Changes
From Biolecture.org
Created page with "<p>A+ grade to Daeyeol Ye: self-evaluation on genomics class</p> <p> &nbs..."
<p>A+ grade to Daeyeol Ye: self-evaluation on genomics class</p>
<p> Daeyeol Ye</p>
<p> </p>
<p><strong>Abstract</strong></p>
<p><strong>It is reasonable that A+ grade is gotten to Daeyeol Ye (the rest is Daeyeol) when the several activities that Daeyeol did are taken into consideration. After a hiatus, classes which Daeyeol took are generally relevant to one keyword: genome. Daeyeol accumulated diverse knowledge based on two viewpoints: genomic and genomic-related knowledge themselves and means which transport the knowledge (i.e. English writing, communication posture) using several media. Then, several materials have been made during the semester and arranged with following one criterion: a paper on a banana pandemic, by Daeyeol.</strong></p>
<p> </p>
<p><strong>Introduction</strong></p>
<p><strong>Background</strong></p>
<p> Daeyeol Ye returned to UNIST at this semester with finishing the military service. For this reason, Daeyeol was short of general knowledge about the major including the genome. Daeyeol took several classes: molecular biotechnology, bioinformatics, genetics, and genomics. And all these classes are involved in the one topic which is the genome. It was considerable that correlation among these classes was helpful to Daeyeol to accumulate the knowledge.</p>
<p> </p>
<p><strong>Learning on the genomic and its related parts</strong></p>
<p>Daeyeol learned a basic genetic and genomic knowledge and used several web-based protocols and database by learning bioinformatics. And then, Daeyeol concluded that based on genomic information gained by series of processes, these genomes can be applied to make a useful genetically modified organism for several purposes.</p>
<p> </p>
<p>Actually, Daeyeol has been interested in genomic engineering, especially in food security or bioremediation using plant or microorganism. Daeyeol decided to write a paper related to it with applying the genomic knowledge which could be learned during the semester. So, the banana was selected because it is a material easy to be found. And numerous people do not realize its seriousness in spite of the present situation.</p>
<p> </p>
<p> After that, Daeyeol read a book which covered the crisis of the banana. Through the book which Dan Koeppel, it is distinct that the genomic analysis would give the answer for curing the tropical race 4, the panama disease which threats the extant banana industry. Daeyeol started to apply the knowledge learned from genomics and other classes with proposing several hypotheses.</p>
<p> </p>
<p> First of all, Daeyeol searched an influence caused by mutation of organellar genomes and built a hypothesis that the mutation is related to the immunity toward the tropical race 4. In addition, Daeyeol wrote about the essay related in the mutation of theorganellar genome: a three-parent baby. The essay is based on the genomic analysis of the organellar genome and related genomic engineering which can be applied based on the genomic information, because Daeyeol focused not only the analysis of the genome but also the application based on it.</p>
<p> </p>
<p> Also, Daeyeol built a phylogenetic tree about the relationship subspecies between the fungus which affects bananas and other plants. Before the phylogenetic tree was put into the paper, Daeyeol studied how the phylogenetic tree is made based on several media: genomics and bioinformatics textbook and web material. And an essay was written about the mechanism making the phylogenetic tree. Actually, the pylogenetic tree used in the paper was made using the BLAST result. That meant homologous relationship between the BLAST results. In this point, a question about the relationship among paralogous genes was thrown. So, an essay about the human cytoplasmic tRNA was complete.</p>
<p> </p>
<p> Fusarium oxysporum f. sp. cubense, a pathogen of the tropical race 4, is spread by the soil, not through the air. This point raised a question whether sequencing of the organisms in the soil was needed. And from this question, Daeyeol searched information about the metagenomics. So, an essay about the metagenomics was complete combining with the material which Daeyeol has used for research work at a laboratory. Through the flow, Daeyeol built diverse knowledge about the genomics and insight of its application and completed the paper about the banana disease.</p>
<p> </p>
<p><strong>Learning on the non-major parts: communication and English</strong></p>
<p> In addition, Daeyeol had a chance to improve the efficient communication method. By participating in whole class except once, Daeyeol answered some questions which Dr. Jong Bhak gave. And Daeyeol was pointed out due to method of the communication. Through the genomics course, it was valuable not only to learn about the basis of genomics but also to communicate and think efficiently, critically and independently. Daeyeol could experience it through the genomics classes and individual counseling with Dr. Jong Bhak. A simple gesture can be important in the communication. Furthermore, concise but comprehensive answer or writing is the most efficient communication in science. Even though Daeyeol changes the major and do not research genome-related works any more, it is certain that the attitude toward the communication which Daeyeol learned though the course has not to change.</p>
