News This Noon

DNA, RNA and protein extraction is the basic method used in molecular biology. These biomolecules can be isolated from any biological material for subsequent processes, analytical purposes or preparations. In the past, the process of nucleic acid extraction ffpe and purification was complicated, slow, laborious and limited in terms of overall performance. Currently, there are many specialized methods that can be used to extract pure biomolecules, such as solution-based and column-based protocols.

Yuan et al. found that the counting method can double the DNA performance of some phytoplankton species compared to the enzyme method of not counting. He has suggested that extra freezing and thawing lysis could affect the effectiveness of hitting. We recognize the possibility that there is never a universally better extraction method and have designed a modular nucleic acid extraction protocol that yields high nucleic acid yields in a wide range of environmental samples. Most of the samples analyzed are marine sediments ranging from the surface to the deep subsurface, and eutrophic to ultraoligotrophic, but we also include lake sediments, coagulation rocks, water and air samples. With only minor adjustments, This method can be adapted to specific research needs, such as the simultaneous extraction of DNA and RNA, and the separate extraction of two different groups of DNA. In the past, these two DNA groups were called “extracellular DNA” and “intracellular DNA” respectively (Ogram et al. 1987; Corinaldesi et al. 2005; Alawi et al. 2014; for more details see “Discussion”).

Instead of RNA separation with cesium chloride gradients, water-saturated phenol, sodium acetate and chloroform are added to the homogenized and stirred. After a quick spin (no ultracentrifugation!), separate the phenolic and chloroform layers and the RNA is retained in the aqueous top layer, while DNA and other proteins are retained in the interface and the bottom organic layer. This method reduced the high throughput DNA purification time it took to isolate the RNA from more than 20 hours to about 4 hours, and variations in this kit-free method are still widely used . To test whether cell storage in Lugol affects sequencing results, part of the grouped sample was stored in a 1% to + 4 ° C acidic Lugol solution, and the 2 ml aliquots were centrifuged at 3500 g for 10 minutes to obtain 100 μL cell suspension before DNA was extracted.

When the trim requirements at Mothur were relaxed, with a minimum length of 150 bases and without checking the quality of the scroll window, the sequence ratios were less biased. The other trim processes remained similar in both cases, even in up to two mismatched cases in the primer area, a wrong combination in the barcode area and the maximum homopolymer length of eight. In the CLC pipeline, when the 3 ‘endless readings were imported from Torrent Suite and a minimum reading length of 150 was imposed, sequence ratios followed the original distribution better than when starting with 3’ end-cut measurements. A closer look at the cut revealed that the site causing a temporary decrease in quality values was a loop in the structure of the rRNA gene. In the CLC program, the standard modified Mott quality algorithm was used to reduce the ending with an error rate of 0.05. In both software programs, the OTU0.97 group was used to identify comparable sequences and the OTUs were classified at species level compared to the reference library .

The water layer is removed to precipitate the RNA at night with isopropanol and 40 µg glycogen at -20 ° C. All RNA grains are washed twice with 75% ethanol and then dissolved in water (Free RNase / DNase). A volume of 200 ng total RNA for each sample was transcribed in reverse in cDNA using the high capacity cDNA RNA kit, according to the manufacturer’s protocol. For qPCR, 1 µL cDNA is primed with Taqman assays tailored to Applied Biosystems for mRNA target in a final reaction volume of 1X Taqman Universal PCR Master Mix . QPCR was equipped with Gene Expression Master Mix and TaqMan® gene expression primers in the CFX96 real-time detection system (Bio-Rad, Hercules, CA).