Difference between revisions of "Genomics"

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<p><font size="3"><strong>Genomics</strong> is the omics study of genes of individual organisms,&nbsp;populations, and species. <br />
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<p>1) Define Genomics your own way after doing research on what genomes are and how we study.</p>
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</font></p>
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<p><font size="3">It is also a paradigm of performing biological science that deviates from&nbsp;investigating single genes, their functions, and roles. <br />
 
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</font></p>
 
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<p><font size="3">The main reason of an independent biological discipline is that it deals with very large sets of genetic information to automatically analyze information using interaction and network concepts. Genomics inevitably employs high performance computing and bioinformatics technologies.</font><br />
 
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</p>
 
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<p><span class="editsection"></span><span class="mw-headline"><font size="4"><br />
 
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</font></span></p>
 
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<p><strong><span class="mw-headline"><font size="4">History of the field</font></span></strong></p>
 
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<p><font size="3">Genomics was practically founded by Fred Sanger group in 1970s when they developed&nbsp;a gene sequencing technique and completed the first genomes; namely bacteriophage &Phi;-X174; (5,368 bp),&nbsp;the human mitochondrial genome, and lamda virus.</font></p>
 
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<p><font size="3">In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein.<sup class="reference" id="_ref-0">[1]</sup> In 1976, the team determined the complete nucleotide-sequence of bacteriophage MS2-RNA.<sup class="reference" id="_ref-1">[2]</sup> The first DNA-based genome to be sequenced in its entirety was that of bacteriophage &Phi;-X174; (5,368 bp), sequenced by Frederick Sanger in 1977<sup class="reference" id="_ref-2">[3]</sup>. The first free-living organism to be sequenced was that of <em>Haemophilus influenzae</em> (1.8 Mb) in 1995, and since then genomes are being sequenced at a rapid pace. A rough draft of the human genome was completed by Sanger centre and the Human Genome Project in early 2001.</font></p>
 
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<p><font size="3">As of September 2007, the complete sequence was known of about 1879 viruses <sup class="reference" id="_ref-3">[4]</sup>, 577 bacterial species and roughly 23 eukaryote organisms, of which about half are fungi. <sup class="reference" id="_ref-4">[5]</sup> Most of the bacteria whose genomes have been completely sequenced are problematic disease-causing agents, such as <em>Haemophilus influenzae</em>. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast (<em>Saccharomyces cerevisiae</em>) has long been an important model organism for the eukaryotic cell, while the fruit fly <em>Drosophila melanogaster</em> has been a very important tool (notably in early pre-molecular genetics). The worm <em>Caenorhabditis elegans</em> is an often used simple model for multicellular organisms. The zebrafish <em>Brachydanio rerio</em> is used for many developmental studies on the molecular level and the flower <em>Arabidopsis thaliana</em> is a model organism for flowering plants. The Japanese pufferfish (<em>Takifugu rubripes</em>) and the spotted green pufferfish (<em>Tetraodon nigroviridis</em>) are interesting because of their small and compact genomes, containing very little non-coding DNA compared to most species. <sup class="reference" id="_ref-5">[6]</sup> <sup class="reference" id="_ref-6">[7]</sup> The mammals dog (<em>Canis familiaris</em>), <sup class="reference" id="_ref-7">[8]</sup> brown rat (<em>Rattus norvegicus</em>), mouse (<em>Mus musculus</em>), and chimpanzee (<em>Pan troglodytes</em>) are all important model animals in medical research.</font></p>
 
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<p><font size="3">&nbsp;</font></p>
 
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<p><span class="editsection"></span><strong><span class="mw-headline"><font size="4">Bacteriophage Genomics</font></span></strong></p>
 
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<p><font size="3">Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology. Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced was a bacteriophage. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome.<sup class="reference" id="_ref-McGrath_0">[9]</sup></font></p>
 
