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Single-molecule localization microscopy (SMLM) generates data in the form of coordinates of localized fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite a range of cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics to score the success of clustering algorithms in simulated conditions mimicking experimental data. We demonstrate the framework using seven diverse analysis algorithms: DBSCAN, ToMATo, KDE, FOCAL, CAML, ClusterViSu and SR-Tesseler. Given that the best performer depended on the underlying distribution of localizations, we demonstrate an analysis pipeline based on statistical similarity measures that enables the selection of the most appropriate algorithm, and the optimized analysis parameters for real SMLM data. We propose that these standard simulated conditions, metrics and analysis pipeline become the basis for future analysis algorithm development and evaluation.
Assuntos
Algoritmos , Imagem Individual de Molécula , Análise por Conglomerados , BenchmarkingRESUMO
Current imaging approaches limit the ability to perform multi-scale characterization of three-dimensional (3D) organotypic cultures (organoids) in large numbers. Here, we present an automated multi-scale 3D imaging platform synergizing high-density organoid cultures with rapid and live 3D single-objective light-sheet imaging. It is composed of disposable microfabricated organoid culture chips, termed JeWells, with embedded optical components and a laser beam-steering unit coupled to a commercial inverted microscope. It permits streamlining organoid culture and high-content 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour. We demonstrate that the large number of 3D stacks that can be collected via our platform allows training deep learning-based algorithms to quantify morphogenetic organizations of organoids at multi-scales, ranging from the subcellular scale to the whole organoid level. We validated the versatility and robustness of our approach on intestine, hepatic, neuroectoderm organoids and oncospheres.
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Imageamento Tridimensional , Organoides , IntestinosRESUMO
Hippocampal pyramidal neurons are characterized by a unique arborization subdivided in segregated dendritic domains receiving distinct excitatory synaptic inputs with specific properties and plasticity rules that shape their respective contributions to synaptic integration and action potential firing. Although the basal regulation and plastic range of proximal and distal synapses are known to be different, the composition and nanoscale organization of key synaptic proteins at these inputs remains largely elusive. Here we used superresolution imaging and single nanoparticle tracking in rat hippocampal neurons to unveil the nanoscale topography of native GluN2A- and GluN2B-NMDA receptors (NMDARs)-which play key roles in the use-dependent adaptation of glutamatergic synapses-along the dendritic arbor. We report significant changes in the nanoscale organization of GluN2B-NMDARs between proximal and distal dendritic segments, whereas the topography of GluN2A-NMDARs remains similar along the dendritic tree. Remarkably, the nanoscale organization of GluN2B-NMDARs at proximal segments depends on their interaction with calcium/calmodulin-dependent protein kinase II (CaMKII), which is not the case at distal segments. Collectively, our data reveal that the nanoscale organization of NMDARs changes along dendritic segments in a subtype-specific manner and is shaped by the interplay with CaMKII at proximal dendritic segments, shedding light on our understanding of the functional diversity of hippocampal glutamatergic synapses.
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Dendritos/metabolismo , Hipocampo/metabolismo , Neurônios/metabolismo , Receptores de N-Metil-D-Aspartato/metabolismo , Animais , Proteína Quinase Tipo 2 Dependente de Cálcio-Calmodulina/metabolismo , Dendritos/genética , Ratos , Receptores de N-Metil-D-Aspartato/genética , Sinapses/metabolismoRESUMO
The nanoscale co-organization of neurotransmitter receptors facing presynaptic release sites is a fundamental determinant of their coactivation and of synaptic physiology. At excitatory synapses, how endogenous AMPARs, NMDARs, and mGluRs are co-organized inside the synapse and their respective activation during glutamate release are still unclear. Combining single-molecule superresolution microscopy, electrophysiology, and modeling, we determined the average quantity of each glutamate receptor type, their nanoscale organization, and their respective activation. We observed that NMDARs form a unique cluster mainly at the center of the PSD, while AMPARs segregate in clusters surrounding the NMDARs. mGluR5 presents a different organization and is homogenously dispersed at the synaptic surface. From these results, we build a model predicting the synaptic transmission properties of a unitary synapse, allowing better understanding of synaptic physiology.
