Purification and quantitative proteomic analysis of cell bodies and protrusions.

Actin-rich protrusions are membrane extensions generated by actin polymerization that drive mesenchymal-like cell migration. Characterization of protrusions proteome is crucial for understanding their function. We present a complete step-by-step protocol based on microporous filter-based fractionation of protrusive cellular domains coupled with sample preparation for quantitative proteomics, mass spectrometric data acquisition, and data analysis. This protocol enables purification, quantification, and analysis of the distribution of proteins present in protrusions and cell bodies. For complete details on the use and execution of this protocol, please refer to Dermit et al. (2020).

Immunohistochemical mapping of neurotensin in the alpaca diencephalon.

INTRODUCTION: The distribution of the immunoreactive cell bodies and fibers containing neurotensin in the alpaca diencephalon was determined by an immunohistochemical technique. MATERIAL AND METHODS: The study was carried out in four male alpacas that lived at sea level. Brains of deeply anesthetized animals were fixed by perfusion with 4% paraformaldehyde. Cryostat sections were stained by a standard immunohistochemical method. RESULTS: Cell bodies containing neurotensin were observed in the zona incerta and hypothalamus. A low/moderate density of these cell bodies was observed in the lateral hypothalamic area, anterior and dorsal hypothalamic areas, suprachiasmatic nucleus, periventricular region of the hypothalamus and in the ventromedial hypothalamic nucleus. In both thalamus and hypothalamus, immunoreactive fibers showed a widespread distribution. In the thalamus, a high density of these fibers was mainly found in the midline nuclei, whereas in the hypothalamus a high density was in general observed in the whole structure. CONCLUSIONS: In comparison with other mammals, the thalamus of the alpaca showed the most widespread distribution of neurotensin-immunoreactive fibers. The widespread distribution of neurotensin through the alpaca diencephalon suggests that the peptide can be involved in many physiological actions.

Automated Measurement of Cryptococcal Species Polysaccharide Capsule and Cell Body.

The purpose of this technique is to provide a consistent, accurate, and manageable process for large numbers of polysaccharide capsule measurements. First, a threshold image is generated based on intensity values uniquely calculated for each image. Then, circles are detected based on contrast between the object and background using the well-established Circle Hough Transformation (CHT) algorithm. Finally, the detected cell capsules and bodies are matched according to center coordinates and radius size, and data is exported to the user in a manageable spreadsheet. The advantages of this technique are simple but significant. First, because these calculations are performed by an algorithm rather than a human both accuracy and reliability are increased. There is no decline in accuracy or reliability regardless of how many samples are analyzed. Second, this approach establishes a potential standard operating procedure for the Cryptococcus field instead of the current situation where capsule measurement varies by lab. Third, given that manual capsule measurements are slow and monotonous, automation allows rapid measurements on large numbers of yeast cells that in turn facilitates high throughput data analysis and increasingly powerful statistics. The major limitations of this technique come from how the algorithm functions. First, the algorithm will only generate circles. While Cryptococcus cells and their capsules take on a circular morphology, it would be difficult to apply this technique to non-circular object detection. Second, due to how circles are detected the CHT algorithm can detect enormous pseudo-circles based on the outer edges of several clustered circles. However, any misrepresented cell bodies caught within the pseudo-circle can be easily detected and removed from the resulting data sets. This technique is meant for measuring the circular polysaccharide capsules of Cryptococcus species based on India Ink bright field microscopy; though it could be applied to other contrast based circular object measurements.

Phase separation in necrotic cells.

Necrotic cells are known to develop characteristic membrane blebs. We measured protein concentration within necrotic blebs and found that it can be reduced by as much as twenty-fold compared to the main cell body (CB). These results raise two questions: 1. Why do proteins vacate the bleb? 2. How can osmotic equilibrium be maintained between the bleb and CB? Our photobleaching and ultracentrifugation experiments indicate extensive protein aggregation. We hypothesize that protein aggregation within the CB shifts the chemical equilibrium and draws proteins out of the bleb; at the same time, aggregation reduces the effective molar concentration of protein in the CB, so that osmotic equilibrium between high-protein CB and low-protein necrotic blebs becomes possible.

