Monitoring and quantifying dynamic physiological processes in live neurons using fluorescence recovery after photobleaching

Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditis elegans PAQR-2 and Its Mammalian Homolog AdipoR2

The properties of cell membranes are determined mostly by the types of fatty acids that they contain. Bodhicharla et al. report that a key regulator of membrane fluidity, the PAQR-2/IGLR-2 protein complex...

Maintenance of membrane properties is an essential aspect of cellular homeostasis of which the regulatory mechanisms remain mostly uncharacterized. In Caenorhabditis elegans, the PAQR-2 and IGLR-2 proteins act together as a plasma membrane sensor that responds to decreased fluidity by promoting fatty acid desaturation, hence restoring membrane fluidity. Here, we used mosaic analysis for paqr-2 and iglr-2, and tissue-specific paqr-2 expression, to show that membrane homeostasis is achieved cell nonautonomously. Specifically, we found that expression of paqr-2 in the hypodermis, gonad sheath cells, or intestine is sufficient to suppress systemic paqr-2 mutant phenotypes, including tail tip morphology, membrane fluidity in intestinal cells, cold and glucose intolerance, vitellogenin transport to the germline, germ cell development, and brood size. Finally, we show that the cell nonautonomous regulation of membrane homeostasis is conserved in human cells: HEK293 cells that express AdipoR2, a homolog of paqr-2, are able to normalize membrane fluidity in distant cells where AdipoR2 has been silenced. Finally, using C. elegans mutants and small interfering RNA against Δ9 stearoyl-CoA desaturase in HEK293 cells, we show that Δ9 desaturases are essential for the cell nonautonomous maintenance of membrane fluidity. We conclude that cells are able to share membrane components even when they are not in direct contact with each other, and that this contributes to the maintenance of membrane homeostasis in C. elegans and human cells.

Using Fluorescence Recovery After Photobleaching to Study Gap Junctional Communication In Vitro

Fluorescence recovery after photobleaching (FRAP) is a microscopy-based technique to study the movement of fluorescent molecules inside a cell. Although initially developed to investigate intracellular mobility, FRAP can be also used to measure intercellular dynamics. This chapter describes how to perform FRAP experiment to study gap junctional communication in living cells. The procedures described here can be carried out with a laser-scanning confocal microscope and any in vitro cultured cells known to communicate via gap junctions. In addition, the method can be easily adjusted to measure gap junction function in 3D cell cultures as well as ex vivo tissue.

FRAP to Characterize Molecular Diffusion and Interaction in Various Membrane Environments

Fluorescence recovery after photobleaching (FRAP) is a standard method used to study the dynamics of lipids and proteins in artificial and cellular membrane systems. The advent of confocal microscopy two decades ago has made quantitative FRAP easily available to most laboratories. Usually, a single bleaching pattern/area is used and the corresponding recovery time is assumed to directly provide a diffusion coefficient, although this is only true in the case of unrestricted Brownian motion. Here, we propose some general guidelines to perform FRAP experiments under a confocal microscope with different bleaching patterns and area, allowing the experimentalist to establish whether the molecules undergo Brownian motion (free diffusion) or whether they have restricted or directed movements. Using in silico simulations of FRAP measurements, we further indicate the data acquisition criteria that have to be verified in order to obtain accurate values for the diffusion coefficient and to be able to distinguish between different diffusive species. Using this approach, we compare the behavior of lipids in three different membrane platforms (supported lipid bilayers, giant liposomes and sponge phases), and we demonstrate that FRAP measurements are consistent with results obtained using other techniques such as Fluorescence Correlation Spectroscopy (FCS) or Single Particle Tracking (SPT). Finally, we apply this method to show that the presence of the synaptic protein Munc18-1 inhibits the interaction between the synaptic vesicle SNARE protein, VAMP2, and its partner from the plasma membrane, Syn1A.

Using FRAP or FRAPA to Visualize the Movement of Fluorescently Labeled Proteins or Cellular Organelles in Live Cultured Neurons Transformed with Adeno-Associated Viruses

Fluorescence recovery after photobleaching (FRAP) and fluorescence redistribution after photoactivation (FRAPA) are complementary methods used to gauge the movement of proteins or sub-resolution organelles within cells. Using these methods we can determine the nature of the movement of labeled particles, whether it is random, constrained, or active, the coefficient of diffusion if applicable, binding and unbinding constants, and the direction of active transport. These two techniques have been extensively utilized to probe the cell biology of neurons. A practical outline of FRAP and FRAPA in cultured neurons is presented, including the preparation of the neurons and their infection with adeno-associated viral vectors. Considerations in planning such experiments are provided.

Bioinformatics approaches to single-cell analysis in developmental biology

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology.

ATP binding to synaspsin IIa regulates usage and clustering of vesicles in terminals of hippocampal neurons

Synaptic transmission is expensive in terms of its energy demands and was recently shown to decrease the ATP concentration within presynaptic terminals transiently, an observation that we confirm. We hypothesized that, in addition to being an energy source, ATP may modulate the synapsins directly. Synapsins are abundant neuronal proteins that associate with the surface of synaptic vesicles and possess a well defined ATP-binding site of undetermined function. To examine our hypothesis, we produced a mutation (K270Q) in synapsin IIa that prevents ATP binding and reintroduced the mutant into cultured mouse hippocampal neurons devoid of all synapsins. Remarkably, staining for synaptic vesicle markers was enhanced in these neurons compared with neurons expressing wild-type synapsin IIa, suggesting overly efficient clustering of vesicles. In contrast, the mutation completely disrupted the capability of synapsin IIa to slow synaptic depression during sustained 10 Hz stimulation, indicating that it interfered with synapsin-dependent vesicle recruitment. Finally, we found that the K270Q mutation attenuated the phosphorylation of synapsin IIa on a distant PKA/CaMKI consensus site known to be essential for vesicle recruitment. We conclude that ATP binding to synapsin IIa plays a key role in modulating its function and in defining its contribution to hippocampal short-term synaptic plasticity.

Presynaptic and Postsynaptic Scaffolds

The development of methods to follow the dynamics of synaptic molecules in living neurons has radically altered our view of the synapse, from that of a generally static structure to that of a dynamic molecular assembly at steady state. This view holds not only for relatively labile synaptic components, such as synaptic vesicles, cytoskeletal elements, and neurotransmitter receptors, but also for the numerous synaptic molecules known as scaffolding molecules, a generic name for a diverse class of molecules that organize synaptic function in time and space. Recent studies reveal that these molecules, which confer a degree of stability to synaptic assemblies over time scales of hours and days, are themselves subject to significant dynamics. Furthermore, these dynamics are probably not without effect; wherever studied, these seem to be associated with spontaneous changes in scaffold molecule content, synaptic size, and possibly synaptic function. This review describes the dynamics exhibited by synaptic scaffold molecules, their typical time scales, and the potential implications to our understanding of synaptic function.