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Modelos Neurológicos , Neurônios/metabolismo , Receptor de Glutamato Metabotrópico 5/metabolismo , Receptores de AMPA/metabolismo , Receptores de N-Metil-D-Aspartato/metabolismo , Transmissão Sináptica/fisiologia , Animais , Células Cultivadas , Embrião de Mamíferos , Feminino , Ácido Glutâmico/metabolismo , Hipocampo/citologia , Hipocampo/diagnóstico por imagem , Hipocampo/fisiologia , Microscopia Intravital , Neurônios/ultraestrutura , Técnicas de Patch-Clamp , Cultura Primária de Células , Ratos , Ratos Sprague-Dawley , Imagem Individual de MoléculaRESUMO
Super-resolution microscopy offers tremendous opportunities to unravel the complex and dynamic architecture of living cells. However, current super-resolution microscopes are well suited for revealing protein distributions or cell morphology, but not both. We present a super-resolution platform that permits correlative single-molecule imaging and stimulated emission depletion microscopy in live cells. It gives nanoscale access to the positions and movements of synaptic proteins within the morphological context of growth cones and dendritic spines.
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Processamento de Imagem Assistida por Computador/métodos , Microscopia de Fluorescência/métodos , Imagem Individual de Molécula/métodos , Animais , Células Cultivadas , Feminino , Humanos , Camundongos , Ratos , Ratos Sprague-DawleyRESUMO
Neurons receive a large number of active synaptic inputs from their many presynaptic partners across their dendritic tree. However, little is known about how the strengths of individual synapses are controlled in balance with other synapses to effectively encode information while maintaining network homeostasis. This is in part due to the difficulty in assessing the activity of individual synapses with identified afferent and efferent connections for a synapse population in the brain. Here, to gain insights into the basic cellular rules that drive the activity-dependent spatial distribution of pre- and postsynaptic strengths across incoming axons and dendrites, we combine patch-clamp recordings with live-cell imaging of hippocampal pyramidal neurons in dissociated cultures and organotypic slices. Under basal conditions, both pre- and postsynaptic strengths cluster on single dendritic branches according to the identity of the presynaptic neurons, thus highlighting the ability of single dendritic branches to exhibit input specificity. Stimulating a single presynaptic neuron induces input-specific and dendritic branchwise spatial clustering of presynaptic strengths, which accompanies a widespread multiplicative scaling of postsynaptic strengths in dissociated cultures and heterosynaptic plasticity at distant synapses in organotypic slices. Our study provides evidence for a potential homeostatic mechanism by which the rapid changes in global or distant postsynaptic strengths compensate for input-specific presynaptic plasticity.
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Dendritos/fisiologia , Terminações Pré-Sinápticas/fisiologia , Potenciais Sinápticos/fisiologia , Animais , Axônios , Região CA3 Hipocampal/fisiologia , Dendritos/metabolismo , Potenciais Pós-Sinápticos Excitadores , Hipocampo/fisiologia , Homeostase , Camundongos , Camundongos Endogâmicos C57BL , Modelos Neurológicos , Neurônios/fisiologia , Técnicas de Patch-Clamp , Células Piramidais/fisiologia , Sinapses/fisiologiaRESUMO
Super-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ offers an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology.
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Processamento de Imagem Assistida por Computador/métodos , Pescoço/diagnóstico por imagem , Software , Coluna Vertebral/diagnóstico por imagem , Algoritmos , Dendritos/fisiologia , Microscopia Intravital , Microscopia de Fluorescência/métodos , Pescoço/anatomia & histologia , Neurônios/citologia , Neurônios/fisiologia , Distribuição Normal , Distribuição de Poisson , Coluna Vertebral/anatomia & histologia , Fatores de TempoRESUMO
Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.
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Bases de Dados Factuais , Processamento de Imagem Assistida por Computador/métodos , Imagem Individual de Molécula/métodos , Animais , Células COS , Chlorocebus aethiops , Mineração de Dados , Corantes Fluorescentes , Células HeLa , Humanos , Proteínas de Membrana/análise , Transporte Proteico , Receptores de Neurotransmissores/análise , Software , Fluxo de TrabalhoRESUMO
Localization-based super-resolution techniques open the door to unprecedented analysis of molecular organization. This task often involves complex image processing adapted to the specific topology and quality of the image to be analyzed. Here we present a segmentation framework based on Voronoï tessellation constructed from the coordinates of localized molecules, implemented in freely available and open-source SR-Tesseler software. This method allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. We validated our method on simulated data and on various biological experimental data of proteins labeled with genetically encoded fluorescent proteins or organic fluorophores. In addition to providing insight into complex protein organization, this polygon-based method should serve as a reference for the development of new types of quantifications, as well as for the optimization of existing ones.
