briefA theory-driven treatment protocol with heat-killed S. aureus eradicates S. aureus, reduces MDSCs, and reverses T-cell dysfunction in vivo.
Graphical abstract
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systems biology
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Virtual connectomic datasets in Alzheimer's Disease and aging using whole-brain network dynamics modelling Large neuroimaging datasets, including information about structural (SC) and functional connectivity (FC), play an increasingly important role in clinical research, where they guide the design of algorithms for automated stratification, diagnosis or prediction. A major obstacle is, however, the problem of missing features (e.g., lack of concurrent DTI SC and resting-state fMRI FC measurements for many of the subjects).
We propose here to address the missing connectivity features problem by introducing strategies based on computational whole-brain network modeling. Using two datasets, the ADNI dataset and a healthy aging dataset, for proof-of-concept, we demonstrate the feasibility of virtual data completion (i.e., inferring "virtual FC" from empirical SC or "virtual SC" from empirical FC), by using self-consistent simulations of linear and nonlinear brain network models. Furthermore, by performing machine learning classification (to separate age classes or control from patient subjects) we show that algorithms trained on virtual connectomes achieve discrimination performance comparable to when trained on actual empirical data; similarly, algorithms trained on virtual connectomes can be used to successfully classify novel empirical connectomes. Completion algorithms can be combined and reiterated to generate realistic surrogate connectivity matrices in arbitrarily large number, opening the way to the generation of virtual connectomic datasets with network connectivity information comparable to the one of the original data.
Significance statementPersonalized information on anatomical connectivity ("structural connectivity", SC) or coordinated resting state activation patterns ("functional connectivity, FC) is a source of powerful neuromarkers to detect and track the development of neurodegenerative diseases. However, there are often "gaps" in the available information, with only SC (or FC) being known but not FC (or SC). Exploiting whole-brain modelling, we show that gap in databases can be filled by inferring the other connectome through computational simulations. The generated virtual connectomic data carry information analogous to the one of empirical connectomes, so that machine learning algorithms can be trained on them. This opens the way to the release in the future of cohorts of "virtual patients", complementing traditional datasets in data-driven predictive medicine.
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neuroscience
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A role for reward valuation in the serotonergic modulation of impulsivity Impulsive behavior is a deleterious component of a number of mental health disorders but has few targeted pharmacotherapies. One contributing factor to the difficulty in understanding the neural substrates of disordered impulsivity is the diverse presentations of impulsive behavior. Defining the behavioral and cognitive processes which contribute to different subtypes of impulsivity is integral to understanding and treating disorders with dysregulated impulsive behavior. Our approach was to first determine what behavioral and cognitive phenotypes are associated with increased impulsive behavior, and then probe if they could causally contribute to increasing impulsivity. We used a mouse model for disordered impulsivity - mice lacking the serotonin 1B receptor (5-HT1BR) which have deficits specific to impulsive action, and not other components of impulsive behavior. Here we report, that in addition to increased impulsive action, mice lacking expression of 5-HT1BR also have increased goal-directed responding and motivation, with no differences in extinction, development of habitual behavior, delay discounting, or effort-based discounting. Interestingly, mice lacking 5-HT1BR expression did show an overall increase in the choice of higher value rewards, increased hedonic responses to sweet rewards, and responded more to cues that predict reward, compared to controls. We developed a novel paradigm to demonstrate that increasing anticipated reward value could directly increase impulsive action. Furthermore, we found that 5-HT1BR KO-induced impulsivity could be ameliorated by decreasing the reward value relative to controls, suggesting that the increased 5-HT1BR-associated impulsive action is a result of increased reward valuation. Taken together, these data show that the effects of serotonin on impulsive action are mediated through the modulation of hedonic value, which may alter the reward representations that motivate action. Additionally this work supports a role for reward valuation as an important substrate in impulsive action which may drive clinically-relevant increases in impulsivity.
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neuroscience
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DNA damage and macrophage infiltration in the ovaries of the long-lived GH deficient Ames Dwarf and the short-lived bGH transgenic mice ObjectiveThe aim of the study was to evaluate the role of growth hormone (GH) in DNA damage, macrophage infiltration and the granulosa cells number of primordial and primary follicles.
MethodsFor these experiments six groups of female mice were used. Four groups consisted of Ames dwarf (Prop-1df, df/df, n=12) and their normal littermates (N/df, n=12) mice, between sixteen and eighteen month-old, receiving GH (n=6 for df/df, and n=6 for N/df mice) or saline injections (n=6 for df/df, and n=6 for N/df mice). The other two groups consisted of ten to twelve-month-old bGH (n=6) and normal mice (N, n=6). Immunofluorescence for DNA damage (anti-{gamma}H2AX) and macrophage counting (anti-CD68) were performed. Granulosa cells of primordial and primary follicles were counted.
ResultsFemale df/df mice had lower {gamma}H2AX foci intensity in in both oocytes and granulosa cells of primordial and primary follicles (p<0.05), indicating less DNA double strand breaks (DSBs). In addition, GH treatment increased DSBs in both df/df and N/df mice. Inversely, bGH mice had higher quantity of DSBs in both oocytes and granulosa cells of primordial and primary follicles (p<0.05). Df/df mice showed ovarian tissue with less macrophage infiltration than N/df mice (p<0.05) and GH treatment increased macrophage infiltration (p<0.05). On the other hand, bGH mice had ovarian tissue with more macrophage infiltration compared to normal mice (p<0.05). Df/df mice had less granulosa cells on primordial and primary follicles than N/df mice (p<0.05). GH treatment did not affect the granulosa cells number (p>0.05). However, bGH mice had an increased number of granulosa cells on primordial and primary follicles compared to normal mice (p<0.05).
ConclusionThe current study points to the role of the GH/IGF-I axis in maintenance of oocyte DNA integrity and macrophage ovarian infiltration in mice.
