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<font size="4"p> </p> <font size="3"p><strong>20090810:Obese in Genomics</strong> [[A Caucasian human genome was sequenced by Helicos single molecule sequencer]].<br /p> <p> </p> <p><strong>20090805:What is Obese?</strong> [[Recurring Mutations Found by Full length Sequencing of an Acute Myeloid Leukemia Genome (AML)]]. [[N Engl J Med]]<br /p> <strongdiv>20090802-Obesity is a <a href="https:</strong> [[The complete genome sequence of Triticum mosaic virus is published in Arch Vriol/en.wikipedia.]]<br org/wiki/Medical_condition">medical condition<strong/a>20090730in which excess <a href="https:/strong/en.wikipedia.org/wiki/Body_fat">body fat</a>: [[Crocodile genome map published in BMC Genomics]]has accumulated to the extent that it may have a negative effect on health.<br /div> <strongdiv>20090727< </strongdiv> <div>-People are generally considered obese when their <a href="https: [[A new multiplex sequencing method published by MPI group for highly degraded DNA fragments//en.wikipedia. Cave bear mitochondria]]<br org/wiki/Body_mass_index">20090724: DNA Sequencing andbody mass index</a> (BMI), a measurement obtained by dividing a person's weight by the square of the person's height, is over 30 Array Drive 8% Growth for Roche in First Half of 2009. [[454 GS FLX]] and [[Nimblegen]]. [http<a href="https://wwwen.genomewebwikipedia.comorg/sequencingwiki/dna-sequencing-systems-arrays-drive-8-percent-growth-roche-applied-science-first]<br Kilogram">kg</a>/<a href="https://en.wikipedia.org/wiki/Square_metre">m<strong/a>20090724<a href="https://strong>: BGI (Beijing Genomics Institute) in China participates in orchid genome (<emen.wikipedia.org/wiki/Square_metre">[[Phalaenopsis equestris]]) 2</ema>sequencing. [http://www.genomeweb.com/sequencing/bgi-china-partners-sequence-orchids], with the range 25–30 <br />20090716: Navigenics Lowers Health Compass Price to $999 USD. [httpa href="https://wwwen.genomewebwikipedia.comorg/dxpgxwiki/navigenics-lowers-health-compass-price-1k]<br Kilogram">kg</a>20090716: Celera Uses Automated Workflows for Genomics [http/<a href="https://wwwen.bio-itworldwikipedia.comorg/newswiki/2009Square_metre">m</07/17/celera-pushes-boundariesa><a href="https://en.wikipedia.html]<br org/wiki/Square_metre">20090716: [[A draft genomic sequence for a worm, Schistosoma japonicum, was published]].2<br /a>20090716defined as <a href="https: Genomes Of Parasitic Flatworms Decoded: <em>Schistosoma mansoni</em> and <em>Schistosoma japonicum</em> [http://wwwen.sciencedailywikipedia.comorg/releaseswiki/2009Overweight">overweight</07/090715131439.htm]a><br /div> <strongdiv>20090716< </strongdiv>: <!div>-- Obesity increases the likelihood of <a href=http"https://cen.moreoverwikipedia.comorg/clickwiki/here.pl?z2090023735&z=950242273 target=_parent><bObesity-associated_morbidity">Exxon join with DNA pioneer to develop algae biofuelsvarious diseases</ba>, particularly <a href="https:/a --/en.wikipedia.org/wiki/Cardiovascular_diseases">heart disease</fonta>, <a target="_parent" click="" c.moreover.com="" href="httphttps://wwwen.bioportfoliowikipedia.co.ukorg/wiki/Diabetes_mellitus_type_2">type 2 diabetes</a>, <a href="https:/cgi-bin/dialogserveren.exe?CMD=hitwikipedia.displayMdoc&ID=3022030&HITNO=2&MSIZE=634&LANGUAGEorg/wiki/Obstructive_sleep_apnea">obstructive sleep apnea</a>, certain types of <a href="https://en&FILE=doc.NEWSFEED&SAVEQUERY00wikipedia.org/wiki/Cancer">cancer</a>, and <a href=Genomics&SAVEPROP00=L%3den&SAVEDB=news&SAVEORGANISE_CODED=R:date&R=3022030&THISHREF=http"https://c/en.moreoverwikipedia.comorg/clickwiki/hereOsteoarthritis">osteoarthritis</a>.pl%3fz2090023735%26amp%3bz%3d950242273</div> <div>&nbsp;THEHOST=site d.moreover.com"><strong/div> <font colordiv>-Obesity is most commonly caused by a combination of excessive <a href="#0066cc" size="3">Exxon join with DNA pioneer to develop algae biofuels<https://en.wikipedia.org/font><wiki/strongFood_energy">food</a>intake, lack of physical activity, and <font sizea href="3https://en.wikipedia.org/wiki/Polygenic_inheritance">genetic susceptibility</a>.</div> <div> <br /div> <strongdiv>20090715<p> </p> <p><strong>: [[Pathway Arrangement of basic terms in Genomics]] starts the Direct-to-Consumer Genomics service as 23andme and Decodeme [http:</strong></www.bio-itworld.com/news/2009/07/15/pathway-consumer-genomics.html]p> <p> <br /p> <p><strong>20090714What is Genomics?</strong>: OryzaSNP Consortium IDs Thousands of Variants in Rice Genome: [</p></div> <p>Genomics is the <a href="http://wwwbiopedia.genomeweborg/index.comphp/arraysOmics">omics</oryzasnp-consortium-ids-thousands-variants-rice-genome] a> study of <br a href="http://biopedia.org/index.php/Gene"><strong>20090709genes</stronga>: [[The second Korean pesonal genome was sequenced by a Korean team and analyzed by US researchers]] (Macrogen of individual organisms, populations, and Seoul University Medical School)<br a href="http://biopedia.org/index.php/Species">species<strong/a>20090630.</strongp> <p>: [[Genomic linkage map Paradigm of the human blood fluke Schistosoma mansoni]]:performing biological science that deviates from <em>Genome Biologyinvestigating single genes, their functions, and roles.</emp> 2009, <strongp>10 </strongp> <p><strong>:What is Omics?</strong>R71<span class="pseudotab">doi:10.1186/gb-2009-10-6-r71</spanp> <br /p>20090629: [[Melon Genome Map was publicized by US researchers]]General term for a broad discipline of science and engineering<br /p> <strongp>20090616Analyzing the interactions of biological information objects in various </strong>: Illumina Launches Personal Genome-Sequencing Service Using Genome Analyzer II. [a href="http://scienceblogsomics.com/geneticfuture/2009org/06/illumina_launches_personal_genindex.php]?title=Omes&action=edit">omes</a> in biology<br /p> <p><strong>20090604Main focus</strong>: [[An integrated genetic and cytogenetic map of the cucumber genome was announced in PLOS One]]<br /p> <strongdiv>20090603</strong>: [[Neanderthal genome sequeced by MPI Germany 1)mapping information objects such as genes and Roche]]proteins<br /div> <div><strong>20090601</strongu>: Microsoft buys Rosetta Biosoftware from Merck. Merck becomes 2)finding interaction relationships among the client of Microsoft.objects<br /u></strong>20090529: </strongdiv>[[A new malaria agent in African chimpanzees found]]. <div>3)engineering the networks and objects to understand and manipulate the regulatory mechanisms<br /div> <strongdiv>20090526 </strongdiv> <div>: [[The first Korean Genome Sequence analysis]] by two Korean teams published in [http://genome.cshlp.org/content/early/2009/05/26/gr.092197.109.full.pdf+html Genome Research article]<br /div>20081208: [[Soybean genome, G. max data publicized]]<br /div><strong>20081204What is Proteomics?</strong></div> <div> </div> <div><p>Omics study of proteins, particularly their structures, sequences, and functions.