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p><span class="editsection"></span><strong><span class="mw-headline"><font size="4">Cyanobacteria Genomics</font></span></strong></p>
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<p><font size="3">At present there are 24 cyanobacteria for which a total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six <em>Prochlorococcus</em><em>Synechococcus</em> strains, <em>Trichodesmium erythraeum</em> IMS101 and <em>Crocosphaera watsonii</em> [[WH8501. Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further <em>Prochlorococcus</em> and marine <em>Synechococcus</em> isolates, <em>Acaryochloris</em> and <em>Prochloron</em>, the N<sub>2</sub>-fixing filamentous cyanobacteria <em>Nodularia spumigena</em>, <em>Lyngbya aestuarii</em> and <em>Lyngbya majuscula</em>, as well as bacteriophages infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into the evolutionary origin of photosynthesis, or estimation of the contribution of horizontal gene transfer to the genomes that have been analyzed.<sup class="reference" id="_ref-Herrero_0">[10]</sup></font></p>
 
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<p><font size="4">[[Genome sequencing and genomics]]</font></p>
 
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<p><span class="editsection"></span><strong><span class="mw-headline"><font size="4">See also</font></span></strong></p>
 
 
<ul>
 
<ul>
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    <li><font size="3">[[Pangenomics]] and [[Pangenome]]</font> </li>
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<li>It is about sequencing of DNA&nbsp;/ mRNA / proteome and analyzing the function and structure of genome (especially whole genome in a cell or organism)</li>
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    <li><font size="3">[[Personal Genome Project]]</font> </li>
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<li>difference from genetics : genetic study the detail of function or composition of a single gene whereas genomics cover all genes and their relationship.</li>
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    <li><font size="3">[[Omics]] </font></li>
 
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    <li><font size="3">[[Proteomics]] </font></li>
 
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    <li><font size="3">[[Interactomics]] </font></li>
 
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    <li><font size="3">[[Functional genomics]] </font></li>
 
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    <li><font size="3">[[Computational genomics]] </font></li>
 
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    <li><font size="3">[[Nitrogenomics]]</font> </li>
 
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    <li><font size="3">[[Pathogenomics]]</font></li>
 