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physiology
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A simple, cheap, and robust protocol for the identification of mating type in Saccharomyces cerevisiae Saccharomyces cerevisiae is an exceptional genetic system, with genetic crosses facilitated by its ability to be maintained in haploid and diploid forms. Such crosses are straightforward if the mating type/ploidy of the strains are known. Several techniques can be used to determine mating type (or ploidy), but all have limitations. Here we validate a simple, cheap and robust method to rapidly identify S. cerevisiae mating types. When cells of opposite mating type are mixed in liquid media, they "creep" up the culture vessel sides, a phenotype that can be easily detected visually. In contrast, mixtures of the same mating type or with a diploid simply settle out. The phenotype is robust to different media, cell densities, temperatures and strains, and is observable for several days. Microscopy suggests that cell aggregation during mating is responsible for the phenotype. Yeast knockout collection analysis identified 107 genes required for the creeping phenotype, with these being enriched for mating-specific genes. Surprisingly, the RIM101 signalling pathway was strongly represented. We propose that RIM101 signalling regulates aggregation as part of a wider, previously-unrecognized role in mating. The simplicity and robustness of this method makes it ideal for routine verification of S. cerevisiae mating type, with future studies required to verify its molecular basis.
|
microbiology
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Genome-wide discovery of lupus genetic risk variant allelic regulatory activity Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second, larger class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE.
|
genomics
|
A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and D. yakuba. We designed a semi-automatic measurement pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches in D. yakuba but that in D. santomea ventral branches tend to morph into a D. yakuba-like shape at lower temperature. Our results suggest that speciation of D. santomea and D. yakuba was associated with a change in genitalia plasticity.
|
evolutionary biology
|
Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
|
biochemistry
|
A signal of competitive dominance in mid-latitude herbaceous plant communities Understanding the main determinants of species coexistence across space and time is a central question in ecology. However, ecologists still know little about the scales and conditions at which biotic interactions matter and how these interact with the environment to structure species assemblages. Here we use recent theory developments to analyze plant distribution and trait data across Europe and find that plant height clustering is related to both evapotranspiration and gross primary productivity. This clustering is a signal of interspecies competition between plants, which is most evident in mid-latitude ecoregions, where conditions for growth (reflected in actual evapotranspiration rates and gross primary productivities) are optimal. Away from this optimum, climate severity likely overrides the effect of competition, or other interactions become increasingly important. Our approach bridges the gap between species-rich competition theories and large-scale species distribution data analysis.
|
ecology
|
Description of a widespread bacterial secretion system with chemically diverse substrates In host-associated bacteria, surface and secreted proteins mediate acquisition of nutrients, interactions with host cells, and specificity of tissue-localization. In Gram-negative bacteria, the mechanism by which many proteins cross or become tethered to the outer membrane remains unclear. The domain of unknown function (DUF)560 occurs in outer membrane proteins throughout Proteobacteria and has been implicated in host-bacteria interactions and lipoprotein surface exposure. We used sequence similarity networking to reveal three subfamilies of DUF560 homologs. One subfamily includes those DUF560 proteins experimentally characterized to date: NilB, a host-range determinant of the nematode-mutualist Xenorhabdus nematophila, and the surface lipoprotein assembly modulators Slam1 and Slam2, which facilitate msurface exposure of lipoproteins in Neisseria meningitidis (1, 2). We show that DUF560 proteins from a second subfamily facilitate secretion of soluble, non-lipidated proteins across the outer membrane. Using in silico analysis, we demonstrate that DUF560 gene complement correlates with bacterial environment at a macro level and host association at a species level. The DUF560 protein superfamily represents a newly characterized Gram-negative secretion system capable of lipoprotein surface exposure and soluble protein secretion with conserved roles in facilitating symbiosis. In light of these data, we propose that it be titled the type eleven secretion system (TXISS).
ImportanceThe microbial constituents of a host associated microbiome are decided by a complex interplay of microbial colonization factors, host surface conditions, and host immunological responses. Filling such niches requires bacteria to encode an arsenal of surface and secreted proteins to effectively interact with the host and co-occurring microbes. Bioinformatic predictions of the localization and function of putative bacterial colonization factors are essential for assessing the potential of bacteria to engage in pathogenic, mutualistic, or commensal activities. This study uses publicly available genome sequence data, alongside experimental results from representative gene products from Xenorhabdus nematophila, to demonstrate a role for DUF560 family proteins in the secretion of bacterial effectors of host interactions. Our research delineates a broadly distributed family of proteins and enables more accurate predictions of the localization of colonization factors throughout Proteobacteria.
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microbiology
|
Desmosomes polarize mechanical signaling to govern epidermal tissue form and function The epidermis is a stratified epithelium in which structural and functional features are polarized across multiple cell layers. This type of polarity is essential for establishing the epidermal barrier, but how it is created and sustained is poorly understood. Previous work identified a role for the classical cadherin/filamentous-actin network in establishment of epidermal polarity. However, little is known about potential roles of the most prominent epidermal intercellular junction, the desmosome, in establishing epidermal polarity, in spite of the fact that desmosome constituents are patterned across the apical to basal cell layers. Here, we show that desmosomes and their associated intermediate filaments (IF) are key regulators of mechanical polarization in epidermis, whereby basal and suprabasal cells experience different forces that drive layer-specific functions. Uncoupling desmosomes and IF or specific targeting of apical desmosomes through depletion of the superficial desmosomal cadherin, desmoglein 1, impedes basal stratification in an in vitro competition assay and suprabasal tight junction barrier functions in 3D reconstructed epidermis. Surprisingly, disengaging desmosomes from IF also accelerated the expression of differentiation markers, through precocious activation of the mechanosensitive transcriptional regulator serum response factor (SRF) and downstream activation of Epidermal Growth Factor Receptor family member ErbB2 by Src family kinase (SFK) mediated phosphorylation. This Dsg1-SFK-ErbB2 axis also helps maintain tight junctions and barrier function later in differentiation. Together, these data demonstrate that the desmosome-IF network is a critical contributor to the cytoskeletal-adhesive machinery that supports the polarized function of the epidermis.
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cell biology
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Use of high-refractive index hydrogels and tissue clearing for large biological sample imaging Recent advances in tissue clearing and light sheet fluorescence microscopy have improved insights into and understanding of tissue morphology and disease pathology by imaging large samples without the requirement of histological sectioning. However, sample handling and conservation of sample integrity during lengthy staining and acquisition protocols remains a challenge. This study overcomes these challenges with acrylamide hydrogels synthesised to match the refractive index of solutions typically utilised in aqueous tissue clearing protocols. These hydrogels have a high-water content (82.0{+/-}3.7% by weight). The gels are stable over time and FITC-IgG readily permeated into, and effluxed out of them. Whilst the gels deformed and/or swelled over time in some commonly used solutions, this was overcome by using a previously described custom refractive index matched solution. To validate their use, CUBIC cleared mouse tissues and whole embryos were embedded in hydrogels, stained using fluorescent small molecule dyes, labels and antibodies and successfully imaged using light sheet fluorescence microscopy. In conclusion, the high-water content, high refractive index hydrogels described in this study have a broad applicability to research that delves into pathophysiological processes by stabilising and protecting large and fragile samples.
