GiJeong Kim

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BIOPROGRAMMING

what is programming? programming is a process of making series of instuction enabling computer to do particular task. program gives logical flow of instructions to computer and also provides ease to handle and readability to user. programming is progressive work, it needs consistant reforming, editing, and correction. it is the reason why program should be user-friendly.
How to make a compiler? compiler translates programming languages into executive instructions for computer. for making compiler, compiler must involves functions such as interpreting programming languages, matching interprted programming languages with set of instructions what computer could be acceptable.
what is a language? computer is basically operated according to arrangement of 1 and 0. so, it is hard for programmer to impart instruction(programm) directly. programming languages mediate languages of 0 and 1(low-level language), and real human language(high-level language) to make easy to programming. there are lots of languages having different levels according to its purpose and property, such as C, java, R, python, so on.
what is a computer? computer is programmable machine. It consists of hardware and software. hardwares are physical components of computer, which process instructions, receive and reperesent informations, and store what it did. software is program. it falls into two types - operating system and application software. Operating system controls hardware of computers to optimize its functionality. application software is so called program, making computer "work".
what is a grammer? grammer is rule making order of sentence of language. it indicates the position of key word, punctuation of sentence. programming languages also has grammer, which is especially called syntax.

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ppt from DoYeon Lim and YeonSoo Jun - programmable C.elegans. there was debate about the C.elegans is living thing. some poeple rejects that the C.elegans can't reproduce or evolution, it turns out that it is also programmable. in my opinion, it is kind of life. although it is confined virtual dimension, it metabolizes, moves, responses to stimuli, reproduces, evolves, and makes decision in the universe for "virtual" C.elegans. Who knows? it is same as human being. we also confined dimension, and "coded" by physical rules. it may be helpful to answer "What is real?". Reality is the program. it repeats same procedure under the same input - reproducibility. it is amenable and flexable under the determined algorithms still one cannot reform that algorith itself. living things on earth seems to be programmed with natural selection. According to its environment, living things regulates its gene expression(biological switch) by turning on and off. Such decision making is the set of insturction engraved over billion years and enables living things to be "real" thing

What is lecture?

what is lecture? lecture is a talk or speech givne to a group to teach them about a particular subject[1].
from the ancient to the information-orieted age, teaching methods changes and are invented. Among them, lecture provides the best way to transfer the knowledge and information in terms of personal contact. according to the definition of lecture, it is essential for lecturer and student to be in same place and time. Book, for example, is widely used material for storage knowledge, however, it is poor at teaching alone. because it requires for reader to stand on the author's position. lots of factors printed with knowledge, such as nuance, traditional background, and even historical background of author oneself. another poor example for teaching may be "online lecture". it has no communication between lecturer and student in realtime. it is possible to ask e-mail to the lecturer, however, it deprives the opportunity to discuss fresh and thoughtful question in prompt from both lecturer and student. Lecture resolves such problems by placing all members together. such arrangement could enable student to reach the basis of knowledge and penetrate the center of understanding - giving insight.

GENOMICS

Define genomics your own way after doing research on what genomes are and how we study. Genomics is understanding of genome supported with sequencing in terms of the relationship between organism and surrounding environments. Genomics should be not only defining genetic sequence but provide the comprehension of interaction between genome and phenomena. For example, there is a TRIA project(i.e. Turning Risk Into Action for the mountain pine beetle epidemic) in Canada which investigates correlation between pine beetle, fungus, and pine tree in genome level to protect pine tree forest in western Canada[6].
What is the origin of genomics? genomics is first used by Dr. Thomas H. Roderick while discussion of starting new journal - which is now known as Genomics[7].
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.
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.
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.

TRANSCRIPTOMICS

what is transcriptomics? transcript + omics. it is study of all set of RNAs including mRNA, rRNA, tRNA, so on.
relationship bewteen genomics. genome is the basis for the transcriptome. although only small portion of gene is transcribed (less than 5%[2]), it is useful to figure out the pattern of gene expression. especially multicellular organism, there are different type of cells having same genome, which is called genomic equivalence. transcription of genes is the first stage of gene expression, transcriptomic is the valuable source for understanding the gene expression of genome.
what is mRNA? mRNA is the molecule carrying genetic information for protein synthesis. it is trasncripted from nucleus, exported to cytosol, and recognized by ribosome with its unique modification moiety such as 5'-cap and poly A tail.
how to measure mRNA expression[5]? to measure mRNA expression, extracted mRNA should be identified and quantified. there're largely two methods - microarray and RNA-seq. 1)microarray is blotting method with hybridization probe on solid(microchip). only RNAs complementary to probes bind to the probes and quantified under fluoroscent microscopy. such hybridization can occurs simultaneously, it provides high throughput. Microarray has limitation that it could detect RNAs only complementary to probes, being improper to detect novel RNA. Also, fluoroscent light gives good comparison for quantification, however, it does not give absolute quantification. Finally, microarray can't distinguish difference in expression of isoforms. 2)RNA-seq is kind of second-generation sequencing, which offers robust sequencing. It consists of three steps - library preparation, deep sequencing, and data analysis. Compared to microarray, this technique sequences RNA de novo - which is called "hypothesis-free approach" - so that it provides absolute abundance of RAN and is good at detecting low abundant or novel RNA. However, its data analysis is more complex than microarray, and expansive.
relationship between trasncriptome & proteome. to cell function, a set of proteins are needed. Due to the fact that mRNA translates proteins it is easy to consider that linear correlation bewteen transcriptome and proteome, low correlation sometimes come up with the post translational modification[3]. but still transcriptomic is the middle step of understanding bewteen genetic code and the functioning molecule.
what is UTR[4]? UTR is abbreviation for untranslated region. it is the portion of mRNA which is not translated. there are two UTR - one is on the 5' end(5'-UTR), another on the 3' end(3'-UTR). those UTRs are related to modification and lifespan of mRNA. for example, polyadenylation is an addition of 200 ~ 300 adenine to 3' end of mRNA making poly A tail. this process depends on AATAAA sequence on the 3'-UTR.
what is ncRNA? ncRNA is abbreviation for non-coding RNA, which means RNA does not encode protein. rather than encoding RNA, such RNAs included regulatory pathway in gene expression. For example, miRNA is transcribed from nucleus and forms complex with proteins. the complex is called RISC(RNA-induced silencing complex), widely regulating eukaryotic gene expression
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.

PROTEOMICS

What is proteome? proteome is the total set of proteins expressed as the product of genes.
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.

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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.
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].
discussion of Foldit - by SoonGu Kim

EPIGENOMICS

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.
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].
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].

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