<p> </p>
<p> Also, Dr. Jong Bhak had emphasis on improving English skill during undergraduate. So, Daeyeol did additional works to improve the English skill. Daeyeol focused on writing because the writing is the basis in a scientific paper. Daeyeol kept training on the English writing and got a grade of TOFLE on November. Daeyeol concluded that these kinds of non-major factors are also as important as the major knowledge.</p>
<p> </p>
<p><strong>Conclusion</strong></p>
<p>Daeyeol Ye progressed to write the scientific paper with the hypotheses based on the genomics and other courses. In the process of writing the paper, Daeyeol learned genomic information and implemented web-based data base and genomic analyzing tool such as NCBI, EBI, UCSC genome browser and BLSAT etc. And several essays are completed based on the topics mentioned in the process of writing the paper. Daeyeol built and applied the genomic knowledge for present interesting research field: genomic engineering. And in terms of this viewpoint, the genomics class was helpful.</p>
<p> </p>
<p>Furthermore, Daeyeol realized the efficient communication for critical and independent thinking. These advices were acquired in the classes and personal meeting with Dr. Jong Bhak. Lastly, as well as the genomic knowledge, Daeyeol tried to improve English skill, especially in writing. Daeyeol tried to pick up diverse knowledge from diverse sources during the genomic courses. As a result, it is reasonable that Daeyeol get A+ grade, because Daeyeol realized the most basic method and tool in research: efficient communication, independent thinking and English skill as well as the genomic knowledge. These can be applied in any scientific fields.</p>
<p> </p>
<p><strong>Additional information and method</strong></p>
<p>No personal pronoun was used at all in this paper, except for impersonal one (i.e. it, this etc.). Daeyeol Ye only used the name rather than ‘I’. This was an attempt for excluding any self-defense during self-evaluation as third-person.</p>
<p> Several materials are made during the semester. They can be checked in this site: biolecture (<a href="http://biolecture.org/index.php/Daeyeol_Ye">http://biolecture.org/index.php/Daeyeol_Ye</a>). Basically, whole processes about the learning genomics are based on the paper of the banana disease: the tropical race 4</p>
<p>(<a href="http://biolecture.org/index.php/Banana_Pandemic:_spread_of_tropical_race_4_and_effort_to_surmount_it">http://biolecture.org/index.php/Banana_Pandemic:_spread_of_tropical_race_4_and_effort_to_surmount_it</a>). By advancing the process, the related essays were made with using genomic knowledge (<a href="http://biolecture.org/index.php/Essay_list">http://biolecture.org/index.php/Essay_list</a>). As well as the major knowledge, the English skills, especially in writing, were improved during this semester</p>
<p>(<a href="http://biolecture.org/index.php/TOFLE_score">http://biolecture.org/index.php/TOFLE_score</a>). Knowledge was basically from several text books for the semester. In addition, some web-sites are referred for learning.</p>
<p> </p>
<p><strong>Reference</strong></p>
<p>"Phylogeny." <em>Restless Leg Syndrome (BTBD9)</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Pevsner, Jonathan. <em>Bioinformatics and Functional Genomics</em>. Hoboken, NJ: Wiley-Liss, 2003. Print.</p>
<p> </p>
<p>Zhang, J., H. Liu, S. Luo, A. Chavez-Badiola, Z. Liu, M. Yang, S. Munne, M. Konstantinidis, D. Wells, and T. Huang. "First Live Birth Using Human Oocytes Reconstituted by Spindle Nuclear Transfer for Mitochondrial DNA Mutation Causing Leigh Syndrome." <em>Fertility and Sterility</em> 106, no. 3 (2016). doi:10.1016/j.fertnstert.2016.08.004.</p>
<p> </p>
<p>@NewsfromScience. "Unanswered Questions Surround Baby Born to Three Parents." Science. 2016. Accessed September 28, 2016. http://www.sciencemag.org/news/2016/09/unanswered-questions-surround-baby-born-three-parents.</p>
<p> </p>
<p>"Banana Genome Hub." <em>Welcome to the Banana Genome Hub | Banana Genome Hub</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Koeppel, Dan. <em>Banana: The Fate of the Fruit That Changed the World</em>. New York: Hudson Street, 2008. Print.</p>
<p> </p>
<p>"Metagenomics Lake Tyrrell USC Dana and David Dornsife College of Letters, Arts and Sciences." <em>Lake Tyrrell USC Dana and David Dornsife College of Letters, Arts and Sciences</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Hartwell, Leland. <em>Genetics: From Genes to Genomes</em>. Boston, MA: McGraw-Hill Higher Education, 2004. Print.</p>
<p> </p>