|
pathology
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Evidence of Absence Regression: A Binomial N-Mixture Model for Estimating Fatalities at Wind Power Facilities Estimating bird and bat fatalities caused by wind-turbine facilities is challenging when carcass counts are rare and produce counts that are either exactly zero or very near zero. The rarity of found carcasses is exacerbated when live members of a particular species are rare and when carcasses degrade quickly, are removed by scavengers, or are not detected by observers. With few observed carcass counts, common statistical methods like logistic, Poisson, or negative binomial regression are unreliable (statistically biased) and often fail to provide answers (i.e., fail to converge). Here, we propose a binomial N-mixture model that estimates fatality rates as well as the total number of carcass counts when these rates are expanded. Our model extends the evidence of absence model (Huso et al., 2015; Dalthorp, Huso, and Dail, 2017) by relating carcass deposition rates to study covariates and by incorporating terms that naturally scale counts from facilities of different sizes. Our model, which we call Evidence of Absence Regression (EoAR), can estimate the total number of birds or bats killed at a single wind energy facility or a fleet of wind energy facilities based on covariate values. Furthermore, with accurate prior distributions the models results are extremely robust to sparse data and unobserved combinations of covariate values. In this paper, we describe the model, show its low bias and high precision via computer simulation, and apply it to bat carcass counts observed at 21 wind energy facilities in Iowa.
|
ecology
|
Development of early postnatal inhibitory function in the mouse medial prefrontal and primary somatosensory cortex The prefrontal cortex (PFC) is characterized by protracted maturation. The cellular mechanisms controlling the early development of prefrontal circuits are still largely unknown. Our study delineates the developmental cellular processes in the mouse medial PFC (mPFC) during the second and third postnatal weeks and characterizes their contribution to the changes in network activity. We show that spontaneous inhibitory postsynaptic currents (sIPSC) are increased while spontaneous excitatory postsynaptic currents (sEPSC) are reduced from the second to the third postnatal week. Drug application suggested that the increased sEPSC frequency in mPFC at P10 is due to depolarizing GABAA receptor (GABAAR) function. To further validate this, perforated patch-clamp recordings were obtained and the expression levels of K-Cl co-transporter 2 (KCC2) protein were examined. The reversal potential of IPSCs in response to current stimulation was significantly more depolarized at P10 compared to P20 while KCC2 expression is decreased. Moreover, the number of parvalbumin-expressing GABAergic interneurons increase from P10 to P20 in the mPFC and their intrinsic electrophysiological properties significantly mature. Using computational modeling, we show that the developmental changes in synaptic and intrinsic properties of mPFC neurons contribute to the enhanced network activity in the juvenile compared to neonatal mPFC.
|
neuroscience
|
Not only compulsivity: The SAPAP3-KO mouse reconsidered as a comorbid model expressing a spectrum of pathological repetitive behaviors. Symptom comorbidity is present amongst neuropsychiatric disorders with repetitive behaviours, complicating clinical diagnosis and impeding appropriate treatments. This is of particular importance for obsessive-compulsive disorder (OCD) and Tourette syndrome. Here, we meticulously analysed the behaviour of Sapap3 knockout mice, the recent rodent model predominantly used to study compulsive-like behaviours, and found that its behaviour is more complex than originally and persistently described. Indeed, we detected previously unreported elements of distinct pathologically repetitive behaviours, which do not form part of rodent syntactic cephalo-caudal self-grooming. These repetitive behaviours include sudden, rapid body and head twitches, resembling tic-like movements. We also observed that another type of repetitive behaviours, aberrant hindpaw scratching, is responsible for the flagship-like skin lesions of this mouse model, rather than originally suspected self-grooming. In order to characterize the symptomatological nature of observed repetitive behaviours, we pharmacologically challenged these phenotypes by systemic aripiprazole administration, a first-line treatment for tic-like symptoms in Tourette Syndrome and trichotillomania. A single treatment of aripiprazole significantly reduced the number of tic-like movements but not syntactic grooming events. These observations are in line with the high comorbidity of tic- and compulsive-like symptoms in Tourette, OCD and trichotillomania patients as well as with the hypothesis of shared neurobiological mechanisms.
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neuroscience
|
Disentangling the roles of neocortical alpha/beta and hippocampal theta/gamma oscillations in human episodic memory formation To form an episodic memory, we must first process a vast amount of sensory information about a to-be-encoded event and then bind these sensory representations together to form a coherent memory. While these two cognitive capabilities are thought to have two distinct neural origins, with neocortical alpha/beta oscillations supporting information representation and hippocampal theta-gamma phase-amplitude coupling supporting mnemonic binding, evidence for a dissociation between these two neural markers is conspicuously absent. To address this, seventeen human participants completed a sequence-learning task that first involved processing information about three stimuli, and then binding these stimuli together into a coherent memory trace, all the while undergoing MEG recordings. We found that decreases in neocortical alpha/beta power during sequence perception, but not mnemonic binding, correlated with enhanced memory performance. Hippocampal theta/gamma phase-amplitude coupling, however, showed the opposite pattern; increases during mnemonic binding (but not sequence perception) correlated with enhanced memory performance. These results demonstrate that memory-related decreases in neocortical alpha/beta power and memory-related increases in hippocampal theta/gamma phase-amplitude coupling arise at distinct stages of the memory formation process. We speculate that this temporal dissociation reflects a functional dissociation in which neocortical alpha/beta oscillations could support the processing of incoming information relevant to the memory, while hippocampal theta-gamma phase-amplitude coupling could support the binding of this information into a coherent memory trace.
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neuroscience
|
Short hydrogen bonds enhance non-aromatic protein-related fluorescence Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, we show that specific hydrogen bonding networks can significantly affect fluorescence employing a combined experimental and computational approach. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared to L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease non-radiative transition probabilities. Our findings open the doors for the design of new photoactive materials with biophotonic applications.
Significance statementIntrinsic fluorescence of non-aromatic amino acids is a puzzling phenomenon with an enormous potential for technological and biomedical applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds in the networks on the ensuing fluorescence and we provide a detailed molecular mechanism to explain this unusual non-aromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.
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biophysics
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Prolonged disturbance of proteostasis induces cellular senescence via temporal mitochondrial dysfunction and enhanced mitochondrial biogenesis in human fibroblasts Proteolytic activities decline with age, resulting in the accumulation of aggregated proteins in aged organisms. To investigate how disturbance in proteostasis causes cellular senescence, we developed a stress-induced premature senescence (SIPS) model, in which normal human fibroblast MRC-5 cells were treated with either the proteasome inhibitor MG132 or the V-ATPase inhibitor bafilomycin A1 (BAFA1) for 5 days. Time-course studies revealed significant increase in intracellular and mitochondrial reactive oxygen species (ROS) during and after drug treatment. Mitochondrial membrane potential initially decreased, but recovered along with PGC-1-mediated mitochondrial biogenesis, especially after drug treatment. Mitochondrial antioxidant enzymes SOD2 and GPx4 were temporally depleted in mitochondria on day 1 of the treatment, which in turn could cause excess production of mitochondrial ROS. Extra-mitochondrial SOD2 colocalized with protein aggregates and lysosomes in MG132-treated cells on day 1. SOD2 partially interacted with HSC70 and LAMP2, implying that dysfunctional SOD2 was degraded through chaperon-mediated autophagy (CMA) and caused SOD2 depletion in mitochondria. SIPS induction by MG132 or BAFA1 was partially attenuated by co-treatment with rapamycin, in which generation of excess ROS and mitochondrial biogenesis were suppressed. Rapamycin co-treatment also augmented the upregulation of HSP70 and decreased protein aggregates after drug treatment. Our study proposes a possible pathway from the disturbance of proteostasis to cellular senescence via functional changes in mitochondria.
