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== What is Sequencing in Genomics and Omics? (as an approach of understanding life) ==
<p>What is Sequencing in Genomics and Omics?</p>
<p>(as an approach of understanding life) Sequencing</p>
<p>Madina Seidualy 20132023 09/09/2016<br />
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<p> First of all, I would like to describe my point of view about life. What is life? Actually, this word correlated with verb “live”, which can be expressed in diverse words like breath, staying alive, surviving, reproducing. “Live your life”, where only living organisms can achieve that. Thereby, Life is noun state of live, only living things own life. All living organisms distinguished from material things as they were constructed from cells, the basic unit of life. All cells are consisted of variety functional organelles or particles, those give priority to survive. The special thing that exist in all cells of entire organisms is DNA, which carrier with them live survival instructions.</p>
<p>It is proved scientifically that DNA in chromosomes of living organisms own information about whole function in the cell, and any mismatch in their structure will lead fail in the function of appropriate organelle or another cell blocks. DNA is the molecule consists of two antiparallel strands of four nucleic acids, which coiled forming double helix. Those four nucleic acids are the monomers of this huge molecule and their base pair were distinguished, either Thymine (T), Cytosine (C), Adenine (A) and Guanine (G). These bases forms with each other, like A-T, G-C, parallel strands. According to the researches, number of base pairs in one cell of human is around 6x10^9, and fascinating fact is that 2,5 m of DNA coiled in so tiny cell nucleus.</p>
<p>Every cell of the human organism equally have that number and length of DNA molecule, however according cell’s function only several sections of the DNA could be read and transcribed and translated. Consequently, whole cell DNA molecule have information of life of that organisms, and variety part of organism cells only read pieces they required and save other parts condensed in nucleus.</p>
<p> Genomics, if we simplify, want to read those whole DNA base pairs in a cell, so that they could understand their function, effect on, place in and response for their whole genome networks. Moreover, reading possible only by Sequencing DNA, which make scientist to list whole 6 billion codes, consists of A,T,C,G. Until nowadays, most famous and efficient way of Sequencing DNA were Sanger sequencing and Next-generation sequencing.</p>
<p> In following two paragraphs I will describe shortly about above two sequencing methods. In 1977 – 80 years first Fred Sanger introduced this method to the world, and have been used till mid 2000s. In any sequencing it is impossible to read it without cutting long DNA or interested gene to tiny splices, by restriction enzymes after isolating gene. Afterwards, we have to amplify it to thousands strands, which it possible by PCR (polymerase Chain reaction). Now we have extreme numbers of single strands, the thing we have to do now copy or make its second strands. For that, we require polymer, to start the polymerization, and polymerase, enzyme that makes that action, and a quantity of dNTP, building blocks of DNA. In addition, we need the crucial feature of this method is ddNTP, terminator nucleotides. If ddNTP binds to the elongating strands it stops elongation, and terminated strand at that position. Correspondingly, all four ddNTP will be labelled with different colors, so later we detect them with UV. This experiment should done four times for the same splice of the strand with four ddATP,ddGTP,ddCTP, ddTTP. As a result, different strands terminated at different strands. Those strands we will run on electrophoresis gel, where short sequences run first, the longest ones run as latest. Thereby, that splice’s or gene’s DNA code will be sequenced by analyzing result of the gel electrophoresis. </p>
<p><img alt="Картинки по запросу sanger sequencing" src="https://www.researchgate.net/profile/Martin_Kircher/publication/44614816/figure/fig1/AS:267595626577984@1440811177410/Figure-1-Schematic-representation-of-the-Sanger-sequencing-process-Input-DNA-is.png" /></p>
<p>The second method of the sequencing is next-generation sequencing(NGS), which were applied recently, about 10 years ago. This method also have same beginnings such as isolating DNA, restriction them. The difference is on further steps, in NGS amplification of multiple strands can be used and sequenced at the same. Thereby, PCR of multiple strands have been done, fragment clusters were placed on a flow cell, glass plate. The tremendous feature of this method is that, nucleotides were terminated by labelling fluorescent dyes to the 3’-OH on sugar, which enabled them to form phosphodiester bond and called as reversible terminators. However, in this experiment no need to normal nucleotides. Firstly, all strands will be bind with primers after to that plate added all reversible terminators, then that plate was screened under the UV light. So we can get all strands first base block. After that, plate were washed in order to get rid of fluorescent labels, only nucleotides left. The same passage repeats again and again, until we get whole strand sequence.</p>
<p><img alt="Reversible 3'-O-blocked reversible terminator" src="https://binf.snipcademy.com/binf/img/lessons/sequencing-techniques/reversible-terminator.svg" style="height:300px; width:500px" /></p>
<p><img alt="Картинки по запросу next generation sequencing" src="http://www.intechopen.com/source/html/49419/media/image2.png" style="height:383px; width:500px" /></p>
<p> The NGS gives chance to sequence huge amount of strands at the same time quickly, so it is the indeed technology for sequencing huge organisms genome. However, Sanger sequencing also one of the effective methods, and it can used in sequencing small genes in detail, in order to get accurate data.</p>
<p><strong>Sequencing is key of the life</strong>. Since all living organism’s codes written in those sequenced DNA, close investigation of the code will give valuable information about our life. Actually, there millions of actions can be done after we get all organisms’ DNA sequence. As an example, all diseases features can identified, by comparing healthy individual’s DNA with patient. Every individual’s tension to disease can easily identified, lead to prevention from incurable diseases. Moreover, also helps to find correlations between close species, that can lead to find all disappeared animal and plants around the world.</p>
<p>Majority of scientists, after getting more of the organisms DNA sequences, they want to afford way to correct mismatches and mutation in organisms. I support the idea of using codes in order to cure fatal diseases, like cancers. But, what if scientists try to get new animal or organism, which might bring harm to society. If scientists create some genetically modified animal, it will be hard to control it. There is still no guarantee to that corrections in DNA will lead to only positive changes. I am little bit concerned about ethical issues of genomics. Who will have access to these individual’s sequences? What if it used in reproductive decisions, like changing gender of the offspring in the fetus? </p>
<p>Thereafter, those accomplished DNA sequences of variety organisms can lead to totally diverse world. All limitations of this life might considerably changed or at the same may open up new avenues, which we might be something we have never imagined.</p>
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<p>References:</p>
<p><a href="http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_1.shtml">http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_1.shtml</a></p>
<p><a href="https://www.thermofisher.com/kr/ko/home/life-science/sequencing/sequencing-education/sanger-next-generation-technology.html">https://www.thermofisher.com/kr/ko/home/life-science/sequencing/sequencing-education/sanger-next-generation-technology.html</a></p>
<p>http://hypertextbook.com/facts/1998/StevenChen.shtml “Length of a Human DNA molecule”(<a href="http://hypertextbook.com/facts/" target="_top">The Physics Factbook</a>, edited by Glenn Elert -- Written by his students)</p>
<p><a href="https://www.youtube.com/watch?v=LSfQPSXQbb4">https://www.youtube.com/watch?v=LSfQPSXQbb4</a> “The Human Genome Project - Next Generation Sequencing (NGS) Part 1,2,3”</p>
