Tissue preparation protocols approaches

This chapter summarizes our experience with this approach and describes some of the critical parameters involved in the preparation of rat neural tissue for LCM, with particular emphasis on protocols applied to the Arcturus Autopix LCM. This instrument has been superceded by more recent models, which are now marketed and distributed by MDS Analytical Technologies (http // www.moleculardevices.com). The principles described here, however, are applicable to tissue preparation for most LCM instruments. We describe two basic protocols for the isolation of samples of rat brain, first from unstained microdissected regions, and second, from brain cells that express specific antigens identified by immunostaining. In addition, we compare the effects of different fixation conditions on tissue recovery and RNA content using real-time QPCR. 

Two variations of conventional SIMS have evolved. In one, known as matrix-enhanced SIMS, the MALDI sample preparation protocol is used to coat the sample surface with an organic acid (e.g., 2,5-dihydroxybenzoic acid) or other suitable matrix material to improve ionization efficiency [24,25], This approach has been used to image brain tissue samples from freshwater snails (Lymnaea stagnalis). Another variation employs a coating of a thin layer of gold or other metals to enhance analytical signals [26], This method, known as metal-assisted SIMS, provides images with improved spatial and chemical resolution. 

Classical approaches to plant DNA isolation aim to produce large quantities of highly purified DNA. However, smaller quantities of crudely extracted plant DNA are often acceptable for PCR analysis. Another efficient method for preparation of plant DNA for PCR is a single-step protocol that involves heating a small amount of plant tissue in a simple solution. Several factors influence nucleic acid release from tissue salt, EDTA, pH, incubation time and temperature. These factors must be optimized for different sample substrates. EDTA in the sample solution binds the Mg + cofactor required by the Taq polymerase in the PCR, so the EDTA concentration in the solution, or the Mg + concentration in the PCR, must be carefully optimized. 

The usual method of sample preparation for tissue remains as formalin fixation and paraffin embedment (FFPE). This venerable approach may be satisfactory for the preservation of morphologic detail, but does adversely affect the antigenicity of many target molecules in the tissue, to degrees that are unknown. The enormous variation in protocols (including fixation times) employed for FFPE among different laboratories, or within the same laboratory from specimen to specimen, compounds the problem, and contributes to the current poor reproducibility. 

Successful application of this experimental approach depends on several factors synthesis of high-quality hybridization probes, appropriate fixation of the sample, the hybridization procedure, and the fluorescence microscopy approach used to image the specimen. In adapting the technique of three-dimensional in situ hybridization to different organisms and tissue types, the simplest and most invariant aspect of the technology has proved to be the hybridization procedure. Probes must be developed on a custom basis to address the particular questions of the investigator, and equally crucially, fixation conditions need to be adapted with special attention to the physical attributes of the individual specimen. However, once appropriate preparation conditions are established for a particular type of sample, it has been unnecessary to reoptimize the basic hybridization protocol. We discuss each of these experimental issues separately below. 

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