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cell biology
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Establishment of a Human RNA Pol II Pausing System and the Identification of O-GlcNAc Cycling Regulating Pol II Pausing and Elongation Paused RNA polymerase II is the major regulated step of transcription in metazoans. We describe here a unique human cell-free transcription system that recapitulates RNA pol II pausing and assemble paused pol IIs on the human CMV IE, SV40, and heat shock promoters, all is the case in vivo. We then use the system to show that PARP-1 and CDK12/13 inhibitors directly affect pausing and elongation. We then show that O-GlcNAcylation is required for the establishment of a paused pol II: inhibition of OGT allowed pol II to bypass pausing and begin to elongate. Addback of rOGT or the pausing factor NELF re-established the pausing. In vivo nascent RNA measurements showed that OGA inhibition blocks elongation. These data show that cell-free systems can recapitulate RNA pol II pausing, that PARP-1 and CDK12/13 directly regulate RNA pol II elongation, and identify O-GlcNAc cycling regulating both pausing and pause release.
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biochemistry
|
Entropy of city street networks linked to future spatial navigation ability Cultural and geographical properties of the environment have been shown to deeply influence cognition and mental health[1-6]. While living near green spaces has been found to be strongly beneficial [7-11], urban residence has been associated with a higher risk of some psychiatric disorders [12-14] (although see [15]). However, how the environment one grew up in impacts later cognitive abilities remains poorly understood. Here, we used a cognitive task embedded in a video game[16] to measure non-verbal spatial navigation ability in 397,162 people from 38 countries across the world. Overall, we found that people who grew up outside cities are better at navigation. More specifically, people were better at navigating in environments topologically similar to where they grew up. Growing up in cities with low Street Network Entropy (e.g. Chicago) led to better results at video game levels with a regular layout, while growing up outside cities or in cities with higher Street Network Entropy (e.g. Prague) led to better results at more entropic video game levels. This evidences the impact of the environment on human cognition on a global scale, and highlights the importance of urban design on human cognition and brain function.
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neuroscience
|
Single molecule imaging reveals the collective and independent search mechanisms of cFos and cJun on DNA AP-1 proteins are members of the basic leucine zipper (bZIP) family of dimeric transcription factors, which facilitate a multitude of cellular processes, but are primarily known for their oncogenic potential in several cancer types. The oncogenic transcription factor AP-1 binds a specific DNA target site (5TCA[G/C]TGA), however the physical mechanism of how this is achieved has not been determined. The archetypal AP-1 complex is formed by cFos and cJun, which heterodimerize via their leucine zipper domains. We investigated the DNA-binding bZIP domains of AP-1 interacting with DNA tightropes using real-time single molecule fluorescence imaging in vitro. We find that AP-1 bZIP domains comprising cFos:cJun and cJun:cJun rapidly scan DNA using a 1D diffusional search with average diffusion constants of 0.14 m2s-1 and 0.26 m2s-1 respectively. We also report for the first time that cFos is able to bind to and diffuse on DNA (0.29 m2s-1) as a mixed population of monomers and homodimers, despite previous studies suggesting that it is incapable of independent DNA binding. Additionally, we note increased pause lifetimes for the cFos:cJun heterodimer compared to the cJun:cJun homodimer, and were able to detect distinct pausing behaviours within diffusion data. Understanding how cFos:cJun and other transcription factors identify their targets is highly relevant to the development of new therapeutics which target DNA binding proteins using these search mechanisms.
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biochemistry
|
Climate change will drive novel cross-species viral transmission At least 10,000 species of mammal virus are estimated to have the potential to spread in human populations, but the vast majority are currently circulating in wildlife, largely undescribed and undetected by disease outbreak surveillance 1-3 . In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species 4, 5 . In some cases, this will inevitably facilitate spillover into humans 6, 7 --a possible mechanistic link between global environmental change and emerging zoonotic disease 8 . Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of potential geographic range shifts for 3,139 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the novel cross-species transmission of their viruses an estimated 4,000 times. Counter to expectations, holding warming under 2{degrees}C within the century does not reduce new viral sharing, due to greater potential range expansions-- highlighting the need to invest in surveillance even in a low-warming future. Most projected viral sharing is driven by diverse hyperreservoirs (rodents and bats) and large-bodied predators (carnivores). Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that could facilitate future emergence in humans. Our findings highlight the urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking species range shifts, especially in tropical countries that harbor the most emerging zoonoses.
|
ecology
|
Adaptive divergence generates distinct plastic responses in two closely related Senecio species The evolution of plastic responses to external cues allows species to track the environmental variation they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity is associated with recent adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled c.40 genotypes of each species from natural populations on and around Mt Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient representing each species native range, the edge of their range, and conditions outside their native range. At each elevation we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content and gene expression. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Traits and differentially expressed genes that changed with elevation in one species often showed little change in the other species, or changed in the opposite direction. Adaptive divergence is therefore associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.
|
evolutionary biology
|
TMEM184b is necessary for IL-31 induced itch Nociceptive and pruriceptive neurons in the dorsal root ganglia (DRG) convey sensations of pain and itch to the spinal cord, respectively. One subtype of mature DRG neurons, comprising about 5% of neurons in the ganglia, is responsible for sensing mediators of acute itch and atopic dermatitis, including the cytokine IL-31. How itch-sensitive (pruriceptive) neurons are specified is unclear. Here we show that Tmem184b, a gene with roles in axon degeneration and nerve terminal maintenance, is required for the expression of a large cohort of itch receptors, including those for IL-31, Leukotriene C4, and Histamine. Male and female mice lacking Tmem184b show reduced responses to IL-31, but maintain normal responses to pain and mechanical force, indicating a specific behavioral defect in pruriception. Calcium imaging experiments indicate that a reduction in IL-31 induced calcium entry is a likely contributor to this phenotype. We identify an early failure of proper Wnt-dependent transcriptional signatures and signaling components in Tmem184b mutant mice that may explain the improper DRG neuronal subtype specification. Accordingly, lentiviral re-expression of Tmem184b in mutant embryonic neurons restores Wnt signatures. Together, these data demonstrate that Tmem184b promotes adult somatosensation through developmental Wnt signaling and promotion of proper pruriceptive gene expression. Our data illuminate a new key regulatory step in the processes controlling the establishment of diversity in the somatosensory system.
