Your browser does not fully support modern features. Please upgrade for a smoother experience.
Submitted Successfully!
Thank you for your contribution! You can also upload a video entry or images related to this topic. For video creation, please contact our Academic Video Service.
Version Summary Created by Modification Content Size Created at Operation
1 Maria Oczkowicz -- 1293 2023-02-13 11:01:10 |
2 format correct Catherine Yang Meta information modification 1293 2023-02-14 02:51:23 |

Video Upload Options

We provide professional Academic Video Service to translate complex research into visually appealing presentations. Would you like to try it?
No, upload directly Yes
Cite
If you have any further questions, please contact Encyclopedia Editorial Office.
Steg, A.; Oczkowicz, M.; Smołucha, G. Molecular Techniques Most often Used in Omic. Encyclopedia. Available online: https://encyclopedia.pub/entry/41153 (accessed on 02 April 2026).
Steg A, Oczkowicz M, Smołucha G. Molecular Techniques Most often Used in Omic. Encyclopedia. Available at: https://encyclopedia.pub/entry/41153. Accessed April 02, 2026.
Steg, Anna, Maria Oczkowicz, Grzegorz Smołucha. "Molecular Techniques Most often Used in Omic" Encyclopedia, https://encyclopedia.pub/entry/41153 (accessed April 02, 2026).
Steg, A., Oczkowicz, M., & Smołucha, G. (2023, February 13). Molecular Techniques Most often Used in Omic. In Encyclopedia. https://encyclopedia.pub/entry/41153
Steg, Anna, et al. "Molecular Techniques Most often Used in Omic." Encyclopedia. Web. 13 February, 2023.
Molecular Techniques Most often Used in Omic
Edit
This entry is adapted from the peer-reviewed paper 10.3390/nu14245305

Techniques used in omics have proven to be useful in studying dietary supplements. Techniques used in omics have proven to be useful in studying dietary supplements. In nutrigenomic research, it is necessary to precisely determine the influence of the tested substances on biological processes in the organism at the following levels: transcriptome, genome, proteome, and metabolome. Advanced, high-throughput techniques that generate a massive amount of data must be used to obtain a holistic view of a given subject. 

omics dietary supplements vitamins plant extracts

1. NGS

It took over 12 years of hundreds of scientists’ work and cost almost USD 3 billion to obtain the sequence of the human genome [1].
The Human Genome Project relied on a first-generation sequencing technique called the Sanger technique, and although it allowed for the achievement of groundbreaking results, by the end of the project in 2002, it was known that a much more efficient, large-scale, and less expensive technique was needed, in order for these efforts to contribute to the development of genomic personalized medicine accessible for millions of patients [2]. Several years later, NGS (next-generation sequencing) techniques are in use, that overcome the limitation of Sanger sequencing methods and allow the entire genome to be sequenced in one day for about USD 1000 [3]. NGS-based tests rely on identifying the differences between the genome of the test sample and the reference genome. These differences may arrive from changes to the DNA sequence, e.g., single-nucleotide polymorphisms (SNPs), or large (the whole gene) deletions/duplications [2]. There are two major categories of NGS techniques, sequencing by hybridization and sequencing by synthesis (SBS), while the second approach is the predominant one [4]; therefore, the following descriptions focus on this method.
The basic NGS process involves three steps: library preparation which involves fragmenting DNA/RNA into multiple pieces and adding adapters (oligonucleotides of known sequence) at each end of the template fragments; then, sequencing of the library; and the last step is data analysis.
The vast majority of the sequencing data are generated using Illumina technology, where fragments of DNA with ligated adaptors at the ends, are hybridized to the flow cell surface and then amplified into a clonal cluster through bridge amplification cycles. Proprietary modified and fluorescently labeled nucleotides are incorporated and identified directly by fluorophore excitation during synthesis reactions. The process is repeated for at least 300 rounds. As all four reversible terminator dNTPs are present during each cycle, natural competition reduces incorporation bias and raw error rates. NGS platforms allow research of the genome, transcriptome, or epigenome of any organisms, with the use of a wide variety of methods such as whole-genome sequencing, de novo sequencing, targeted sequencing, total and mRNA sequencing, methylation sequencing or CHiP sequencing (chromatin immunoprecipitation sequencing) [5]. SBS methods rely on much shorter reads (up to 300–500 bases) and have an intrinsically higher error rate than Sanger sequencing. Another limitation of this approach is the reliance on high sequence coverage to obtain an accurate sequence [4].
Although typical, bulk RNA sequencing (RNA-seq) is extremely useful in studying gene expression, gene variants, alternative splicing, etc., and it illustrates an average of numerous cell transcriptomes present in the sample, disregarding the differences between individual cells. Therefore, shortly after introducing high-throughput RNA-seq, a technique for performing single-cell RNA-seq (scRNA-seq) emerged. This approach first requires tissue dissociation and then the isolation of single cells using fluorescence-activated cell sorting (FACS) or microfluidics-based techniques, or mechanical micromanipulation. The individual cells are lysed and converted into cDNA, which is the amplifier and is used to create RNA-seq libraries. scRNA-seq is successfully used in several fields, helping to study cancer heterogeneity and its microenvironment, immunology, neuroscience, and developmental biology [6]. It can also be useful in establishing the effect of a given factor on a particular type of cells, for instance, neurons or immune cells.
NGS techniques contributed to the rapid development and are now leading methods in omics fields such as genomics, transcriptomics, metagenomics, and nutritional genomics. NGS techniques can be used to determine human’ or animal’ genomes and can also be useful for both the qualitative and quantitative assessment and the identification of included in supplements species of, for instance, herbs. NGS techniques can also reveal a diverse community of fungi that are associated with live plant material [7].

