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Learning valence-based responses to favorable and unfavorable options requires judgments of the relative value of the options, a process necessary for species survival. We found, using engineered mice, that circuit connectivity and function of the striosome compartment of the striatum are critical for this type of learning. Calcium imaging during valence-based learning exhibited a selective correlation between learning and striosomal but not matrix signals. This striosomal activity encoded discrimination learning and was correlated with task engagement, which, in turn, could be regulated by chemogenetic excitation and inhibition. Striosomal function during discrimination learning was disturbed with aging and severely so in a mouse model of Huntington's disease. Anatomical and functional connectivity of parvalbumin-positive, putative fast-spiking interneurons (FSIs) to striatal projection neurons was enhanced in striosomes compared with matrix in mice that learned. Computational modeling of these findings suggests that FSIs can modulate the striosomal signal-to-noise ratio, crucial for discrimination and learning.
Assuntos
Envelhecimento/patologia , Corpo Estriado/patologia , Doença de Huntington/patologia , Aprendizagem , Potenciais de Ação , Animais , Comportamento Animal , Biomarcadores/metabolismo , Corpo Estriado/fisiopatologia , Aprendizagem por Discriminação , Modelos Animais de Doenças , Doença de Huntington/fisiopatologia , Interneurônios/patologia , Camundongos Transgênicos , Modelos Neurológicos , Rede Nervosa/fisiopatologia , Parvalbuminas/metabolismo , Fotometria , Recompensa , Análise e Desempenho de TarefasRESUMO
Effective evaluation of costs and benefits is a core survival capacity that in humans is considered as optimal, "rational" decision-making. This capacity is vulnerable in neuropsychiatric disorders and in the aftermath of chronic stress, in which aberrant choices and high-risk behaviors occur. We report that chronic stress exposure in rodents produces abnormal evaluation of costs and benefits resembling non-optimal decision-making in which choices of high-cost/high-reward options are sharply increased. Concomitantly, alterations in the task-related spike activity of medial prefrontal neurons correspond with increased activity of their striosome-predominant striatal projection neuron targets and with decreased and delayed striatal fast-firing interneuron activity. These effects of chronic stress on prefronto-striatal circuit dynamics could be blocked or be mimicked by selective optogenetic manipulation of these circuits. We suggest that altered excitation-inhibition dynamics of striosome-based circuit function could be an underlying mechanism by which chronic stress contributes to disorders characterized by aberrant decision-making under conflict. VIDEO ABSTRACT.
Assuntos
Tomada de Decisões , Córtex Pré-Frontal/fisiopatologia , Estresse Fisiológico , Animais , Gânglios da Base/metabolismo , Interneurônios/fisiologia , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Vias Neurais , Optogenética , Ratos , Ratos Long-EvansRESUMO
Activity-regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment responses for many neuropsychiatric disorders. The HPC contains discrete classes of neurons with specialized functions, but cell type-specific activity-regulated transcriptional programs are not well characterized. Here, we used single-nucleus RNA-sequencing (snRNA-seq) in a mouse model of acute electroconvulsive seizures (ECS) to identify cell type-specific molecular signatures associated with induced activity in HPC neurons. We used unsupervised clustering and a priori marker genes to computationally annotate 15,990 high-quality HPC neuronal nuclei from N = 4 mice across all major HPC subregions and neuron types. Activity-induced transcriptomic responses were divergent across neuron populations, with dentate granule cells being particularly responsive to activity. Differential expression analysis identified both upregulated and downregulated cell type-specific gene sets in neurons following ECS. Within these gene sets, we identified enrichment of pathways associated with varying biological processes such as synapse organization, cellular signaling, and transcriptional regulation. Finally, we used matrix factorization to reveal continuous gene expression patterns differentially associated with cell type, ECS, and biological processes. This work provides a rich resource for interrogating activity-regulated transcriptional responses in HPC neurons at single-nuclei resolution in the context of ECS, which can provide biological insight into the roles of defined neuronal subtypes in HPC function.