|
neuroscience
|
Schizophrenia Risk Alleles Often Affect The Expression of Many Genes and Each Gene May Have a Different Effect On The Risk; A Mediation Analysis. Variants identified by genome-wide association studies (GWAS) are often expression quantitative trait loci (eQTLs), suggesting they are proxies or are themselves regulatory. Across many datasets analyses show that variants often affect multiple genes. Lacking data on many tissue types, developmental time points and homogeneous cell types, the extent of this one-to-many relationship is underestimated. This raises questions on whether a disease eQTL target gene explains the genetic association or is a by-stander and puts into question the direction of expression effect of on the risk, since the many variant - regulated genes may have opposing effects, imperfectly balancing each other. We used two brain gene expression datasets (CommonMind and BrainSeq) for mediation analysis of schizophrenia-associated variants. We confirm that eQTL target genes often mediate risk but the direction in which expression affects risk is often different from that in which the risk allele changes expression. Of 38 mediator genes significant in both datasets 33 showed consistent mediation direction (Chi2 test P=6*10-6). One might expect that the expression would correlate with the risk allele in the same direction it correlates with disease. For 15 of these 33 (45%), however, the expression change associated with the risk allele was protective, suggesting the likely presence of other target genes with overriding effects. Our results identify specific risk mediating genes and suggest caution in interpreting the biological consequences of targeted modifications of gene expression, as not all eQTL targets may be relevant to disease while those that are, might have different than expected directions.
|
genetics
|
Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions? In Bayesian phylogenetics, the coalescent process provides an informative framework for inferring changes in the effective size of a population from a phylogeny (or tree) of sequences sampled from that population. Popular coalescent inference approaches such as the Bayesian Skyline Plot, Skyride and Skygrid all model these population size changes with a discontinuous, piecewise-constant function but then apply a smoothing prior to ensure that their posterior population size estimates transition gradually with time. These prior distributions implicitly encode extra population size information that is not available from the observed coalescent data i.e., the tree. Here we present a novel statistic, {Omega}, to quantify and disaggregate the relative contributions of the coalescent data and prior assumptions to the resulting posterior estimate precision. Our statistic also measures the additional mutual information introduced by such priors. Using {Omega} we show that, because it is surprisingly easy to over-parametrise piecewise-constant population models, common smoothing priors can lead to overconfident and potentially misleading inference, even under robust experimental designs. We propose {Omega} as a useful tool for detecting when effective population size estimates are overly reliant on prior assumptions and for improving quantification of the uncertainty in those estimates.
|
genetics
|
Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor How a cell changes from one stable phenotype to another one is a fundamental problem in developmental and cell biology. Epithelial-to-mesenchymal transition (EMT) is a phenotypic transition process extensively studied recently but mechanistic details remain elusive. Through time-lapse imaging we recorded single cell trajectories of human A549/Vim-RFP cells undergoing EMT induced by different concentrations of TGF-{beta} in a multi-dimensional cell feature space. The trajectories cluster into two distinct groups, indicating that the transition dynamics proceeds through parallel paths. We then reconstructed the reaction coordinates and corresponding pseudo-potentials from the trajectories. The potentials reveal a plausible mechanism for the emergence of the two paths as the original stable epithelial attractor collides with two saddle points sequentially with increased TGF-{beta} concentration, and relaxes to a new one. Functionally the directional saddle-node bifurcation ensures a CPT proceeds towards a specific cell type, as a mechanistic realization of the canalization idea proposed by Waddington.
|
biophysics
|
Contrasting Effects of Western vs. Mediterranean Diets on Monocyte Inflammatory Gene Expression and Social Behavior in a Primate Model Dietary changes associated with industrialization substantially increase the prevalence of chronic diseases, such as obesity, type II diabetes, and cardiovascular disease, which are major contributors to the public health burden. The high prevalence of these chronic diseases is often attributed to an "evolutionary mismatch," between human physiology and modern nutritional environments. In support of this idea, Western diets enriched with foods that were scarce throughout human evolutionary history (e.g., simple sugars and saturated fats) promote inflammation and disease relative to diets more akin to hunter-gatherer diets, such as a Mediterranean diet; however, the mechanisms linking dietary mismatch to inflammation and chronic disease are poorly understood. We used a macaque model and whole diet manipulations to evaluate one possible mechanism - inflammatory polarization of monocytes - that potentially leads to this evolutionary mismatch. After consuming a Western- or Mediterranean-like diet for 15 months, monocytes from Western diet consumers exhibited a more proinflammatory phenotype, with 40% of their genes differentially expressed (FDR<0.05). Compared to the Mediterranean diet, the Western diet shifted the co-expression of 445 gene pairs, including small RNAs and transcription factors associated with metabolism and adiposity in humans, and dramatically altered animal behavior. For example, Western-fed individuals were more anxious and less socially integrated compared to the Mediterranean-fed subjects. These behavioral changes were also associated with some of the effects of diet on gene expression, suggesting an interaction between diet, central nervous system activity, and monocyte gene expression. The results of this study provide new insights into evolutionary mismatch at the molecular level and uncover new pathways through which Western diets generate inflammation and disease.
|
genomics
|
MazeMaster: an open-source Python-based software package for controlling virtual reality experiments AO_SCPLOWBSTRACTC_SCPLOWIn the last 15 years, virtual realities have revolutionized behavior experiments in particular for rodents. In combination with treadmills, running wheels, or air-floating balls, the implementation of a virtual reality (VR) provides not only the opportunity to simultaneously explore behavior and neuronal activity in head-fixed animals under nearly natural conditions, but also allows full control over the visual sensory input presented to the animal. Furthermore, VRs can be combined with other sensory modalities such as auditory, tactile or olfactory stimuli. Despite the power of using VRs in animal experiments, available software packages are very limited, expensive and lack the required flexibility to design appropriate behavior and neurophysiology experiments. For this reason, we have developed the versatile, adaptable and easy to use VR environment MazeMaster, an open-source, Python-based software package for controlling virtual reality setups and behavior experiments. The software package includes a graphical user interface (GUI) and can be integrated into standard electrophysiology and imaging setups even by non-programmers. Ready-made behavioral experiments such as multisensory discrimination in T-mazes are already implemented including full control for reward supply and bias correction. For more individual setup designs, the modularity of MazeMaster allows more programming-affine users to extend the software with potentially missing features. With MazeMaster, we offer a free and easy-to-use VR controller that will facilitate the implementation of VR setups in scientific laboratories. In addition, MazeMaster allows the design and control of common head-fixed rodent behavior paradigms with extensive acquisition of meta-data required for reproducible VR experiments. The MazeMaster VR package, therefore, offers a collaboration tool for reproducible research within and across neuroscience laboratories according to the FAIR principles.