Assuntos
Processamento de Imagem Assistida por Computador/métodos , Microscopia de Fluorescência/métodos , Receptores de Glicina/metabolismo , Algoritmos , Animais , Células COS , Chlorocebus aethiops , Análise por Conglomerados , Biologia Computacional , Simulação por Computador , Corantes Fluorescentes/química , Humanos , Neurônios/metabolismo , Neurônios/fisiologia , Oócitos/metabolismo , Reconhecimento Automatizado de Padrão , Software , Xenopus laevisRESUMO
Intellectual disorders (IDs) have been regularly associated with morphological and functional deficits at glutamatergic synapses in both humans and rodents. How these synaptic deficits may lead to the variety of learning and memory deficits defining ID is still unknown. Here we studied the functional and behavioral consequences of the ID gene il1rapl1 deficiency in mice and reported that il1rapl1 constitutive deletion alters cued fear memory formation. Combined in vivo and in vitro approaches allowed us to unveil a causal relationship between a marked inhibitory/excitatory (I/E) imbalance in dedicated amygdala neuronal subcircuits and behavioral deficits. Cell-targeted recordings further demonstrated a morpho-functional impact of the mutation at thalamic projections contacting principal cells, whereas the same afferents on interneurons are unaffected by the lack of Il1rapl1. We thus propose that excitatory synapses have a heterogeneous vulnerability to il1rapl1 gene constitutive mutation and that alteration of a subset of excitatory synapses in neuronal circuits is sufficient to generate permanent cognitive deficits.
Assuntos
Potenciais Pós-Sinápticos Excitadores/genética , Deficiência Intelectual/complicações , Transtornos da Memória/etiologia , Tonsila do Cerebelo/citologia , Anestésicos Locais/farmacologia , Animais , Aprendizagem por Associação/fisiologia , Córtex Cerebral/citologia , Channelrhodopsins , Condicionamento Psicológico/fisiologia , Espinhas Dendríticas/metabolismo , Espinhas Dendríticas/ultraestrutura , Modelos Animais de Doenças , Potenciais Pós-Sinápticos Excitadores/efeitos dos fármacos , Potenciais Pós-Sinápticos Excitadores/fisiologia , Medo/fisiologia , Antagonistas GABAérgicos/farmacologia , Glutamato Descarboxilase/genética , Proteínas de Fluorescência Verde/genética , Técnicas In Vitro , Deficiência Intelectual/genética , Proteína Acessória do Receptor de Interleucina-1/genética , Proteína Acessória do Receptor de Interleucina-1/metabolismo , Potenciação de Longa Duração/efeitos dos fármacos , Potenciação de Longa Duração/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Proteínas do Tecido Nervoso/metabolismo , Inibição Neural/efeitos dos fármacos , Inibição Neural/genética , Neurônios/fisiologia , Neurônios/ultraestruturaRESUMO
Super-resolution imaging provides unprecedented visualization of sub-cellular structures, but the two main techniques used, single-molecule localization microscopy (SMLM) and stimulated emission depletion (STED), are not easily reconciled. We present a protocol to super-impose nanoscale protein distribution reconstructed with SMLM to sub-cellular morphology obtained in STED. We describe steps for tracking cells on etched coverslips and registering images from two different microscopes with 30-nm accuracy. In this protocol, synaptic proteins are mapped in the dendritic spines of primary neurons. For complete details on the use and execution of this protocol, please refer to Inavalli et al.1.
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Introduction: The synaptic adhesion molecule neuroligin-1 (NLGN1) is involved in the differentiation of excitatory synapses, but the precise underlying molecular mechanisms are still debated. Here, we explored the role of NLGN1 tyrosine phosphorylation in this process, focusing on a subset of receptor tyrosine kinases (RTKs), namely FGFR1 and Trks, that were previously described to phosphorylate NLGN1 at a unique intracellular residue (Y782). Methods: We used pharmacological inhibitors and genetic manipulation of those RTKs in dissociated hippocampal neurons, followed by biochemical measurement of NLGN1 phosphorylation and immunocytochemical staining of excitatory synaptic scaffolds. Results: This study shows that: (i) the accumulation of PSD-95 at de novo NLGN1 clusters induced by neurexin crosslinking is reduced by FGFR and Trk inhibitors; (ii) the increase in PSD-95 puncta caused by NLGN1 over-expression is impaired by FGFR and Trk inhibitors; (iii) TrkB activation by BDNF increases NLGN1 phosphorylation; and (iv) TrkB knock-down impairs the increase of PSD-95 puncta caused by NLGN1 over-expression, an effect which is not seen with the NLGN1 Y782A mutant. Discussion: Together, our data identify TrkB as one of the major RTKs responsible for NLGN1 tyrosine phosphorylation, and reveal that TrkB activity is necessary for the synaptogenic effects of NLGN1.