2. LC/MS

Sometimes, a combination of several seemingly different techniques allows the discovery of their new possibilities and usefulness in many scientific fields. An example of such a successful combination is the LC-MS method, which combines the physical separation capabilities of liquid chromatography (LC) with the mass analysis capabilities of mass spectroscopy (MS). The coupling of chromatography and mass spectroscopy has been a subject of interest for over 60 years. The first one, reported in 1958 was a combination of gas chromatography (GC) with MS [8]. In GC, the analytes are eluted from the separation column as a gas and can be directly electrically (EI) or chemically (CI) ionized in order to produce mass spectra. This is not possible in the case of liquid chromatography; thus coupling LC with MS was technically a much more significant challenge, and hence it was not commercially available until the 1970s [8][9].
Nowadays, besides liquid chromatography and mass spectrometry devices, the LC-MS system also includes an interface based on atmospheric pressure ionization (API) strategies, that is used to transfer components from the LC column to the MS ion source. Therefore, the sample is pumped through the high-performance liquid chromatography (HPLC) column, where analytes move through at different migration rates. This step separates mixtures with multiple components such as biological fluids, drugs, food, or pesticides. Then, the eluent is directed to MS, where mass determines the mass-to-charge ratio of ions. These data can be used to determine the exact molecular mass that helps to establish the exact molecular mass and structural information about the components of such samples.
The LC-MS offers high selectivity, resolution, precise mass, and specificity compared to other chromatography techniques. However, at the same time, it is also expensive in terms of capital and running costs, and is high maintenance.
This method is used successfully in a variety of fields, for instance in proteomic or metabolomic studies for peptide mass fingerprinting, the metabolite profiling of human/animal tissue, and for the analysis of natural products or secondary metabolites in plants [10][11].

3. NMR

At the end of World War II, the nuclear magnetic resonance (NMR) phenomenon was discovered independently by two groups of scientists Felix Bloch and Edward Purcell. It began to be tested within just a few years, mainly in chemistry, leading to the observation that different compounds give different signals [12]. NMR is a physical event that occurs in all nuclei that contain an odd number of protons and/or neutrons (in other words: nonzero nuclear spin) (most frequently used are 1H and 13C), and it means that at a characteristic and specific resonance frequency it comes to the absorption and re-emission of electromagnetic radiation [13].
Nowadays, NMR spectroscopy is a powerful tool that can provide detailed and quantitative physical, chemical, electronic and structural information about molecules in solutions and in the solid state. Many varieties of NMR techniques have been developed, which are used in various fields, e.g., in medicine, in which the so-called magnetic resonance imaging (MRI) is used for cancer diagnosis, and in chemistry, where proton NMR is used to identify the constituent parts of compounds. Furthermore, NMR is also a leading technique in proteomics and metabolomics to obtain information from biological fluids about the state of the disease or the level of toxins, as well as in foodomics to measure, for example, the ratio between water and fat and a given food product [14]. However, it should be mentioned that the disadvantage of this method is its low sensitivity, which means that it can only be used for the detection and measurement of metabolites in relatively high concentrations [15].