|
neuroscience
|
Abnormal center of mass control during balance: a new biomarker of falls in people with Parkinson's disease Although Parkinson disease (PD) causes profound balance impairments, we know very little about how PD impacts the sensorimotor networks we rely on for automatically maintaining balance control. In young healthy people and animals, muscles are activated in a precise temporal and spatial organization when the center of body mass (CoM) is unexpectedly moved that is largely automatic and determined by feedback of CoM motion. Here, we show that PD alters the sensitivity of the sensorimotor feedback transformation. Importantly, sensorimotor feedback transformations for balance in PD remain temporally precise, but become spatially diffuse by recruiting additional muscle activity in antagonist muscles during balance responses. The abnormal antagonist muscle activity remains precisely time-locked to sensorimotor feedback signals encoding undesirable motion of the body in space. Further, among people with PD, the sensitivity of abnormal antagonist muscle activity to CoM motion varies directly with the number of recent falls. Our work shows that in people with PD, sensorimotor feedback transformations for balance are intact but disinhibited in antagonist muscles, likely contributing to balance deficits and falls.
|
neuroscience
|
Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 {+/-} 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
|
microbiology
|
Between-subject prediction reveals a shared representational geometry in the rodent hippocampus The rodent hippocampus constructs statistically independent representations across environments ("global remapping") and assigns individual neuron firing fields to locations within an environment in an apparently random fashion, processes thought to contribute to the role of the hippocampus in episodic memory. This random mapping implies that it should be challenging to predict hippocampal encoding of a given experience in one subject based on the encoding of that same experience in another subject. Contrary to this prediction, we find that by constructing a common representational space across rats in which neural activity is aligned using geometric operations (rotation, reflection, and translation; "hyperalignment"), we can predict data of "right" trials (R) on a T-maze in a target rat based on 1) the "left" trials (L) of the target rat, and 2) the relationship between L and R trials from a different source rat. These cross-subject predictions relied on ensemble activity patterns including both firing rate and field location, and outperformed a number of control mappings, such as those based on permuted data that broke the relationship between L and R activity for individual neurons, and those based solely on within-subject prediction. This work constitutes proof-of-principle for successful cross-subject prediction of ensemble activity patterns in the hippocampus, and provides new insights in understanding how different experiences are structured, enabling further work identifying what aspects of experience encoding are shared vs. unique to an individual.
|
neuroscience
|
Energetics of stochastic BCM type synaptic plasticity and storing of accurate information Excitatory synaptic signaling in cortical circuits is thought to be metabolically expensive. Two fundamental brain functions, learning and memory, are associated with long-term synaptic plasticity, but we know very little about energetics of these slow biophysical processes. This study investigates the energy requirement of information storing in plastic synapses for an extended version of BCM plasticity with a decay term, stochastic noise, and nonlinear dependence of neurons firing rate on synaptic current (adaptation). It is shown that synaptic weights in this model exhibit bistability. In order to analyze the system analytically, it is reduced to a simple dynamic mean-field for a population averaged plastic synaptic current. Next, using the concepts of nonequilibrium thermodynamics, we derive the energy rate (entropy production rate) for plastic synapses and a corresponding Fisher information for coding presynaptic input. That energy, which is of chemical origin, is primarily used for battling fluctuations in the synaptic weights and presynaptic firing rates, and it increases steeply with synaptic weights, and more uniformly though nonlinearly with presynaptic firing. At the onset of synaptic bistability, Fisher information and memory lifetime both increase sharply, by a few orders of magnitude, but the plasticity energy rate changes only mildly. This implies that a huge gain in the precision of stored information does not have to cost large amounts of metabolic energy, which suggests that synaptic information is not directly limited by energy consumption. Interestingly, for very weak synaptic noise, such a limit on synaptic coding accuracy is imposed instead by a derivative of the plasticity energy rate with respect to the mean presynaptic firing, and this relationship has a general character that is independent of the plasticity type. An estimate for primate neocortex reveals that a relativemetabolic cost of BCM type synaptic plasticity, as a fraction of neuronal cost related to fast synaptic transmission and spiking, can vary from negligible to substantial, depending on the synaptic noise level and presynaptic firing.
|
neuroscience
|
Extreme hot weather has stronger impacts on avian reproduction in forests than in cities Climate change and urbanization are among the most salient human-induced changes affecting Earths biota. Extreme weather events can have high biological impacts and are becoming more frequent recently. In cities, the urban heat island can amplify the intensity and frequency of hot weather events. However, the joint effects of heat events and urban microclimate on wildlife are unclear, as urban populations may either suffer more from increased heat stress or become adapted to warmer temperatures. Here we test whether the effects of hot weather on reproductive success of great tits (Parus major) are exacerbated or dampened in urban environments compared to forest habitats. By studying two urban and two forest populations over six years, we show that 14-16 days-old nestlings have smaller body mass and tarsus length, and suffer increased mortality when they experience a higher number of hot days during the nestling period. The negative effects of hot weather on body mass and survival are significantly stronger in forests than in urban areas, where these effects are dampened or even reversed. These results suggest that urban birds are less vulnerable to extreme hot weather conditions than their non-urban conspecifics, possibly by adaptively evolving or flexibly adjusting nestling physiology to tolerate heat stress, and/or by adjusting parental behavior in response to heat. This finding highlights that endothermic vertebrates may be able to adapt to heat stress, which may help their populations cope with the joint challenges of climate change and urbanization.
Significance statementExtreme weather events are becoming more frequent due to climate change and can have substantial effects on reproduction and survival of wild animals. Urban heat island can amplify the frequency of extreme hot weather events, making it potentially more harmful for city-dwelling organisms. Alternatively, urban populations living in warmer environments may adapt to better tolerate heat. We investigated these alternatives by comparing nestling development and survival between urban and forest great tit (Parus major) populations. We found that urban populations are less vulnerable to heat: nestling body mass and survival decreased rapidly with the increasing number of hot days in forests, while these effects were dampened in urban broods. Thus, urban populations may become adapted to better tolerate heat events.
