Hydrogel-Tissue Chemistry: Principles and Applications

Abstract

Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons—even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants—or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout—is stimulating innovation across biology and medicine.

Features Of Hippocampal Astrocytic Domains And Their Spatial Relation To Excitatory And Inhibitory Neurons

“…Recently developed brain clearing techniques allow large scale, three dimensional, single-cell resolution characterization of multiple cell types simultaneously (Gradinaru et al, 2018;Treweek and Gradinaru, 2016;Ye et al, 2016). Such methods can be adopted to investigate astrocytic domains, and indeed a few studies have already used transgenic mice to show that fluorescent astrocytes can be imaged in the cleared mouse cortex (Chai et al, 2017;Gaire et al, 2018;Lanjakornsiripan et al, 2018;Miller and Rothstein, 2016).…”

Exploring single cells in space and time during tissue development, homeostasis and regeneration

“…This is especially true of deep tissues in which auto-fluorescence masks fluorescently labeled molecules, and light scattering hampers reliable signal read-out, resulting in low efficiency and accuracy (Lein et al, 2017). In a recently developed method called spatially resolved transcript amplicon read-out mapping (STARmap; Wang et al, 2018b), Wang et al combined hydrogel-tissue chemistry (Gradinaru et al, 2018) with in situ sequencing to facilitate sequencing of targeted sequences within intact 3D-tissues. In this approach, the cross-linking of selected intracellular biomolecules to a network of polymer allowed the preservation of three-dimensional tissue-structural relationships whilst also improving optical properties by clearing lipids and proteins.…”

Three dimensional nanoscopy of whole cells and tissues within situpoint spread function retrieval

“…The combination of adaptive optics (AO) [29,30,[58][59][60][61][62][63][64] with INSPR will allow restoring emission pattern information and pin-pointing 3D location of single molecules with high accuracy simultaneously. In addition, INSPR can be combined with light-sheet illumination approaches [65][66][67] and tissue clearing and expansion methods [68][69][70] to further reduce the fluorescence background and increase the achievable resolution, therefore opening doors to observe the static and dynamic conformation of complex intra-and extra-cellular constituents over large tissue volumes at the nanoscale level.…”