References

  1. National Human Genome Research Institute. Human Genome Project FAQ, National Institute of Health. 2010. Available online: https://www.genome.gov/11006943/human-genome-project-completion-frequently-asked-questions/ (accessed on 8 January 2021).
  2. Muzzey, D.; Evans, E.A.; Lieber, C. Understanding the Basics of NGS: From Mechanism to Variant Calling. Curr. Genet. Med. Rep. 2015, 3, 158–165.
  3. Metzker, M.L. Sequencing technologies the next generation. Nat. Rev. Genet. 2010, 11, 31–46.
  4. Slatko, B.E.; Gardner, A.F.; Ausubel, F.M. Overview of Next-Generation Sequencing Technologies. Curr. Protoc. Mol. Biol. 2018, 122, e59.
  5. Sequencing Technology Sequencing by Synthesis. Available online: https://www.illumina.com/science/technology/next-generation-sequencing/sequencing-technology.html (accessed on 25 November 2021).
  6. Olsen, T.K.; Baryawno, N. Introduction to Single-Cell RNA Sequencing. Curr. Protoc. Mol. Biol. 2018, 122, e57.
  7. Ivanova, N.V.; Kuzmina, M.L.; Braukmann, T.W.A.; Borisenko, A.V.; Zakharov, E.V. Authentication of herbal supplements using next-generation sequencing. PLoS ONE 2016, 11, e0156426.
  8. Chatfield, D.A.; Fitzgerald, R.L. Liquid Chromatography—Mass Spectrometry: An Introduction; Ardrey, R.E., Ed.; Wiley: Hoboken, NJ, USA, 2003; Volume 50, p. 276. ISBN 0471497991.
  9. Pitt, J.J. Principles and applications of liquid chromatography-mass spectrometry in clinical biochemistry. Clin. Biochem. Rev. 2009, 30, 19–34.
  10. Stobiecki, M.; Skirycz, A.; Kerhoas, L.; Kachlicki, P.; Muth, D.; Einhorn, J.; Mueller-Roeber, B. Profiling of phenolic glycosidic conjugates in leaves of Arabidopsis thaliana using LC/MS. Metabolomics 2006, 2, 197–219.
  11. Gika, H.G.; Theodoridis, G.A.; Plumb, R.S.; Wilson, I.D. Current practice of liquid chromatography-mass spectrometry in metabolomics and metabonomics. J. Pharm. Biomed. Anal. 2014, 87, 12–25.
  12. Marion, D. An introduction to biological NMR spectroscopy. Mol. Cell. Proteom. 2013, 12, 3006–3025.
  13. Rhodes, C.J. Magnetic resonance spectroscopy. Sci. Prog. 2017, 100, 241–292.
  14. Rinck, P. Magnetic Resonance in Medicine. In The Basic Textbook of the European Magnetic Resonance Forum, 11th ed.; Wiley: Hoboken, NJ, USA, 2017.
  15. Horgan, R.P.; Kenny, L.C. ‘Omic’ technologies: Genomics, transcriptomics, proteomics and metabolomics. Obstet. Gynaecol. 2011, 13, 189–195.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license; additional terms may apply. By using this site, you agree to the Terms and Conditions and Privacy Policy.
Upload a video for this entry
Information
Subjects: Biochemistry & Molecular Biology
Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register : Anna Steg , Maria Oczkowicz , Grzegorz Smołucha
View Times: 714
Revisions: 2 times (View History)
Update Date: 14 Feb 2023
Table of Contents
    Notice
    You are not a member of the advisory board for this topic. If you want to update advisory board member profile, please contact office@encyclopedia.pub.
    OK
    Confirm
    Only members of the Encyclopedia advisory board for this topic are allowed to note entries. Would you like to become an advisory board member of the Encyclopedia?
    Yes
    No
    ${ textCharacter }/${ maxCharacter }
    Submit
    Cancel
    There is no comment~
    ${ textCharacter }/${ maxCharacter }
    Submit
    Cancel
    ${ selectedItem.replyTextCharacter }/${ selectedItem.replyMaxCharacter }
    Submit
    Cancel
    Confirm
    Are you sure to Delete?
    Yes No
    Academic Video Service
    Feedback