<p>Lesk, Arthur M. <em>Introduction to Genomics</em>. Oxford: Oxford UP, 2007. Print.</p>
<p> </p>
<p> Daeyeol Ye</p>
<p> </p>
<p><strong>Abstract</strong></p>
<p><strong>It is reasonable that A+ grade is gotten to Daeyeol Ye (the rest is Daeyeol) when the several activities that Daeyeol did are taken into consideration. After a hiatus, classes which Daeyeol took are generally relevant to one keyword: genome. Daeyeol accumulated diverse knowledge based on two viewpoints: genomic and genomic-related knowledge themselves and means which transport the knowledge (i.e. English writing, communication posture) using several media. Then, several materials have been made during the semester and arranged with following one criterion: a paper on a banana pandemic, by Daeyeol.</strong></p>
<p> </p>
<p><strong>Introduction</strong></p>
<p><strong>Background</strong></p>
<p> Daeyeol Ye returned to UNIST at this semester with finishing the military service. For this reason, Daeyeol was short of general knowledge about the major including the genome. Daeyeol took several classes: molecular biotechnology, bioinformatics, genetics, and genomics. And all these classes are involved in the one topic which is the genome. It was considerable that correlation among these classes was helpful to Daeyeol to accumulate the knowledge.</p>
<p> </p>
<p><strong>Learning on the genomic and its related parts</strong></p>
<p>Daeyeol learned a basic genetic and genomic knowledge and used several web-based protocols and database by learning bioinformatics. And then, Daeyeol concluded that based on genomic information gained by series of processes, these genomes can be applied to make a useful genetically modified organism for several purposes.</p>
<p> </p>
<p>Actually, Daeyeol has been interested in genomic engineering, especially in food security or bioremediation using plant or microorganism. Daeyeol decided to write a paper related to it with applying the genomic knowledge which could be learned during the semester. So, the banana was selected because it is a material easy to be found. And numerous people do not realize its seriousness in spite of the present situation.</p>
<p> </p>
<p> After that, Daeyeol read a book which covered the crisis of the banana. Through the book which Dan Koeppel, it is distinct that the genomic analysis would give the answer for curing the tropical race 4, the panama disease which threats the extant banana industry. Daeyeol started to apply the knowledge learned from genomics and other classes with proposing several hypotheses.</p>
<p> </p>
<p> First of all, Daeyeol searched an influence caused by mutation of organellar genomes and built a hypothesis that the mutation is related to the immunity toward the tropical race 4. In addition, Daeyeol wrote about the essay related in the mutation of theorganellar genome: a three-parent baby. The essay is based on the genomic analysis of the organellar genome and related genomic engineering which can be applied based on the genomic information, because Daeyeol focused not only the analysis of the genome but also the application based on it.</p>
<p> </p>
<p> Also, Daeyeol built a phylogenetic tree about the relationship subspecies between the fungus which affects bananas and other plants. Before the phylogenetic tree was put into the paper, Daeyeol studied how the phylogenetic tree is made based on several media: genomics and bioinformatics textbook and web material. And an essay was written about the mechanism making the phylogenetic tree. Actually, the pylogenetic tree used in the paper was made using the BLAST result. That meant homologous relationship between the BLAST results. In this point, a question about the relationship among paralogous genes was thrown. So, an essay about the human cytoplasmic tRNA was complete.</p>
<p> </p>
<p> Fusarium oxysporum f. sp. cubense, a pathogen of the tropical race 4, is spread by the soil, not through the air. This point raised a question whether sequencing of the organisms in the soil was needed. And from this question, Daeyeol searched information about the metagenomics. So, an essay about the metagenomics was complete combining with the material which Daeyeol has used for research work at a laboratory. Through the flow, Daeyeol built diverse knowledge about the genomics and insight of its application and completed the paper about the banana disease.</p>
<p> </p>
<p><strong>Learning on the non-major parts: communication and English</strong></p>
<p> In addition, Daeyeol had a chance to improve the efficient communication method. By participating in whole class except once, Daeyeol answered some questions which Dr. Jong Bhak gave. And Daeyeol was pointed out due to method of the communication. Through the genomics course, it was valuable not only to learn about the basis of genomics but also to communicate and think efficiently, critically and independently. Daeyeol could experience it through the genomics classes and individual counseling with Dr. Jong Bhak. A simple gesture can be important in the communication. Furthermore, concise but comprehensive answer or writing is the most efficient communication in science. Even though Daeyeol changes the major and do not research genome-related works any more, it is certain that the attitude toward the communication which Daeyeol learned though the course has not to change.</p>
