Neocortical microdissection at columnar and laminar resolution for molecular interrogation

The heterogeneous organization of the mammalian neocortex poses a challenge to elucidate the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. Here we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA-sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general as it is applicable to any brain structure that can be identified using optical landmarks in living slices.

Microelastic mapping of the rat dentate gyrus

The lineage commitment of many cultured stem cells, including adult neural stem cells (NSCs), is strongly sensitive to the stiffness of the underlying extracellular matrix. However, it remains unclear how well the stiffness ranges explored in culture align with the microscale stiffness values stem cells actually encounter within their endogenous tissue niches. To address this question in the context of hippocampal NSCs, we used atomic force microscopy to spatially map the microscale elastic modulus ( E ) of specific anatomical substructures within living slices of rat dentate gyrus in which NSCs reside during lineage commitment in vivo . We measured depth-dependent apparent E -values at locations across the hilus (H), subgranular zone (SGZ) and granule cell layer (GCL) and found a two- to threefold increase in stiffness at 500 nm indentation from the H (49 ± 7 Pa) and SGZ (58 ± 8 Pa) to the GCL (115 ± 18 Pa), a fold change in stiffness we have previously found functionally relevant in culture. Additionally, E exhibits nonlinearity with depth, increasing significantly for indentations larger than 1 µm and most pronounced in the GCL. The methodological advances implemented for these measurements allow the quantification of the elastic properties of hippocampal NSC niche at unprecedented spatial resolution.

Lamina-specific cell adhesion on living slices of hippocampus

Laminar distribution of fiber systems is a characteristic feature of hippocampal organization. Ingrowing afferents, e.g. the fibers from the entorhinal cortex, terminate in specific layers, which implies the existence of laminar recognition cues. To identify cues that are involved in the laminar segregation of fiber systems in the hippocampus, we used an in vitro assay to study the adhesion of dissociated entorhinal cells on living hippocampal slices. Here we demonstrate that dissociated entorhinal cells adhere to living hippocampal slices with a lamina-specific distribution that reflects the innervation pattern of the entorhino-hippocampal projection. In contrast, laminae which are not invaded by entorhinal fibers are a poor substrate for cell adhesion. Lamina-specific cell adhesion does not require the neural cell adhesion molecule or the extracellular matrix glycoprotein reelin, as revealed in studies with mutants. However, the pattern of adhesive cues in the reeler mouse hippocampus mimics characteristic alterations of the entorhinal projection in this mutant, suggesting a role of layer-specific adhesive cues in the pathfinding of entorhinal fibers. Lamina-specific cell adhesion is independent of divalent cations, is abolished after cryofixation or paraformaldehyde fixation and is recognized across species. By using a novel membrane adhesion assay, we show that lamina-specific cell adhesion can be mimicked by membrane-coated fluorescent microspheres. Recognition of the adhesive properties of different hippocampal laminae by growing axons, as either a growth permissive or a non-permissive substrate, may provide a developmental mechanism underlying the segregation of lamina-specific fiber projections.

From light to electron microscopic analysis of neurons intracellularly injected in fixed slices with “miniruby”, a fluorescent biocyttn compound

Intracellular labeling of neurons in fixed slices is a very useful method for studying morphological structures of neurons both at light and electron microscopic levels. Recently, biocytin has been widely used for intracellular labeling in living slices because this molecule is highly soluble, has high electrophoretic mobility and has high affinity for avidin. However, biocytin cannot be used in fixed slices because in fixed slices membrane potential cannot be used to signify that a cell is impaled. Thus, in fixed slices it is necessary to inject cells with a fluorescent compound so that impalement and filling can be visualized under fluorescent microscope. We have developed a fluorescent biocytin compound, “Miniruby” (MR), dextran-tetramethylrhodamine-biocytin. previously, we showed that mis molecule provides excellent intracellular labels in fixed slices at the light microscopic level. Here, we demonstrate MR can also be visualized at the electron microscopic level.Fixed slices (200-400 ¼m) of adult rat olfactory bulb, piriform cortex and periaqeductal gray were used.