Assuntos
Hipocampo , Neurônios , Camundongos , Animais , Hipocampo/fisiologia , Neurônios/fisiologia , Aprendizagem/fisiologia , Regulação da Expressão Gênica/genética , Convulsões , Expressão GênicaRESUMO
The hippocampus contains many unique cell types, which serve the structure's specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and infer the expression of these patterns in the SRT data. With this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
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Pathophysiology of many neuropsychiatric disorders, including schizophrenia (SCZD), is linked to habenula (Hb) function. While pharmacotherapies and deep brain stimulation targeting the Hb are emerging as promising therapeutic treatments, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in SCZD. Here we define the molecular neuroanatomy of the human Hb and identify transcriptomic changes in individuals with SCZD compared to neurotypical controls. Utilizing Hb-enriched postmortem human brain tissue, we performed single nucleus RNA-sequencing (snRNA-seq; n=7 neurotypical donors) and identified 17 molecularly defined Hb cell types across 16,437 nuclei, including 3 medial and 7 lateral Hb populations, several of which were conserved between rodents and humans. Single molecule fluorescent in situ hybridization (smFISH; n=3 neurotypical donors) validated snRNA-seq Hb cell types and mapped their spatial locations. Bulk RNA-sequencing and cell type deconvolution in Hb-enriched tissue from 35 individuals with SCZD and 33 neurotypical controls yielded 45 SCZD-associated differentially expressed genes (DEGs, FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. eQTL analysis identified 717 independent SNP-gene pairs (FDR < 0.05), where either the SNP is a SCZD risk variant (16 pairs) or the gene is a SCZD DEG (7 pairs). eQTL and SCZD risk colocalization analysis identified 16 colocalized genes. These results identify topographically organized cell types with distinct molecular signatures in the human Hb and demonstrate unique genetic changes associated with SCZD, thereby providing novel molecular insights into the role of Hb in neuropsychiatric disorders. One Sentence Summary: Transcriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.
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The B domain of staphylococcal protein A (BdpA) is a small helical protein that has been studied intensively in kinetics experiments and detailed computer simulations that include explicit water. The simulations indicate that BdpA needs to reorganize in crossing the transition barrier to facilitate folding its C-terminal helix (H3) onto the nucleus formed from helices H1 and H2. This process suggests frustration between two partially ordered forms of the protein, but recent varphi value measurements indicate that the transition structure is relatively constant over a broad range of temperatures. Here we develop a simplistic model to investigate the folding transition in which properties of the free energy landscape can be quantitatively compared with experimental data. The model is a continuation of the Muñoz-Eaton model to include the intermittency of contacts between structured parts of the protein, and the results compare variations in the landscape with denaturant and temperature to varphi value measurements and chevron plots of the kinetic rates. The topography of the model landscape (in particular, the feature of frustration) is consistent with detailed simulations even though variations in the varphi values are close to measured values. The transition barrier is smaller than indicated by the chevron data, but it agrees in order of magnitude with a similar alpha-carbon type of model. Discrepancies with the chevron plots are investigated from the point of view of solvent effects, and an approach is suggested to account for solvent participation in the model.
Assuntos
Entropia , Proteína Estafilocócica A/química , Modelos Moleculares , Dobramento de Proteína , Estrutura Terciária de ProteínaRESUMO
Recently diverged butterfly populations in North America have been found to exhibit high levels of divergence on the Z chromosome relative to autosomes, as measured by fixation index, F st . The pattern of divergence appears to result from accumulation of incompatible alleles, obstructing introgression on the Z chromosome in hybrids (i.e., the large-Z effect); however, it is unknown whether this mechanism is sufficient to explain the data. Here, we simulate the effects of hybrid incompatibility on interbreeding butterfly populations using a model in which populations accumulate cross-incompatible alleles in allopatry prior to contact. We compute statistics for introgression and population divergence during contact between model populations and compare our results to those for 15 pairs of butterfly species interbreeding along a suture zone in central Texas. Time scales for allopatry and contact in the model are scaled to glacial and interglacial periods during which real populations evolved in isolation and contact. We find that the data for butterflies are explained well by an otherwise neutral model under slow fusion conditions. In particular, levels of divergence on the Z chromosome increase when interacting clusters of genes are closely linked, consistent with clusters of functionally related genes in butterfly genomes.