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Over the last decade, single-molecule localization microscopy (SMLM) has revolutionized cell biology, making it possible to monitor molecular organization and dynamics with spatial resolution of a few nanometers. Despite being a relatively recent field, SMLM has witnessed the development of dozens of analysis methods for problems as diverse as segmentation, clustering, tracking or colocalization. Among those, Voronoi-based methods have achieved a prominent position for 2D analysis as robust and efficient implementations were available for generating 2D Voronoi diagrams. Unfortunately, this was not the case for 3D Voronoi diagrams, and existing methods were therefore extremely time-consuming. In this work, we present a new hybrid CPU-GPU algorithm for the rapid generation of 3D Voronoi diagrams. Voro3D allows creating Voronoi diagrams of datasets composed of millions of localizations in minutes, making any Voronoi-based analysis method such as SR-Tesseler accessible to life scientists wanting to quantify 3D datasets. In addition, we also improve ClusterVisu, a Voronoi-based clustering method using Monte-Carlo simulations, by demonstrating that those costly simulations can be correctly approximated by a customized gamma probability distribution function.
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Completion of neuronal migration is critical for brain development. Kif21b is a plus-end-directed kinesin motor protein that promotes intracellular transport and controls microtubule dynamics in neurons. Here we report a physiological function of Kif21b during radial migration of projection neurons in the mouse developing cortex. In vivo analysis in mouse and live imaging on cultured slices demonstrate that Kif21b regulates the radial glia-guided locomotion of newborn neurons independently of its motility on microtubules. We show that Kif21b directly binds and regulates the actin cytoskeleton both in vitro and in vivo in migratory neurons. We establish that Kif21b-mediated regulation of actin cytoskeleton dynamics influences branching and nucleokinesis during neuronal locomotion. Altogether, our results reveal atypical roles of Kif21b on the actin cytoskeleton during migration of cortical projection neurons.
Assuntos
Cinesinas , Neurônios , Animais , Camundongos , Citoesqueleto de Actina/metabolismo , Movimento Celular , Interneurônios/metabolismo , Cinesinas/metabolismo , Microtúbulos/metabolismo , Neurônios/metabolismoRESUMO
Bronchi of chronic obstructive pulmonary disease (COPD) are the site of extensive cell infiltration, allowing persistent contact between resident cells and immune cells. Tissue fibrocytes interaction with CD8+ T cells and its consequences were investigated using a combination of in situ, in vitro experiments and mathematical modeling. We show that fibrocytes and CD8+ T cells are found in the vicinity of distal airways and that potential interactions are more frequent in tissues from COPD patients compared to those of control subjects. Increased proximity and clusterization between CD8+ T cells and fibrocytes are associated with altered lung function. Tissular CD8+ T cells from COPD patients promote fibrocyte chemotaxis via the CXCL8-CXCR1/2 axis. Live imaging shows that CD8+ T cells establish short-term interactions with fibrocytes, that trigger CD8+ T cell proliferation in a CD54- and CD86-dependent manner, pro-inflammatory cytokines production, CD8+ T cell cytotoxic activity against bronchial epithelial cells and fibrocyte immunomodulatory properties. We defined a computational model describing these intercellular interactions and calibrated the parameters based on our experimental measurements. We show the model's ability to reproduce histological ex vivo characteristics, and observe an important contribution of fibrocyte-mediated CD8+ T cell proliferation in COPD development. Using the model to test therapeutic scenarios, we predict a recovery time of several years, and the failure of targeting chemotaxis or interacting processes. Altogether, our study reveals that local interactions between fibrocytes and CD8+ T cells could jeopardize the balance between protective immunity and chronic inflammation in the bronchi of COPD patients.
Assuntos
Linfócitos T CD8-Positivos , Doença Pulmonar Obstrutiva Crônica , Humanos , Brônquios/patologia , Células Epiteliais/patologia , Inflamação/patologiaRESUMO
Excitatory synapses are typically described as single synaptic boutons (SSBs), where one presynaptic bouton contacts a single postsynaptic spine. Using serial section block-face scanning electron microscopy, we found that this textbook definition of the synapse does not fully apply to the CA1 region of the hippocampus. Roughly half of all excitatory synapses in the stratum oriens involved multi-synaptic boutons (MSBs), where a single presynaptic bouton containing multiple active zones contacted many postsynaptic spines (from 2 to 7) on the basal dendrites of different cells. The fraction of MSBs increased during development (from postnatal day 22 [P22] to P100) and decreased with distance from the soma. Curiously, synaptic properties such as active zone (AZ) or postsynaptic density (PSD) size exhibited less within-MSB variation when compared with neighboring SSBs, features that were confirmed by super-resolution light microscopy. Computer simulations suggest that these properties favor synchronous activity in CA1 networks.