<p> </p>
<p> Also, Dr. Jong Bhak had emphasis on improving English skill during undergraduate. So, Daeyeol did additional works to improve the English skill. Daeyeol focused on writing because the writing is the basis in a scientific paper. Daeyeol kept training on the English writing and got a grade of TOFLE on November. Daeyeol concluded that these kinds of non-major factors are also as important as the major knowledge.</p>
<p> </p>
<p><strong>Conclusion</strong></p>
<p>Daeyeol Ye progressed to write the scientific paper with the hypotheses based on the genomics and other courses. In the process of writing the paper, Daeyeol learned genomic information and implemented web-based data base and genomic analyzing tool such as NCBI, EBI, UCSC genome browser and BLSAT etc. And several essays are completed based on the topics mentioned in the process of writing the paper. Daeyeol built and applied the genomic knowledge for present interesting research field: genomic engineering. And in terms of this viewpoint, the genomics class was helpful.</p>
<p> </p>
<p>Furthermore, Daeyeol realized the efficient communication for critical and independent thinking. These advices were acquired in the classes and personal meeting with Dr. Jong Bhak. Lastly, as well as the genomic knowledge, Daeyeol tried to improve English skill, especially in writing. Daeyeol tried to pick up diverse knowledge from diverse sources during the genomic courses. As a result, it is reasonable that Daeyeol get A+ grade, because Daeyeol realized the most basic method and tool in research: efficient communication, independent thinking and English skill as well as the genomic knowledge. These can be applied in any scientific fields.</p>
<p> </p>
<p><strong>Additional information and method</strong></p>
<p>No personal pronoun was used at all in this paper, except for impersonal one (i.e. it, this etc.). Daeyeol Ye only used the name rather than ‘I’. This was an attempt for excluding any self-defense during self-evaluation as third-person.</p>
<p> Several materials are made during the semester. They can be checked in this site: biolecture (<a href="http://biolecture.org/index.php/Daeyeol_Ye">http://biolecture.org/index.php/Daeyeol_Ye</a>). Basically, whole processes about the learning genomics are based on the paper of the banana disease: the tropical race 4</p>
<p>(<a href="http://biolecture.org/index.php/Banana_Pandemic:_spread_of_tropical_race_4_and_effort_to_surmount_it">http://biolecture.org/index.php/Banana_Pandemic:_spread_of_tropical_race_4_and_effort_to_surmount_it</a>). By advancing the process, the related essays were made with using genomic knowledge (<a href="http://biolecture.org/index.php/Essay_list">http://biolecture.org/index.php/Essay_list</a>). As well as the major knowledge, the English skills, especially in writing, were improved during this semester</p>
<p>(<a href="http://biolecture.org/index.php/TOFLE_score">http://biolecture.org/index.php/TOFLE_score</a>). Knowledge was basically from several text books for the semester. In addition, some web-sites are referred for learning.</p>
<p> </p>
<p><strong>Reference</strong></p>
<p>"Phylogeny." <em>Restless Leg Syndrome (BTBD9)</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Pevsner, Jonathan. <em>Bioinformatics and Functional Genomics</em>. Hoboken, NJ: Wiley-Liss, 2003. Print.</p>
<p> </p>
<p>Zhang, J., H. Liu, S. Luo, A. Chavez-Badiola, Z. Liu, M. Yang, S. Munne, M. Konstantinidis, D. Wells, and T. Huang. "First Live Birth Using Human Oocytes Reconstituted by Spindle Nuclear Transfer for Mitochondrial DNA Mutation Causing Leigh Syndrome." <em>Fertility and Sterility</em> 106, no. 3 (2016). doi:10.1016/j.fertnstert.2016.08.004.</p>
<p> </p>
<p>@NewsfromScience. "Unanswered Questions Surround Baby Born to Three Parents." Science. 2016. Accessed September 28, 2016. http://www.sciencemag.org/news/2016/09/unanswered-questions-surround-baby-born-three-parents.</p>
<p> </p>
<p>"Banana Genome Hub." <em>Welcome to the Banana Genome Hub | Banana Genome Hub</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Koeppel, Dan. <em>Banana: The Fate of the Fruit That Changed the World</em>. New York: Hudson Street, 2008. Print.</p>
<p> </p>
<p>"Metagenomics Lake Tyrrell USC Dana and David Dornsife College of Letters, Arts and Sciences." <em>Lake Tyrrell USC Dana and David Dornsife College of Letters, Arts and Sciences</em>. N.p., n.d. Web. 29 Nov. 2016.</p>
<p> </p>
<p>Hartwell, Leland. <em>Genetics: From Genes to Genomes</em>. Boston, MA: McGraw-Hill Higher Education, 2004. Print.</p>
<p> </p>
<p>Lesk, Arthur M. <em>Introduction to Genomics</em>. Oxford: Oxford UP, 2007. Print.</p>
<p> </p>