</p> <p> (which proteins interact)</p> <p> </p> <p>The set of proteins produced by it during its life, and its genome is its set of genes.</p> <p> </p> <p>A proteome differs from cell to cell and constantly changes through its biochemical interactions with the genome and the environment.</p> <p>=> One organism has radically different protein expression in different parts of its body, different stages of its life cycle and different environmental conditions</p> <p>*There are far fewer protein-coding genes in the human genome than proteins in the human proteome (20,000 to 25,000 genes vs. > 500,000 proteins)</p> <p>=> Protein diversity is thought to be due to alternative splicing and post-translational modification of proteins</p> <p> </p> <p>New methods include protein microarrays, <u><strong>immunoaffinity chromatography followed by mass spectrometry(MALDI-TOF mass spectrometry),</strong> </u>and combinations of experimental methods such as phage display and computational methods.</p> <p> </p> <p><strong>What is Metabolome?</strong></p> <p> </p> <p>Interaction between an organism’s genome and its environment</p> <p> </p> <p>Complete set of <a href="https: [http://www.koreatimes.co.kr/www/news/tech/2008/12/133_35578.html Korean Genome Publicized]. The sequencing and bioinformatic analyses were carried out by two Korean teams. <br /></font>//en.wikipedia.org/wiki/Small_molecule">small-molecule</a> chemicals found within a biological sample.</p> <p> </p> <p>The <a href="https://en.wikipedia.org/wiki/Small_molecule">small molecule</a> chemicals found in a given metabolome may include both endogenous <a href="https://en.wikipedia.org/wiki/Metabolites">metabolites</a> that are naturally produced by an <a href="https://en.wikipedia.org/wiki/Organism">organism</a> as well as exogenous chemicals</p> <p> </p> <p><strong>The endogenous metabolome</strong></p> <p>-> primary metabolome</p> <p>-> Secondary metabolome</p> <p> </p> <p><a href="https://en.wikipedia.org/wiki/Primary_metabolite">* primary metabolite</a> is directly involved in the normal growth, development, and reproduction.</p> <p><a href="https://en.wikipedia.org/wiki/Secondary_metabolite">*secondary metabolite</a> is not directly involved in those processes, but usually has important ecological function(ex: <a href="https://en.wikipedia.org/wiki/Pigments">pigments</a>, <a href="https://en.wikipedia.org/wiki/Antibiotics">antibiotics</a> or waste products derived from partially metabolized <a href="https://en.wikipedia.org/wiki/Xenobiotics">xenobiotics</a>)</p> <p><a href="https://en.wikipedia.org/wiki/NMR_spectroscopy">Use NMR spectroscopy</a> and <a href="https://en.wikipedia.org/wiki/Mass_spectrometry">mass spectrometry</a>.</p> <p> </p> <p> </p> <p><strong>The Human Metabolome Database</strong></p> <p> </p> <p>Contain detailed data on more than 40,000 metabolites that have already been identified or are likely to be found in the human body</p> <p> </p> <div>1)Chemical information</div> <p>- includes >40,000 metabolite structures with detailed descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties</p> <div> </div> <div>2)Clinical information</div> <p>- includes data on >10,000 <a href="https://en.wikipedia.org/wiki/Metabolite">metabolite</a>-<a href="https://en.wikipedia.org/wiki/Biofluid">biofluid</a> concentrations, metabolite concentration information on more than 600 different human diseases and pathway data for more than 200 different inborn errors of metabolism.