Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples.

BACKGROUND: Different cytology preparations can be used for molecular diagnostics, however the influence of pre-analytical and analytical steps on the results are not yet well defined. We aimed to determine optimal steps for efficient extraction of DNA and RNA from fresh cells for molecular diagnostics. METHODS: MCF7 and FaDu human cell lines, were used as a model to determine fresh cells storage conditions (temperature: 25°C, 4°C, -20°C, -80°C; duration: 0 h, 4 h, 12 h, 24 h, 48 h) and optimal nucleic acids extraction method. Besides, the minimal number of total cells and minimal percentage of mutated cells needed for successful extraction of nucleic acids and subsequent determination of present mutation were evaluated. RESULTS: Extraction of nucleic acids using spin columns yielded the highest quantity and quality of nucleic acids. Isolation of nucleic acids was feasible in all storage conditions, however higher temperature and longer duration of fresh cells storage were associated with lower quality of isolated nucleic acids and similar quantification cycle of housekeeping genes. Successful molecular testing was feasible with least 104 cells, while specific mutation was detected in as low as 5% of mutated cells. CONCLUSIONS: Our cell line model, mimicking fresh cytology samples, showed that quantity of extracted either DNA or RNA declined with higher temperatures and longer duration of storage but regardless of the storage conditions, we successfully detected both housekeeping genes and mutated gene using qPCR.

DNA and RNA extraction from low amount of blood volume.

Clinical and research-based tests in molecular biology require a substantial amount of DNA and RNA, unfortunately, a considerable number of cells is needed for this amount of sample. Blood is one of the best and easiest source of cells, but is not used due to its invasive drawing methods and the needed volume. Another considerable point is the low amount of samples detected in crime scenes. TRI reagent is one of the most available methods for DNA, RNA and protein extraction. However, based on unsuccessful results, this method has not been widely used on blood samples. In this study, for the first time, the use of TRI reagent on micro scale blood volume was reported, resulting in high yield of DNA and RNA with great quality.

Comparison of methods for extraction of short RNA-DNA hybrids / 军事医学

Objective To compare the effects of three different methods for extracting short RNA-DNA hybrids, including the TRI reagent method , the phenol saturated with water method and the phenol saturated with Tris buffer method in order to facilitate studies on the biological function of RNA-DNA hybrids .Methods Short RNA fragments modifiedwith FAM at the 5′end and those modified with Cy 5 at the 5′end were synthesized .RNA and DNA fragments were annealed to form RNA-DNA hybrids.They were extracted with the above-mentioned 3 methods respectively .The extracted products were analyzed with electrophoresis .Results and Conclusion Short RNA-DNA hybrids can be extracted by the phenol saturated with water method and by the phenol saturated with Tris buffer method .The results can help study the function of short RNA-DNA hybrids .

RNA Isolation from Early Drosophila Larval Ovaries.

In the fruit fly Drosophila melanogaster, ovarian germline stem cells (GSCs) and their niches form during larval development. This process is poorly studied partly due to technical difficulties in isolating early larval ovaries. In addition, purifying RNA from larval ovaries proves to be more challenging than purifying it from other organs. Here we describe a technique for dissecting ovaries from early larvae and advise on how to extract RNA with maximum yield and purity. RNA isolation allows assaying gene expression in a direct and quantitative manner, which is invaluable for understanding molecular events underlying ovarian niche formation and GSC establishment.

A Simple Protocol for High Efficiency Protein Isolation After RNA Isolation from Mouse Thyroid and Other Very Small Tissue Samples.

As a dedicated hormone-secreting organ, the thyroid gland possesses a complement of proteostatic systems, including antioxidant, unfolded protein, and autophagic responses. The vast majority of animal investigations of thyroid physiology and, more recently, proteostasis, have utilized as model the rat, rather than the mouse. This is due to the very small size of the thyroid gland in the latter, with a total weight of ~2 mg (~1 mg per thyroid lobe). However, this strategy has limited the utilization of genetic approaches, such as taking advantage of the various transgenic and knockout mouse models. Here, we describe a simple and highly efficient protocol for the simultaneous isolation of mRNA, micro-RNA and 150-200 µg of protein from as little as 1 mg of mouse thyroid tissue, the average weight of one of the two thyroid lobes, thus preserving the other lobe for immunohistochemical or other analyses. While our workflow is similar to other protocols published in the literature and/or proposed by commercial reagent providers, we have introduced a key modification that addresses efficiently the most challenging step of the protein isolation process: the solubilization of the protein pellet after RNA extraction and protein precipitation. We demonstrate the feasibility of our approach and its utility for downstream analyses (including Western blotting) that facilitate the comparative study of proteostatic pathways in the mouse thyroid. We have also successfully applied this protocol on samples from mouse liver, brown and white adipose tissue, as well as from rodent cell lines.

Sample preparation for two-dimensional gel electrophoresis: considering the composition of biological material.

Comparative proteomic analyses in ecotoxicology and related fields require reproducible display of as many proteins as possible. In addition, it should be possible to carry out a quantitative comparison in a reliable manner. Sample preparation represents one of the essential steps toward these aims. In their work, Wu et al. describe how to deal with different recalcitrant tissues of varying species (Proteomics 2013, 13, 3205-3210). Their work underlines the necessity to adapt sample preparation to the specific requirements of the biological material. Beyond that Wu et al. present TRIzol® as feasible means for combined extraction of proteins and RNA. Indeed, using TRI-reagent extraction for proteomics, they resolve two problems at a time: that of removing contaminating compounds and that of simultaneous analysis of gene and protein expression.