|
ecology
|
The Landscape of Precision Cancer Combination Therapy: A Single-Cell Perspective The availability of single-cell transcriptomics data opens new opportunities for rational design of combination cancer treatments. Mining such data, we employed combinatorial optimization techniques to explore the landscape of optimal combination therapies in solid tumors including brain, head and neck, melanoma, lung, breast and colon cancers. We assume that each individual therapy can target any one of 1269 genes encoding cell surface receptors, which may be targets of CAR-T, conjugated antibodies or coated nanoparticle therapies. As a baseline case, we studied the killing of at least 80% of the tumor cells while sparing more than 90% of the non-tumor cells in each patient, as a putative regimen. We find that in most cancer types, personalized combinations composed of at most four targets are then sufficient. However, the number of distinct targets that one would need to assemble to treat all patients in a cohort accordingly would be around 10 in most cases. Further requiring that the target genes be also lowly expressed in healthy tissues uncovers qualitatively similar trends. However, as one asks for more stringent and selective killing beyond the baseline regimen we focused on, we find that the number of targets needed rises rapidly. Emerging individual promising receptor targets include PTPRZ1, which is frequently found in the optimal combinations for brain and head and neck cancers, and EGFR, a recurring target in multiple tumor types. In sum, this systematic single-cell based characterization of the landscape of combinatorial receptor-mediated cancer treatments establishes first of their kind estimates on the number of targets needed, identifying promising ones for future development.
|
bioinformatics
|
eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs An increasing number of gene expression quantitative trait locus (eQTL) studies have made summary statistics publicly available, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and colocalisation. However, differences between these datasets, in their variants tested, allele codings, and in the transcriptional features quantified, are a barrier to their widespread use. Consequently, target genes for most GWAS signals have still not been identified. Here, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl/), a resource which contains quality controlled, uniformly recomputed QTLs from 21 eQTL studies. We find that for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies, enabling the integrative analysis of these data. Although most cis-eQTLs were shared between most bulk tissues, the analysis of purified cell types identified a greater diversity of cell-type-specific eQTLs, a subset of which also manifested as novel disease colocalisations. Our summary statistics can be downloaded by FTP, accessed via a REST API, and visualised on the Ensembl genome browser. New datasets will continuously be added to the eQTL Catalogue, enabling the systematic interpretation of human GWAS associations across many cell types and tissues.
|
genomics
|
The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes. The histone variant macroH2A1.1 (mH2A1.1) plays a role in cancer development and metastasis-related processes. To determine the underlying molecular mechanisms, we mapped genome-wide localization of endogenous mH2A1.1 in the human breast cancer cell MDA-MB 231. We demonstrate that mH2A1.1 specifically binds to active promoters and enhancers in addition to facultative heterochromatin. Selective knock-down of mH2A1.1 deregulates expression of hundreds of highly active genes. Depending on the chromatin landscape, mH2A1.1 acts through two distinct molecular mechanisms. The first is to limit excessive transcription in a predefined environment and relies on domain recruitment of mH2A1.1 at the promoter and gene body. The second mechanism is specific to RNA Pol II (Pol II) paused genes. It requires recruitment of mH2A1.1 restricted to the TSS of these genes. Moreover, we show that these processes occur in a predefined local 3D genome organization and are largely independent of enhancer-promoter looping. Among the genes activated by mH2A1.1, genes regulating mammary tumor cell migration are mostly dependent on Pol II release for their expression level, unlike other categories of mH2A1.1-regulated genes. We thus identified an intriguing new mode of transcriptional regulation by mH2A1.1 and propose that mH2A1.1 serves as a transcriptional modulator with a potential role in assisting the conversion of promoter-locked RNA polymerase II into a productive and elongated Pol II.
|
genomics
|
Learning to Integrate an Artificial Sensory Device: Early Bayesian Integration and Conscious Perception The present study examines how artificial tactile stimulation from a novel non-invasive sensory device is learned and integrated with information from another sensory system. Participants were trained to identify the direction of visual dot motion stimuli with a low, medium, and high signal-to-noise ratio. In bimodal trials, this visual direction information was paired with reliable symbolic tactile information. Over several training blocks, discrimination performance in unimodal tactile test trials and subjects confidence in their decision improved, indicating that participants were able to associate the visual and tactile information consciously and thus learned the meaning of the symbolic tactile cues. Formal analysis of the results in bimodal trials showed that both modalities are being integrated already in the early learning phases. Our modeling results revealed that this integration is consistent with a Bayesian model, which is an optimal integration of sensory information. Furthermore, we showed that a confidence-based Bayesian integration explains the observed behavioral data better than the classical variance-based Bayesian integration. Thus, the present study demonstrates that humans can consciously learn and integrate an artificial sensory device that delivers symbolic tactile information. This finding connects the field of multisensory integration research to the development of sensory substitution systems.
|
neuroscience
|
Dynamic landscape of protein occupancy across the Escherichia coli chromosome Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (IPOD-HR), and present a pilot application to E. coli. We observe that the E. coli protein-DNA interactome organizes into two distinct prototypic features: (1) highly dynamic condition-dependent transcription factor occupancy, and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence-specificity models for the majority of active transcription factors. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria which are not amenable to routine genetic manipulation.
|
systems biology
|
Insights into Cross-species Evolution of Novel Human Coronavirus SARS-CoV-2 and Defining Immune Determinants for Vaccine Development Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in the city of Wuhan, China during December 2019, has now spread to various countries across the globe triggering a heightened containment effort. This human pathogen is a member of betacoronavirus genus carrying 30 kilobase of single positive-sense RNA genome. Understanding the evolution, zoonotic transmission, and source of this novel virus would help accelerating containment and prevention efforts. The present study reported detailed analysis of SARS-CoV-2 genome evolution and potential candidate peptides for vaccine development. This new coronavirus genotype might have been evolved from a bat-coronavirus by accumulating non-synonymous mutations, indels, and recombination events. Structural proteins Spike (S), and Membrane (M) had extensive mutational changes, whereas Envelope (E) and Nucleocapsid (N) proteins were very conserved suggesting differential selection pressures exerted on SARS-CoV-2 during evolution. Interestingly, SARS-CoV-2 Spike protein contains a 39 nucleotide sequence insertion relative to SARS-like bat-SL-CoVZC45/2017. Furthermore, we identified eight high binding affinity (HBA) CD4 T-cell epitopes in the S, E, M and N proteins, which can be commonly recognized by HLA-DR alleles of Asia and Asia-Pacific Region population. These immunodominant epitopes can be incorporated in universal subunit SARS-CoV-2 vaccine. Diverse HLA types and variations in the epitope binding affinity may contribute to the wide range of immunopathological outcomes of circulating virus in humans. Our findings emphasize the requirement for continuous surveillance of SARS-CoV-2 strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic SARS-CoV-2 strains.
|
microbiology
|
Interpretable detection of novel human viruses from genome sequencing data Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.