 
</ul>
 
</ul>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p><span class="editsection"></span><strong><span class="mw-headline"><font size="4">References</font></span></strong></p>
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<ol class="references">
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<p>&nbsp;</p>
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    <li id="_note-0"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-0">^</a></strong> Min Jou W, Haegeman G, Ysebaert M, Fiers W., Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein, Nature. 1972 May 12;237(5350):82-8 </font></li>
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    <li id="_note-1"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-1">^</a></strong> Fiers W et al., Complete nucleotide-sequence of bacteriophage MS2-RNA - primary and secondary structure of replicase gene, Nature, 260, 500-507, 1976 </font></li>
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<p>2) What is the origin of genomics?</p>
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    <li id="_note-2"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-2">^</a></strong> Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., Nucleotide sequence of bacteriophage phi X174 DNA, Nature. 1977 Feb 24;265(5596):687-95 </font></li>
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    <li id="_note-3"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-3">^</a></strong> <a class="external text" title="http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/virostat.html" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/virostat.html"><em>The Viral Genomes Resource</em>, NCBI Friday, 14 September, 2007</a></font> </li>
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<ul>
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    <li id="_note-4"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-4">^</a></strong> <a class="external text" title="http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html"><em>Genome Project Statistic</em>, NCBI Friday, 14 September, 2007</a></font> </li>
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<li>genomics = gene + omics</li>
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    <li id="_note-5"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-5">^</a></strong> <a class="external text" title="http://news.bbc.co.uk/1/hi/sci/tech/3760766.stm" rel="nofollow" href="http://news.bbc.co.uk/1/hi/sci/tech/3760766.stm">BBC article <em>Human gene number slashed</em> from Wednesday, 20 October, 2004</a></font> </li>
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<li>
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    <li id="_note-6"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-6">^</a></strong> <a class="external text" title="http://www.cbse.ucsc.edu/news/2003/10/16/pufferfish_fruitfly/index.shtml" rel="nofollow" href="http://www.cbse.ucsc.edu/news/2003/10/16/pufferfish_fruitfly/index.shtml">CBSE News, Thursday October 16, 2003</a></font> </li>
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<ul>
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    <li id="_note-7"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-7">^</a></strong> <a class="external text" title="http://www.genome.gov/12511476" rel="nofollow" href="http://www.genome.gov/12511476">NHGRI, pressrelease of the publishing of the dog genome</a></font> </li>
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<li>gene = &nbsp;locus of DNA containing genetic information which is mostly related to phenotype</li>
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    <li id="_note-McGrath"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-McGrath_0">^</a></strong> <cite class="book" style="FONT-STYLE: normal">Mc Grath S and van Sinderen D (editors). (2007). <em><a class="external text" title="http://www.horizonpress.com/phage" rel="nofollow" href="http://www.horizonpress.com/phage">Bacteriophage: Genetics and Molecular Biology</a></em>, 1st ed., Caister Academic Press. <a class="external text" title="http://www.horizonpress.com/phage" rel="nofollow" href="http://www.horizonpress.com/phage">ISBN 978-1-904455-14-1</a> .</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=book&amp;rft.btitle=Bacteriophage%3A+Genetics+and+Molecular+Biology&amp;rft.au=Mc+Grath+S+and+van+Sinderen+D+%28editors%29.&amp;rft.edition=1st+ed.&amp;rft.pub=Caister+Academic+Press&amp;rft_id=http%3A%2F%2Fwww.horizonpress.com%2Fphage">&nbsp;</span></font> </li>
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<li>omics = field of study in biology class &gt;&gt; proteomics ,metabolomics ,lipidomics , transcriptomics...</li>
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    <li id="_note-Herrero"><font size="3"><strong><a title="" href="http://en.wikipedia.org/wiki/Genomics#_ref-Herrero_0">^</a></strong> <cite class="book" style="FONT-STYLE: normal">Herrero A and Flores E (editor). (2008). <em><a class="external text" title="http://www.horizonpress.com/cyan" rel="nofollow" href="http://www.horizonpress.com/cyan">The Cyanobacteria: Molecular Biology, Genomics and Evolution</a></em>, 1st ed., Caister Academic Press. <a class="external text" title="http://www.horizonpress.com/cyan" rel="nofollow" href="http://www.horizonpress.com/cyan">ISBN 978-1-904455-15-8</a> .</cite></font><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=book&amp;rft.btitle=The+Cyanobacteria%3A+Molecular+Biology%2C+Genomics+and+Evolution&amp;rft.au=Herrero+A+and+Flores+E+%28editor%29.&amp;rft.edition=1st+ed.&amp;rft.pub=Caister+Academic+Press&amp;rft_id=http%3A%2F%2Fwww.horizonpress.com%2Fcyan"><font size="3"> </font><br />
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</ul>
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    </span></li>
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</li>
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</ol>
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</ul>
 +
 
 +
<p>3) History of genomics?</p>
 +
 
 +
<ul>
 +
<li>1952 : helical structure of DNA (Rosaline Franklin)</li>
 +
<li>1953 : structure of DNA ( James D, Watson , Francis Crick )</li>
 +
<li>1955 : Amino acid sequence of insulin (Fred Sanger)</li>
 +
<li>1964 : first nucleic acid sequence &gt;&gt; ribonucleotide sequence of alanine tRNA (Robert W.Holley)</li>
 +
<li>1972 : gene sequence for Bacteriophage MS2 ( Walter Fiers)&nbsp;</li>
 +
</ul>
 +
 
 +
<p>4) The future of genomics?</p>
 +
 
 +
<ul>
 +
<li>Personal genomics</li>
 +
<li>
 +
<ul>
 +
<li>definition : sequencing individual genomes</li>
 +
<li>why needed? every personal genome sequencing are different, so there may be some side effect from public drug or chemicals If certain person has specific gene sensitive to the drugs. personal genomics is able to carry genome sequencing from each person and by doing this, we can reach ideal drugs optimum to each person.</li>
 +
<li>application (effect) : physiology / drugs / personal information of genetic disease / genetic variants</li>
 +
</ul>
 +
</li>
 +
</ul>
 +
 
 +
<p>5) What is the relationship with other omics?</p>
 +
 
 +
<ul>
 +
<li>functional genomics looks for the protein function and interaction, so they sometimes use transcriptomics or proteomics to know what kinds of function certain protein or transcriptome have&nbsp;</li>
 +
</ul>
 +
 