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To escape from local fitness peaks, a population must navigate across valleys of low fitness. How these transitions occur, and what role they play in adaptation, have been subjects of active interest in evolutionary genetics for almost a century. However, to our knowledge, this problem has never been addressed directly by considering the evolution of a gene, or group of genes, as a whole, including the complex effects of fitness interactions among multiple loci. Here, we use a precise model of protein fitness to compute the probability P ( s , Δ t ) that an allele, randomly sampled from a population at time t, has crossed a fitness valley of depth s during an interval t - Δ t , t in the immediate past. We study populations of model genes evolving under equilibrium conditions consistent with those in mammalian mitochondria. From this data, we estimate that genes encoding small protein motifs navigate fitness valleys of depth 2 N s â³ 30 with probability P â³ 0 . 1 on a time scale of human evolution, where N is the (mitochondrial) effective population size. The results are consistent with recent findings for Watsonâ»Crick switching in mammalian mitochondrial tRNA molecules.
Assuntos
Adaptação Fisiológica/genética , Motivos de Aminoácidos/genética , Evolução Biológica , Aptidão Genética/genética , Epistasia Genética , Genótipo , Humanos , Modelos Genéticos , Mutação/genética , Densidade Demográfica , RNA de Transferência/genética , Seleção GenéticaRESUMO
We use Potts model inference to predict pair epistatic effects in a key mitochondrial protein-cytochrome c oxidase subunit 2-for ray-finned fishes. We examine the effect of phylogenetic correlations on our predictions using a simple exact fitness model, and we find that, although epistatic effects are underpredicted, they maintain a roughly linear relationship to their true (model) values. After accounting for this correction, epistatic effects in the protein are still relatively weak, leading to fitness valleys of depth 2Ns≃-5 in compensatory double mutants. Interestingly, positive epistasis is more pronounced than negative epistasis, and the strongest positive effects capture nearly all sites subject to positive selection in fishes, similar to virus proteins evolving under selection pressure in the context of drug therapy.
Assuntos
Epistasia Genética , Proteínas Mitocondriais/metabolismo , Modelos Genéticos , Animais , Linhagem da Célula , Evolução Molecular , Proteínas de Peixes/metabolismo , Peixes , Aptidão Genética , Modelos Moleculares , MutaçãoRESUMO
A recent study of experimental results for flavodoxin-like folds suggests that proteins from this family may exhibit a similar, signature pattern of folding intermediates. We study the folding landscapes of three proteins from the flavodoxin family (CheY, apoflavodoxin, and cutinase) using a simple nucleation and growth model that accurately describes both experimental and simulation results for the transition state structure, and the structure of on-pathway and misfolded intermediates for CheY. Although the landscape features of these proteins agree in basic ways with the results of the study, the simulations exhibit a range of folding behaviours consistent with two alternate folding routes corresponding to nucleation and growth from either side of the central beta-strand.
Assuntos
Flavodoxina/química , Flavodoxina/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Modelos Biológicos , Dobramento de Proteína , Apoproteínas/química , Apoproteínas/metabolismo , Flavodoxina/classificação , Proteínas de Membrana/classificação , Modelos Moleculares , Estrutura Terciária de ProteínaRESUMO
We study a nucleation-growth model of protein folding and extend it to describe larger proteins with multiple folding units. The model is of one of an extremely simple type in which amino acids are allowed just two states--either folded (frozen) or unfolded. Its energetics are heterogeneous and Go-like, the energy being defined in terms of the number of atom-to-atom contacts that would occur between frozen amino acids in the native crystal structure of the protein. Each collective state of the amino acids is intended to represent a small free energy microensemble consisting of the possible configurations of unfolded loops, open segments, and free ends constrained by the cross-links that form between folded parts of the molecule. We approximate protein free energy landscapes by an infinite subset of these microensemble topologies in which loops and open unfolded segments can be viewed roughly as independent objects for the purpose of calculating their entropy, and we develop a means to implement this approximation in Monte Carlo simulations. We show that this approach describes transition state structures (phi values) more accurately and identifies folding intermediates that were unavailable to previous versions of the model that restricted the number of loops and nuclei.