|
bioinformatics
|
Loss and recovery of transcriptional plasticity after long-term adaptation to global change conditions in a marine copepod Adaptive evolution from standing genetic variation and physiological plasticity will fuel resilience in the geologically unprecedented warming and acidification of the earths oceans. For marine animals, however, we have much to learn about the mechanisms, interactions, and costs of adaptation. Here, using 20 generations of experimental evolution followed by three generations of reciprocal transplantation, we investigate the relationship between adaptation and plasticity in the marine copepod, Acartia tonsa, in future greenhouse conditions (high temperature, high CO2). We find highly parallel genetic adaptation to greenhouse conditions in genes related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production. However, reciprocal transplantation showed that genetic adaptation resulted in a loss of transcriptional plasticity, reduced fecundity, and reduced population growth when greenhouse animals were returned to ambient conditions or reared in low food conditions, suggestive of genetic assimilation after 20 generations of adaptation. Despite the loss of plasticity at F21, after three successive transplant generations, greenhouse-adapted animals were able to match the ambient-adaptive transcriptional profile. Concurrent changes in allele frequencies and erosion of nucleotide diversity suggest that this recovery occurred via adaptation back to ancestral conditions. These results demonstrate the power of experimental evolution from natural populations to reveal the mechanisms, timescales of responses, consequences, and reversibility of complex, physiological adaptation. While plasticity facilitated initial survival in global change conditions, it eroded after 20 generations as populations genetically adapted, limiting resilience to new stressors and previously benign environments.
|
evolutionary biology
|
CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference Single-cell sequencing technologies are becoming increasingly more established, in particular, in the study of tumor heterogeneity. Investigating tumor heterogeneity is imperative to better understand how tumors evolve since each cell subpopulation harbors a unique set of genomic features that yields a unique phenotype, an issue that is bound to have clinical relevance. Clustering of cells based on copy number data, obtained from single-cell DNA sequencing, provides an opportunity to assess different tumor cell subpopulations. Accordingly, computational methods have emerged for single-cell copy number profiling as well as clustering; however, these two tasks have up to now been handled sequentially, and, included various ad-hoc preprocessing steps; hence, prone to introduce clustering artifacts. We propose CopyMix, a mixture model-based method using Variational Inference, to simultaneously cluster cells and infer a single copy number profile for each cluster, revealing the underlying copy number variation pattern for each cluster. CopyMix is evaluated using simulated data as well as published biological data from ovarian cancer. The results reveal high clustering performance and low errors in copy number profiling. These favorable results indicate a considerable potential to obtain clinical impact by using CopyMix in studies of cancer tumor heterogeneity.
|
bioinformatics
|
Arginine-vasopressin mediates counter-regulatory glucagon release and is diminished in type 1 diabetes Insulin-induced hypoglycemia is a major barrier to the treatment of type-1 diabetes (T1D). Accordingly, it is important that we understand the mechanisms regulating the circulating levels of glucagon - the bodys principal blood glucose-elevating hormone which is secreted from alpha-cells of the pancreatic islets. Varying glucose over the range of concentrations that occur physiologically between the fed and fuel-deprived states (from 8 to 4 mM) has no significant effect on glucagon secretion in isolated islets (in vitro) and yet associates with dramatic changes in plasma glucagon in vivo. The identity of the systemic factor(s) that stimulates glucagon secretion remains unknown. Here, we show that arginine-vasopressin (AVP), secreted from the posterior pituitary, stimulates glucagon secretion. Glucagon-secreting alpha-cells express high levels of the vasopressin 1b receptor gene (Avpr1b). Activation of AVP neurons in vivo increased circulating copeptin (the C-terminal segment of the AVP precursor peptide, a stable surrogate marker of AVP) and increased blood glucose; effects blocked by pharmacological antagonism of either the glucagon receptor or vasopressin 1b receptor. AVP also mediates the stimulatory effects of hypoglycemia produced by exogenous insulin and 2-deoxy-D-glucose on glucagon secretion. We show that the A1/C1 neurons of the medulla oblongata drive AVP neuron activation in response to insulin-induced hypoglycemia. Exogenous injection of AVP in vivo increased cytoplasmic Ca2+ in alpha-cells (implanted into the anterior chamber of the eye) and glucagon release. Hypoglycemia also increases circulating levels of AVP in humans and this hormone stimulates glucagon secretion from isolated human islets. In patients with T1D, hypoglycemia failed to increase both plasma copeptin and glucagon levels. These findings suggest that AVP is a physiological systemic regulator of glucagon secretion and that this mechanism becomes impaired in T1D.
|
cell biology
|
Fitting drift-diffusion decision models to trial-by-trial data Drift-diffusion models or DDMs are becoming a standard in the field of computational neuroscience. They extend models from signal detection theory by proposing a simple mechanistic explanation for the observed relationship between decision outcomes and reaction times (RT). In brief, they assume that decisions are triggered once the accumulated evidence in favor of a particular alternative option has reached a predefined threshold. Fitting a DDM to empirical data then allows one to interpret observed group or condition differences in terms of a change in the underlying model parameters. However, current approaches only yield reliable parameter estimates in specific situations (c.f. fixed drift rates vs drift rates varying over trials). In addition, they become computationally unfeasible when more general DDM variants are considered (e.g., with collapsing bounds). In this note, we propose a fast and efficient approach to parameter estimation that relies on fitting a "self-consistency" equation that RT fulfill under the DDM. This effectively bypasses the computational bottleneck of standard DDM parameter estimation approaches, at the cost of estimating the trial-specific neural noise variables that perturb the underlying evidence accumulation process. For the purpose of behavioral data analysis, these act as nuisance variables and render the model "overcomplete", which is finessed using a variational Bayesian system identification scheme. But for the purpose of neural data analysis, estimates of neural noise perturbation terms are a desirable (and unique) feature of the approach. Using numerical simulations, we show that this "overcomplete" approach matches the performance of current parameter estimation approaches for simple DDM variants, and outperforms them for more complex DDM variants. Finally, we demonstrate the added-value of the approach, when applied to a recent value-based decision making experiment.
|
animal behavior and cognition
|
Semantic and Prosodic Threat Processing in Trait Anxiety. The present study attempts to identify how trait anxiety, measured as worry-level, affects the processing of threatening speech. Two experiments using dichotic listening tasks were implemented; where participants had to identify sentences that convey threat through three different information channels: prosody-only, semantic-only and both semantic and prosody (congruent threat). We expected different ear advantages (left or right) depending on task demands, information type, and worry level. We used a full Bayesian approach for statistical modelling and analysis. Results indicate that when participants made delayed responses (Experiment 1), reaction times barely increased as a function of worry level, but under time pressure (Experiment 2) worry level induced clear decreases in reaction times. We explain these results in terms of multistep models of anxiety and language, concluding that present results mainly indicate effects threat aversion-related over-attention to threat, and that we do not provide enough evidence for supporting the integration of anxiety and language multiphasic models.
|
neuroscience
|
Understanding population structure in an evolutionary context: population-specific FST and pairwise FST Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a populations history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to seashores with abundant rainfall, and to the south with dry summers. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable process times and are useful in population genomics studies. The R codes for our method and simulations are available in the Supplemental Material.
|
evolutionary biology
|
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