Question

short essay question:

How to design a bioinformatics pipeline for multi-omics analysis to reconstruct a metabolic pathway.

Answer 1

.So, here’s the answer to your question.

So in order to represent this metabolic pathway, we take the mature acorns extracted from the Holm oak which is a Quercus species. So these acorns when taken to the lab for the sterilization and germination purpose. In the lab, the seeds after getting germinated are being sown in the pots of half a liter composed of perlite and then they are cultivated and grown under a greenhouse with good natural conditions for a period of four months. This will be done until the sapling reaches about ten leaves stage.

Irrigation has to be done periodically at least once a week with specific nutrients like the HOAGLAND. After this, the embryos that are germinated, leaves, the cotyledons, and also the roots have to be separated and then wash thoroughly with the distilled water mixed then kept in liquid nitrogen in frozen conditions.

Later using a mortar the individual tissues are homogenized till it reaches a thin and fine powdered texture is reached. After this, the entire mixture is being stored at -80 degrees celsius. As I have mentioned earlier the homogenized tissues obtained from the acorn's leaves, cotyledons, roots, embryo. Now based on the tissue or the organ different samples are taken from specific trees which after collection are mixed. They range for about a number of eighteen which are the leaves and the roots, to about fifty cotyledons and seed embryos

So after extracting them separately or independently, only a fair or accurate number of proteins are taken in three replicates are being taken into consideration.

There are numerous steps followed after this which include

-RNA Extraction and Sequencing

Data Processing

Gene Ontology

-Proteomics Analysis

Protein Extraction and Digestion

Shotgun LC-MS Analysis

Protein Identification

-Metabolomics Analysis

Metabolite Extraction

GC-MS Analysis

Metabolite Identification

Interspecies Comparison

Integrated Pathway

Hence from the above information and experiment, it is to be noted that the Holm oak is the very significant and definitely the most precious species of trees in the region of Mediterranean.

In the above method as a fresh amount of certain tissues are taken and specific analytical processes are carried.

After the several numbers of steps, metabolic processes are being done to Holm oak mentioned above, it is to be noted and proved that the art of instrumentation is very much convenient

I hope this helps. Please do let me know if I can help you with anything.

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