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Recent analyses of amino acid mutations in proteins reveal that mutations at many pairs of sites are epistatic-i.e., their effects on fitness are non-additive-the combined effect of two mutations being significantly larger or smaller than the sum of their effects considered independently. Interestingly, epistatic sites are not necessarily near each other in the folded structure of a protein, and may even be located on opposite sides of a molecule. However, the mechanistic reasons for long-range epistasis remain obscure. Here, we study long-range epistasis in proteins using a previously developed model in which off-lattice polymers are evolved under ligand binding constraints. Epistatic effects in the model are qualitatively similar to those recently reported for small proteins, and many are long-range. We find that a major reason for long-range epistasis is conformational change-a recurrent theme in both positive and negative epistasis being the transfer, or exchange of material between the ordered nucleus, which supports the binding site, and the liquid-like surface of a folded molecule. These local transitions in phase and folded structure are largely responsible for long-range epistasis in our model.
Assuntos
Epistasia Genética , Mutação , Proteínas/química , Proteínas/metabolismo , Sítios de Ligação , Evolução Molecular , Ligantes , Modelos Genéticos , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Dobramento de Proteína , Proteínas/genéticaRESUMO
We investigate protein evolution using an off-lattice polymer model evolved to imitate the behavior of small enzymes. Model proteins evolve through mutations to nucleotide sequences (including insertions and deletions) and are selected to fold and maintain a specific binding site compatible with a model ligand. We show that this requirement is, in itself, sufficient to maintain an ordered folding domain, and we compare it to the requirement of folding an ordered (but otherwise unrestricted) domain. We measure rates of amino acid change as a function of local environment properties such as solvent exposure, packing density, and distance from the active site, as well as overall rates of sequence and structure change, both along and among model lineages in star phylogenies. The model recapitulates essentially all of the behavior found in protein phylogenetic analyses, and predicts that amino acid substitution rates vary linearly with distance from the binding site.
Assuntos
Evolução Molecular , Proteínas/fisiologia , Sequência de Aminoácidos , Ligantes , Mutação , Filogenia , Dobramento de Proteína , Proteínas/química , Proteínas/genéticaRESUMO
Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n. We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.
Assuntos
Evolução Molecular , Proteínas/química , Proteínas/metabolismo , Difusão , Modelos Moleculares , Mutação , Dobramento de Proteína , Proteínas/genéticaRESUMO
We consider a nonstatistical, computationally fast experiment to identify important topological constraints in folding small globular proteins of about 100-200 amino acids. In this experiment, proteins are expanded mechanically along a path of steepest increase in the free space around residues. The pathways are often consistent with folding scenarios reported in kinetics experiments and most accurately describe obligatory or mechanic folding proteins. The results suggest that certain topological "defects" in proteins lead to preferred, entropically favorable channels down their free energy landscapes.
Assuntos
Aminoácidos/química , Modelos Químicos , Modelos Moleculares , Desnaturação Proteica , Dobramento de Proteína , Proteínas/química , Sequência de Aminoácidos , Simulação por Computador , Elasticidade , Dados de Sequência Molecular , Proteínas/análise , Relação Estrutura-AtividadeRESUMO
The biological function of a protein often depends on the formation of an ordered structure in order to support a smaller, chemically active configuration of amino acids against thermal fluctuations. Here we explore the development of proteins evolving to satisfy this requirement using an off-lattice polymer model in which monomers interact as low resolution amino acids. To evolve the model, we construct a Markov process in which sequences are subjected to random replacements, insertions, and deletions and are selected to recover a predefined minimum number of solid-ordered monomers using the Lindemann melting criterion. We show that polymers generated by this process consistently fold into soluble, ordered globules of similar length and complexity to small protein motifs. To compare the evolution of the globules with proteins, we analyze the statistics of amino acid replacements, the dependence of site mutation rates on solvent exposure, and the dependence of structural distance on sequence distance for homologous alignments. Despite the simplicity of the model, the results display a surprisingly close correspondence with protein data.