Phenotypic clustering: a novel method for microglial morphology analysis.

BACKGROUND: Microglial cells are tissue-resident macrophages of the central nervous system. They are extremely dynamic, sensitive to their microenvironment and present a characteristic complex and heterogeneous morphology and distribution within the brain tissue. Many experimental clues highlight a strong link between their morphology and their function in response to aggression. However, due to their complex "dendritic-like" aspect that constitutes the major pool of murine microglial cells and their dense network, precise and powerful morphological studies are not easy to realize and complicate correlation with molecular or clinical parameters. METHODS: Using the knock-in mouse model CX3CR1(GFP/+), we developed a 3D automated confocal tissue imaging system coupled with morphological modelling of many thousands of microglial cells revealing precise and quantitative assessment of major cell features: cell density, cell body area, cytoplasm area and number of primary, secondary and tertiary processes. We determined two morphological criteria that are the complexity index (CI) and the covered environment area (CEA) allowing an innovative approach lying in (i) an accurate and objective study of morphological changes in healthy or pathological condition, (ii) an in situ mapping of the microglial distribution in different neuroanatomical regions and (iii) a study of the clustering of numerous cells, allowing us to discriminate different sub-populations. RESULTS: Our results on more than 20,000 cells by condition confirm at baseline a regional heterogeneity of the microglial distribution and phenotype that persists after induction of neuroinflammation by systemic injection of lipopolysaccharide (LPS). Using clustering analysis, we highlight that, at resting state, microglial cells are distributed in four microglial sub-populations defined by their CI and CEA with a regional pattern and a specific behaviour after challenge. CONCLUSIONS: Our results counteract the classical view of a homogenous regional resting state of the microglial cells within the brain. Microglial cells are distributed in different defined sub-populations that present specific behaviour after pathological challenge, allowing postulating for a cellular and functional specialization. Moreover, this new experimental approach will provide a support not only to neuropathological diagnosis but also to study microglial function in various disease models while reducing the number of animals needed to approach the international ethical statements.

Localisation of N-acetylaspartate in oligodendrocytes/myelin.

The role of N-acetylaspartate in the brain is unclear. Here we used specific antibodies against N-acetylaspartate and immunocytochemistry of carbodiimide-fixed adult rodent brain to show that, besides staining of neuronal cell bodies in the grey matter, N-acetylaspartate labelling was present in oligodendrocytes/myelin in white matter tracts. Immunoelectron microscopy of the rat hippocampus showed that N-acetylaspartate was concentrated in the myelin. Also neuronal cell bodies and axons contained significant amounts of N-acetylaspartate, while synaptic elements and astrocytes were low in N-acetylaspartate. Mitochondria in axons and neuronal cell bodies contained higher levels of N-acetylaspartate compared to the cytosol, compatible with synthesis of N-acetylaspartate in mitochondria. In aspartoacylase knockout mice, in which catabolism of N-acetylaspartate is blocked, the levels of N-acetylaspartate were largely increased in oligodendrocytes/myelin. In these mice, the highest myelin concentration of N-acetylaspartate was found in the cerebellum, a region showing overt dysmyelination. In organotypic cortical slice cultures there was no evidence for N-acetylaspartate-induced myelin toxicity, supporting the notion that myelin damage is induced by the lack of N-acetylaspartate for lipid production. Our findings also implicate that N-acetylaspartate signals on magnetic resonance spectroscopy reflect not only vital neurons but also vital oligodendrocytes/myelin.

Label-free in vitro visualization of particle uptake into human oral buccal epithelial cells by confocal Raman microscopy.

In this study, we present confocal Raman microscopy for chemically selective analysis of a human buccal epithelial cell layer with a focus on label-free visualization of particle uptake into the cells. We demonstrate the suitability and benefit of this analytical technique in comparison to confocal fluorescence microscopy for three dimensional imaging of in vitro cell models.