 +
<p>6) How can we engineer genomes?</p>
 +
 
 +
<ul>
 +
<li>modify genomic sequence --&gt; repair mutated genes.</li>
 +
</ul>
 +
 
 +
<p>&nbsp;</p>
 +
 
 +
<hr />
 +
<p>&nbsp;</p>
 +
 
 +
<p>Types of genomics</p>
 +
 
 +
<ul>
 +
<li>Cognitive genomics : changes in cognitive processes</li>
 +
<li>Comparative genomics : study the relationship between structure and function</li>
 +
<li>Functional genomics : study of function and interaction of certain genomes</li>
 +
<li>Metagenomics : environmental genomics, study of genetic material recovered directly from environmental samples.</li>
 +
<li>Personal genomics : personalized genomics targeted for individual genome sequencing</li>
 +
<li>Epigenomics : set of epigenetic modification</li>
 +
</ul>
 +
 
 +
<p>&nbsp;</p>
 +
 
 +
<p>effect</p>
 +
 
 +
<ul>
 +
<li>gene-based understanding of complex biomolecules&nbsp;</li>
 +
<li>study of intragenomic phenomena or their mutation</li>
 +
</ul>
 +
 
 +
<p>&nbsp;</p>
 +
 
 +
<p>DNA-sequencing</p>
 +
 
 +
<ul>
 +
<li><a href="http://www.mun.ca/biology/scarr/4241_StepstowardsDNASequencing.html"><em>Plus and minus technique</em></a></li>
 +
<li><a href="https://www.youtube.com/watch?v=iTBTHmhNNbE">Sanger method</a></li>
 +
<li><a href="https://www.youtube.com/watch?v=tiG-rxkhlqg">Maxam-Gilbert method</a></li>
 +
</ul>

Latest revision as of 10:00, 19 June 2016

1) Define Genomics your own way after doing research on what genomes are and how we study.

 

  • It is about sequencing of DNA / mRNA / proteome and analyzing the function and structure of genome (especially whole genome in a cell or organism)
  • difference from genetics : genetic study the detail of function or composition of a single gene whereas genomics cover all genes and their relationship.

 

 

2) What is the origin of genomics?

  • genomics = gene + omics
    • gene =  locus of DNA containing genetic information which is mostly related to phenotype
    • omics = field of study in biology class >> proteomics ,metabolomics ,lipidomics , transcriptomics...

3) History of genomics?

  • 1952 : helical structure of DNA (Rosaline Franklin)
  • 1953 : structure of DNA ( James D, Watson , Francis Crick )
  • 1955 : Amino acid sequence of insulin (Fred Sanger)
  • 1964 : first nucleic acid sequence >> ribonucleotide sequence of alanine tRNA (Robert W.Holley)
  • 1972 : gene sequence for Bacteriophage MS2 ( Walter Fiers) 

4) The future of genomics?

  • Personal genomics
    • definition : sequencing individual genomes
    • why needed? every personal genome sequencing are different, so there may be some side effect from public drug or chemicals If certain person has specific gene sensitive to the drugs. personal genomics is able to carry genome sequencing from each person and by doing this, we can reach ideal drugs optimum to each person.
    • application (effect) : physiology / drugs / personal information of genetic disease / genetic variants

5) What is the relationship with other omics?

  • functional genomics looks for the protein function and interaction, so they sometimes use transcriptomics or proteomics to know what kinds of function certain protein or transcriptome have 

6) How can we engineer genomes?

  • modify genomic sequence --> repair mutated genes.

 

 

Types of genomics

  • Cognitive genomics : changes in cognitive processes
  • Comparative genomics : study the relationship between structure and function
  • Functional genomics : study of function and interaction of certain genomes
  • Metagenomics : environmental genomics, study of genetic material recovered directly from environmental samples.
  • Personal genomics : personalized genomics targeted for individual genome sequencing
  • Epigenomics : set of epigenetic modification

 

effect

  • gene-based understanding of complex biomolecules 
  • study of intragenomic phenomena or their mutation

 

DNA-sequencing

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