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Hipocampo , Terminações Pré-Sinápticas , Sinapses , Neurônios , DendritosRESUMO
The mechanisms governing the recruitment of functional glutamate receptors at nascent excitatory postsynapses following initial axon-dendrite contact remain unclear. We examined here the ability of neurexin/neuroligin adhesions to mobilize AMPA-type glutamate receptors (AMPARs) at postsynapses through a diffusion/trap process involving the scaffold molecule PSD-95. Using single nanoparticle tracking in primary rat and mouse hippocampal neurons overexpressing or lacking neuroligin-1 (Nlg1), a striking inverse correlation was found between AMPAR diffusion and Nlg1 expression level. The use of Nlg1 mutants and inhibitory RNAs against PSD-95 demonstrated that this effect depended on intact Nlg1/PSD-95 interactions. Furthermore, functional AMPARs were recruited within 1 h at nascent Nlg1/PSD-95 clusters assembled by neurexin-1ß multimers, a process requiring AMPAR membrane diffusion. Triggering novel neurexin/neuroligin adhesions also caused a depletion of PSD-95 from native synapses and a drop in AMPAR miniature EPSCs, indicating a competitive mechanism. Finally, both AMPAR level at synapses and AMPAR-dependent synaptic transmission were diminished in hippocampal slices from newborn Nlg1 knock-out mice, confirming an important role of Nlg1 in driving AMPARs to nascent synapses. Together, these data reveal a mechanism by which membrane-diffusing AMPARs can be rapidly trapped at PSD-95 scaffolds assembled at nascent neurexin/neuroligin adhesions, in competition with existing synapses.
Assuntos
Moléculas de Adesão Celular Neuronais/biossíntese , Guanilato Quinases/metabolismo , Hipocampo/fisiologia , Proteínas de Membrana/metabolismo , Moléculas de Adesão de Célula Nervosa/metabolismo , Receptores de AMPA/metabolismo , Transmissão Sináptica/fisiologia , Animais , Proteínas de Ligação ao Cálcio , Moléculas de Adesão Celular Neuronais/genética , Proteína 4 Homóloga a Disks-Large , Feminino , Guanilato Quinases/antagonistas & inibidores , Guanilato Quinases/genética , Hipocampo/metabolismo , Masculino , Potenciais da Membrana/genética , Potenciais da Membrana/fisiologia , Proteínas de Membrana/antagonistas & inibidores , Proteínas de Membrana/genética , Camundongos , Camundongos Knockout , Mutação , Técnicas de Patch-Clamp/métodos , Cultura Primária de Células , Ratos , Receptores de AMPA/fisiologia , Transmissão Sináptica/genética , Transfecção/métodosRESUMO
Dopamine transmission is involved in reward processing and motor control, and its impairment plays a central role in numerous neurological disorders. Despite its strong pathophysiological relevance, the molecular and structural organization of the dopaminergic synapse remains to be established. Here, we used targeted labelling and fluorescence activated sorting to purify striatal dopaminergic synaptosomes. We provide the proteome of dopaminergic synapses with 57 proteins specifically enriched. Beyond canonical markers of dopamine neurotransmission such as dopamine biosynthetic enzymes and cognate receptors, we validated 6 proteins not previously described as enriched. Moreover, our data reveal the adhesion of dopaminergic synapses to glutamatergic, GABAergic or cholinergic synapses in structures we named "dopamine hub synapses". At glutamatergic synapses, pre- and postsynaptic markers are significantly increased upon association with dopamine synapses. Dopamine hub synapses may thus support local dopaminergic signalling, complementing volume transmission thought to be the major mechanism by which monoamines modulate network activity.
Assuntos
Dopamina , Sinapses , Animais , Corpo Estriado/fisiologia , Dopamina/metabolismo , Camundongos , Recompensa , Sinapses/metabolismo , Transmissão Sináptica/fisiologiaRESUMO
Fast-paced innovations in imaging have resulted in single systems producing exponential amounts of data to be analyzed. Computational methods developed in computer science labs have proven to be crucial for analyzing these data in an unbiased and efficient manner, reaching a prominent role in most microscopy studies. Still, their use usually requires expertise in bioimage analysis, and their accessibility for life scientists has therefore become a bottleneck. Open-source software for bioimage analysis has developed to disseminate these computational methods to a wider audience, and to life scientists in particular. In recent years, the influence of many open-source tools has grown tremendously, helping tens of thousands of life scientists in the process. As creators of successful open-source bioimage analysis software, we here discuss the motivations that can initiate development of a new tool, the common challenges faced, and the characteristics required for achieving success.