</p> <div> </div> <div> </div> <div>3)Biochemical information.</div> <p>- includes nearly 6000 protein (and DNA) sequences and more than 5000 biochemical reactions that are linked to these metabolite entries</p></div> <p> </p> <p>---------------------------------------------</p> <p>Obese</p> <p> </p> <p>-> Mainly Influenced by External effects!</p> <p>-> The Disease that can be cured!</p> <p>-> Obese parents usually have obese children!</p> <p> </p> <p><strong><u>Therefore, Focus more on protemoics, Metabolome!</u></strong></p> <p> -----------------------------------------------------------------------</p> <p><strong><span style="font-size:14px">Adipose tissue</span></strong></p> <p> </p> <p><strong>-> Adipokine </strong></p> <p> -> <span style="font-size:12px"><span style="color:black; font-family:맑은 고딕">Adipose tissue secreted multiple mediator</span></span></p> <p><span style="font-size:12px"><span style="color:black; font-family:맑은 고딕"> </span></span>-> Passed through either endocrine or paracrine</p> <p> Ex: Hormone: leptin, adiponectin</p> <p> </p> <p><strong>-> Adiponectin</strong></p> <p><strong> -> </strong>Adipocyte-secreted adipokine</p> <p> -> Increase lipid oxidation& anti-inflammatory, insulin-sensitizing, angiogenic action</p> <p> <strong>=> Anti obesity & Antidiabetic, Decrease insulin resistance </strong></p> <p> [[File:1.png|400px]]</p> <p> </p> <p> </p> <p> [[File:2.gif|400px]]</p> <p>-> Illustration of the major physiological and metabolic</p> <p>processes with which adipose tissue is involved through the secretion</p> <p>of various adipokines from adipocytes. The interactions may be</p> <p>autocrine, paracrine, or endocrine.</p> <p> </p> <p><span style="font-size:16px"><strong><Searching Scientific Reports></strong></span></p> <p> [[File:3.png|400px]]</p> <p> [[File:4.png|400px]]</p> <p> </p> <p><strong><span style="font-size:16px"><What is Col6?></span></strong></p> <p>- COL6 = Collagen type 6</p> <p>- Abundant constituent of white adipose tissue (WAT)</p> <p>- COL6 levels positively correlate with hyperglycaemia and insulin resistance</p> <p>- Composed of three distinct a chains, a1, a2 and a3.(COL6 trimeric building block) and are subsequently secreted into the ECM</p> <p> </p> <p><strong><span style="font-size:16px"><What is a3 Chain?></span></strong></p> <p>-> longest of the three chains</p> <p>- contains an unusually long N terminus and a globular C5 domain at the C-terminus</p> <p> </p> <p>-> C-terminal portion of the a3 subunit is cleaved off during the post-translational processing of COL6 fibrils(COL6a3, Endotrophin)</p> <p> </p> <p><strong><span style="font-size:16px"><What is Endotrophin?></span></strong></p> <p>- Adipokine with potent tumour-promoting effects</p> <p>- Plays a pivotal role in shaping a metabolically unfavorable microenvironment in adipose tissue during consumption of a high-fat diet (HFD)</p> <p>- Powerful co-stimulator of pathologically relevant pathways within the ‘unhealthy’ adipose tissue milieu, triggering fibrosis and inflammation and ultimately leading to enhanced insulin resistance& metabolic dysfunction.</p> <p>- Exerts a major influence in adipose tissue</p> <p>- Endotrophin within the tumor microenvironment serves as a major mediator of COL6-stimulated mammary tumor growth and subsequent chemo resistance</p> <p>- Stimulates fibrosis, activates endothelial cell migration and promotes macrophage infiltration into growing solid tumors.