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<li>History and the future of genomics? Genomics largely depends on sequencing technology. Early sequencing takes advantages of electrophoresis with chain-termination method invented by Frederick Sanger. Nowadays, it is supplemented by "NGS" - next generation sequencing which is automated, and high-throughput method. There is a very descriptive movie about NGS sequencing[8]. In the future, genomics might provide better sequencing method in terms of processivity, cost, and fidelity. </li>
<li>What is the relationship with other omics? other than genomics, there are lot of -omics such as transcriptomics, proteomics, and so on. Genome is set of instructions of organisms containing all essential genetic information to live on. Therefore, genomics is starting point of -omics study. Genomics explains well difference between distinct organisms such as pine tree and pine beetle becuase they have completely diffenent sturcture of their own genome - but still there's lot of common information they have. However, for example, genomics is poor at demonstrating of difference in organs multicellular organims as they have same genomes - which is called "genetic equivalent". Transcriptomics and proteomics are better than genomics in this case. They can figure out what makes difference in terms of RNA and protein. Although those two -omics are based on genomics, it can focus on the smaller differences what genomics can't. Therefore, Genomics gives basis to other omics, and they provides delicate but significant clues about function of genomes.</li>
<li>How can we engineer genomics?Due to the fact that genomes are set of instruction of living things, one can intuitively manipulate organism in genome level. Therefore, by inserting, deleting, altering genetic information, one can change phenotype of organisms - from ill to health, and activating or knock out, for example. Surprisingly, there are some mechanisms discovered as defensive system for microorganism - restriction enzymes. Having specificity and accuracy, restriction enzymes provides the fidelity in the engineering process. Other than that, Some DNA binding proteins are used for specific binding to target sequence - CRISPR/Cas 9 is well known example.</li>
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<li>what is poly A[4]? poly A is the long A sequence on the 3' end of mRNA. it is important for mRNA to fully function as genetic code for protein synthesis. there are 3 roles of poly A tail. 1) providing stability to mRNA, 2)recognizing mRNA for exporting from the nucleus or ribosome binding. 3)involving posttranscriptional modification by interacting with PABP(poly A binding protein), maskin, RISC, and so on.</li>
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<p><b>PROTEOMICS</b></p>
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<li>What is proteome? proteome is the total set of proteins expressed as the product of genes.</li>
<li>Relationship between genomics, transcriptomics, and proteomics. Proteome is the most highly related phenotype of the cell, or organism. In determining the phenotype, some proteins are upregulated and some downregulated or some is undergone modification. genomics and transcriptomics provide the basis of such control mechanism. They're related in terms of sequence. Although polypeptide sequence consists of amino acids, amino acids are designated by codon. </li>
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<li>How many proteins in the cell? proteins are highly aggregated in the membrane enclosed sturcture - cell. such compact clustering is important to study behavior and dynamics of proteins. measuring concentration of individual proteins in vivo is possible by using fluorescent dye that binds specifically to target protein[10]. However, such individual process are not suitable in terms of proteomics. There is estimation of total number of protein molecules per cell volume with known parameters such as average mass, and lenght of proteins. According to that estimation, 2~4 million proteins per cubic micron in bacteria, yeast, and mammalian cells[11]. I thought a little bit more accurate and specific measurment. By using nanoscience, it can be possible to make non-destructive nanoscale needle penetrating cell. antibody with Fluorescent dyes are attached to the needle, and emit light only in case of binding to its target protein. By doing microarray or RNA-seq, we can anticipate what proteins are translated, meaning that specific antibodies could be produced according to the information from transcriptomics. when cell is on the needles, its proteins bind to antibodies attached to needle, and signal produced by fluorescent light. with various kinds of dyes, one can measure the proteins in the cell quantatively and qualitatively. However, as written above, cell is so compact structure that it is hard to detect completely by putting on the cell on the micro surface. Then, it can be possible to combine with flow cytometry. flow cytometry is the cell counting method utilizing the patterns of diffraction of light(or fluorescent light) that come from the cells flowing in a thin capillary. if we make capillary whose inner face is coated nanoscale needle, which is localized differentially, one could gather the quantative and qualitative data while the cell flows the thin capillary.</li>
<li>a-helix is right-handed helix. what determines handness? 20 amino acids that makes up proteins are all L-forms(glycine is achiral), favoring right handed helix. Even more, of around 500 natural exsisting amino acids, only 8 amino acids are D-form. there is argument by Mason that electroweak force of fundamental particles - fermions(quarks, leptons, etc.) - involves such imbalance of L- and D- form amino acid[9].</li>
<li>discussion of Foldit - by SoonGu Kim</li>
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<p><b>EPIGENOMICS</b></p>
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<li>what is epigenomics? set of modifications on a cell's DNA or histones. it largely ocnsists of DNA methylation, histone modification and RNAi affecting on gene expression, which is possible indirect genetic transmission. </li>
<li>Histone code : histone is representative of chromosomal protein coiling DNA compactly. Of course, its modification and combination influence the gene expression. Histones are acetylated/deacetylated, methylated/demethylated, phosphorylated/dephosphorylated, ubiquitinized, and sumoylated. sumoylation is attachment of SUMO(small ubiquitin-related modifier). sumoylation has some stimulation effect on HSF1 or p53, however, it is frequently used for repression through attenuation[12].</li>
<li>Technologies for studying epigenomics : a) bisulfate sequencing; DNA methylation is identified by this mehtod. when sodiumbisulfate is treated, only unmethylated cytosines undergoes deamination, converted into uracil, otherwise methylated cytosines are remained. such difference are shown by sequencing[13]. b) Chip-Seq : it identifies DNA-binding proteins(histones and transcription factor, for example) and detects binding sequence by NGS sequencing method. it is important to study chromatin packaging which is related to histone modification[14].</li>
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<p> -in the class</p>
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<li>Is Darwinian evolution is correct?</li>
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<p>[7] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2392988/#b1-jbt-18-277</p>
<p>[8] https://www.youtube.com/watch?v=77r5p8IBwJk</p>
<p>[9] https://books.google.co.kr/books?id=-nuXW4JPfs0C&pg=PA27&lpg=PA27&dq=handedness+of+helix&source=bl&ots=QuZny1T8Hm&sig=HyOVMNL_9WRcF7TFgzfuhHR7ejE&hl=ko&sa=X&ved=0CHsQ6AEwCWoVChMIzPuE5I-FxgIVwdimCh3sygDX#v=onepage&q=handedness%20of%20helix&f=false</p><p>[10] http://www.the-scientist.com/?articles.view/articleNo/16879/title/Measuring-Protein-Concentrations-in-Live-Cells/</p><p>[11] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910158/</p><p>[12] http://www.pnas.org/content/100/23/13118.full</p><p>[13] http://blog.daum.net/kimuks/7532982</p><p>[14] http://blog.daum.net/kimuks/7533051</p>
