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Poor fixation or hydrogel immersion into tissues can cause the loss of proteins and the distortion of tissue during the tissue clearing process. The whole adult mouse brain should be incubated in 4% paraformaldehyde overnight, followed by immersion in a minimum volume of 20 mL of hydrogel monomer solution for 12 - 18 h with gentle shaking. For large tissues, including human tissue such as brain slices and spinal cord, extended soaking time in the hydrogel monomer solution is required. The ACT protocol is easily applicable to the clearing of fixed tissues because the tissue fixation and polymer infusion steps are separated. After tissue clearing, human tissues were well-stained with several antibodies. Note that the ACT clearing technique is not compatible with alcohol fixatives, such as ethanol and methanol.
The tissue-hydrogel polymerization step is also critical to produce good-quality tissue following the clearing process. Because oxygen inhibits the polymerization of acrylamide, it should be removed by degassing the tissue-containing solution under a nitrogen gas infusion system. Alternatively, de-oxygenation can be executed using a vacuum chamber with a heat block for 23 h.
The clearing rate is dependent upon numerous factors, including the organ size, the contents of lipids or ECM fibrous proteins, the condition of fixation, etc. Most adult mouse tissues can be cleared by ETC overnight. However, there is a risk of unnecessary over-clearing and tissue swelling; thus, the differences in clearing time are of important consideration. Tissue-clearing conditions should be empirically determined. Importantly, the contents of the ECM may affect the appearance of the cleared tissue. The color of the tissues remains white or opaque, even after the ACT in ETC buffer, because ACT does not clear dense protein fibers. However, when these organs were immersed in RI matching solution, they became transparent.
The rate of tissue swelling appears to be dependent upon the ECM contents of the tissues, and soft organs, such as the brain, exhibit a greater swelling ratio than dense organs. Because increased tissue swelling will help the tissue-clearing procedure, ACT routinely utilizes distilled water-based buffer in most cases. In some cases, when tissue swelling or transient deformity is not desirable, such as in embryos, buffer containing 0.1x PBS can be applied for high-resolution imaging. It should be also noted that higher salt concentrations in the buffer could cause the shrinkage of tissues.
The ACT method can clarify whole organs and even the whole body of a mouse14. However, deep-tissue imaging of transparent tissue requires special microscopes and objectives. Thus, brain tissue 1- to 2-mm thick is most effective for imaging with a conventional confocal microscope. In our hands, removal of the labeled antibodies from ACT-processed tissues is antibody-dependent, and rounds of different antibody labeling are not recommended. Several antibodies, such as TH and GFAP, worked especially well for whole-brain immunolabeling14. On the other hand, some antibodies, such as Tuj1 or Map2, often labeled only the surface of the tissues. This might be improved by other methods, such as SWITCH15. Another potential limitation is that it might be difficult to preserve fine protein structures in ACT-processed tissue because of the tissue swelling and shrinkage during the tissue-clearing step.
The PRESTO technique is applicable to a wide variety of tissue-labeling techniques. For example, in tissue-transparent methods using pre-labeled tissue, such as SeeDB4 and iDISCO7, immunolabeling of dense tissue requires incubation periods longer than several days to weeks. However, PRESTO can shorten the incubation time to several hours, enabling the completion of the entire process within a day with 1-mm thick dense tissue. PRESTO can enhance the efficacy of deep-labeling thick, dense tissues, or even un-cleared thick tissues. Because PRESTO uses a table-top centrifuge or syringe pump and does not require any special equipment, it is relatively easy to implement this technique with routine lab procedures.