</p> <p>=> elevated mammary tumor expansion and more pronounced metastatic growth</p> <p> [[File:5.png|400px]]</p> <p>---------------------------------------------------------</p> <p><u><strong><span style="font-size:18px">Problem!</span></strong></u></p> <p> </p> <p><strong>-> Don’t know the mechanism of how ETP works.</strong></p> <p> </p> <p><u><strong><span style="font-size:16px">What I’m going to do!</span></strong></u></p> <p> </p> <div><strong>-> Find the Receptor according to the New method of Protemoics.</strong></div> <div><strong>-> Find the interaction, relationship and mechanisms how they act.(Study of Omics)</strong></div> <div><u><strong> -> Omics could be applied to genomics perspective!</strong></u></div> <p> </p> <p> </p> <p>mETP(204bp, 16.43kda)</p> <p>ACAGAACCATTGTTTCTCACTAAAACAGATATATGTAAGCTGTCCAGAGATGCTGGGACTT</p> <p>GTGTGGACTTCAAGTTACTATGGCACTATGACCTAGAGAGCAAAAGTTGCAAGAGATTCTG</p> <p>GTATGGAGGTTGTGGAGGCAACGAGAACAGATTCCACTCCCAGGAAGAATGTGAAAAGATGTGTAGTCCTGAGTTAACAGTT</p> <p> </p> <p>SpyTag(39bp, 16.43kda)</p> <p>GCCCACATCGTGATGGTGGACGCCTACAAGCCGACGAAG</p> <p> </p> <p>pRL(90bp, 7.48kda)</p> <p>ATGGACAGCAAAGGTTCGTCGCAGAAAGGGTCCCGCCTGCTCCTGCTGCTGGTGGTGTCAAATCTACTCTTGTGCCAGGGTGTGGTCTCC</p> <p> </p> <p>(1)</p> <p> [[File:12.png|600px]]</p> <p> pRA-GFP-EcoR1-pRL-unknown-mETP-SpyTag-Stop</p> <p> </p> <p>-><strong> How to make this cloning?</strong></p> <p>(1)By Using pRL-EcoR1 forward primer, mETP-SpyTag-Stop-Xho1 primer, make pRL-EcoR1-mETP-SpyTag-Stop-Xho1 by Ex-Tag PCR</p> <p>[[File:13.png|500px]]</p> <p>(2) Insert template gained from (1) in T-Vector to check whether it is really pRL-EcoR1-mETP-SpyTag-Stop-Xho1 or not.</p> <p>(3) Use EcoR1, Xho1 Digestion enzyme to double digest T vector</p> <p>(4) Double Digest pRA GFP vector(empty vector) and purify it.</p> <p>(5) ligate (3), (4) product</p> <p> </p> <p><strong>-> Detailed on Each Steps</strong></p> <p>(1) Ex-Tag PCR process</p> <p> </p> <p>->Template(pRA-GFP, 20ng): 1ul</p> <p>->Primer: 1,1ul</p> <p>->dNTP(10nM): 1ul</p> <p>->10X Ex-Tag Buffer: 2.5ul</p> <p>-> Ex-Tag polymerase: 1ul</p> <p>-> D.W: 17.5ul</p> <p>----------------------------------------</p> <p>Total: 25ul</p> <p> </p> <p>PCR</p> <p>->Temperature Gradient : 54,56,58</p> <p>->98 celsius : 2min</p> <p>->98 celsius : 10sec</p> <p>->57 celsius : 30sec</p> <p>->72 celsius : 30sec(insert 300bp)</p> <p>->72 celsius : 5min</p> <p>X35</p> <p> [[File:14.png|400px]]</p> <p>-> Can see the insert(300bp) in both 54,56,58 temperature gradient!</p> <p> </p> <p> (2)</p> <p><T vector ligation></p> <p>Insert DNA mass: 8.607ng(3:1)</p> <p>2X Rapid ligation: 5ul</p> <p>T vector: 0.5ul(25ng)</p> <p>PCR product: 1ul(8.7ng)</p> <p>D.W: 2.5ul</p> <p>T4 DNA Ligase: 1ul</p> <p>----------------------------</p> <p>Total: 10ul</p> <p>RT 1 hour incubation</p> <p>Then, Transformation</p> <p> </p> <p><Colony PCR></p> <p>-> Check whether insert base pairs is inserted in T vector well</p> <p>T.D.W : 14.9</p> <p>10X Buffer : 2</p> <p>M13 primer Forward: 0.5</p> <p>M13 primer Reverse: 0.5</p> <p>2.5mM dNTP: 1.6</p> <p>XL-Taq polymerase: 0.5</p> <p> ---------------------------------</p> <p>[[File:15.jpg|400px]]</p> <p>Can check on 3,5 well(T vector 200bp+ 346bp = 500~600bp)</p> <p> </p> <p> (3)</p> <p> </p> <p> </p> <p>------------------------------------------------------------<br /p><br /><hr /p>[[Genomics News Links20131571 조우빈]] [[Biotechnology News Sites]] [[Science News Sites]]<br /><br /></fontp>