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An efficient strategy for developing microbial cell factories by employing synthetic small regulatory RNAs
A new metabolic engineering tool that allows fine control of gene expression level by employing synthetic small regulatory RNAs was developed to efficiently construct microbial cell factories producing desired chemicals and materials Biotechnologists have been working hard to address the climate change and limited fossil resource issues through the development of sustainable processes for the production of chemicals, fuels and materials from renewable non-food biomass. One promising sustainable technology is the use of microbial cell factories for the efficient production of desired chemicals and materials. When microorganisms are isolated from nature, the performance in producing our desired product is rather poor. That is why metabolic engineering is performed to improve the metabolic and cellular characteristics to achieve enhanced production of desired product at high yield and productivity. Since the performance of microbial cell factory is very important in lowering the overall production cost of the bioprocess, many different strategies and tools have been developed for the metabolic engineering of microorganisms. One of the big challenges in metabolic engineering is to find the best platform organism and to find those genes to be engineered so as to maximize the production efficiency of the desired chemical. Even Escherichia coli, the most widely utilized simple microorganism, has thousands of genes, the expression of which is highly regulated and interconnected to finely control cellular and metabolic activities. Thus, the complexity of cellular genetic interactions is beyond our intuition and thus it is very difficult to find effective target genes to engineer. Together with gene amplification strategy, gene knockout strategy has been an essential tool in metabolic engineering to redirect the pathway fluxes toward our desired product formation. However, experiment to engineer many genes can be rather difficult due to the time and effort required; for example, gene deletion experiment can take a few weeks depending on the microorganisms. Furthermore, as certain genes are essential or play important roles for the survival of a microorganism, gene knockout experiments cannot be performed. Even worse, there are many different microbial strains one can employ. There are more than 50 different E. coli strains that metabolic engineer can consider to use. Since gene knockout experiment is hard-coded (that is, one should repeat the gene knockout experiments for each strain), the result cannot be easily transferred from one strain to another. A paper published in Nature Biotechnology online today addresses this issue and suggests a new strategy for identifying gene targets to be knocked out or knocked down through the use of synthetic small RNA. A Korean research team led by Distinguished Professor Sang Yup Lee at the Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), a prestigeous science and engineering university in Korea reported that synthetic small RNA can be employed for finely controlling the expression levels of multiple genes at the translation level. Already well-known for their systems metabolic engineering strategies, Professor Lee’s team added one more strategy to efficiently develop microbial cell factories for the production of chemicals and materials. Gene expression works like this: the hard-coded blueprint (DNA) is transcribed into messenger RNA (mRNA), and the coding information in mRNA is read to produce protein by ribosomes. Conventional genetic engineering approaches have often targeted modification of the blueprint itself (DNA) to alter organism’s physiological characteristics. Again, engineering the blueprint itself takes much time and effort, and in addition, the results obtained cannot be transferred to another organism without repeating the whole set of experiments. This is why Professor Lee and his colleagues aimed at controlling the gene expression level at the translation stage through the use of synthetic small RNA. They created novel RNAs that can regulate the translation of multiple messenger RNAs (mRNA), and consequently varying the expression levels of multiple genes at the same time. Briefly, synthetic regulatory RNAs interrupt gene expression process from DNA to protein by destroying the messenger RNAs to different yet controllable extents. The advantages of taking this strategy of employing synthetic small regulatory RNAs include simple, easy and high-throughput identification of gene knockout or knockdown targets, fine control of gene expression levels, transferability to many different host strains, and possibility of identifying those gene targets that are essential. As proof-of-concept demonstration of the usefulness of this strategy, Professor Lee and his colleagues applied it to develop engineered E. coli strains capable of producing an aromatic amino acid tyrosine, which is used for stress symptom relief, food supplements, and precursor for many drugs. They examined a large number of genes in multiple E. coli strains, and developed a highly efficient tyrosine producer. Also, they were able to show that this strategy can be employed to an already metabolically engineered E. coli strain for further improvement by demonstrating the development of highly efficient producer of cadaverine, an important platform chemical for nylon in the chemical industry. This new strategy, being simple yet very powerful for systems metabolic engineering, is thus expected to facilitate the efficient development of microbial cell factories capable of producing chemicals, fuels and materials from renewable biomass. Source: Dokyun Na, Seung Min Yoo, Hannah Chung, Hyegwon Park, Jin Hwan Park, and Sang Yup Lee, “Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs”, Nature Biotechnology, doi:10.1038/nbt.2461 (2013)
2013.03.19
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Launched the Saudi Aramco-KAIST CO2 Management Center in Korea
KAIST and Saudi Aramco, a global energy and petrochemicals enterprise, signed on February 20, 2013 the Master Research and Collaboration Agreement (the Agreement) on joint collaborations in research and development of carbon management between the two entities. The Agreement was subsequently concluded upon the signing of the Memorandum of Understanding (MOU) between KAIST and Saudi Aramco, dated January 7th, 2013. In the Agreement, the two organizations specified terms and conditions necessary to conduct joint research projects and stipulated governing body for the operation of the Saudi Aramco-KAIST CO2 Management Center. KAIST and Saudi Aramco, a national oil company for Saudi Arabia, entered into the MOU, in which the two parties shared a common interest in addressing the issue of CO2 capture, CO2storage, CO2 avoidance using efficiency improvements, and converting CO2 into useful chemicals and other materials, and agreed to “create a major research center for CO2” in Korea. As envisioned by the MOU and its subsequent agreement, KAIST and Saudi Aramco decided to operate an interim office of the Saudi Aramco-KAIST CO2 Management Center at KAIST campus in Daejeon, Korea, pending the establishment of the research center. The full-fledged, independent research facility will be built at a location and during a period to be agreed between the two parties. Following the signing of the Agreement, there was a celebration event taken place, including a signboard hanging ceremony for the interim research office. A 10-member delegation from Saudi Aramco, which was headed by Vice President of Engineering Services Samir Al-Tubayyeb, Dr. Nam-Pyo Suh, former president of KAIST, Vice President of Research at KAIST Kyung-Wook Paik, and senior representatives from Korean oil and petrochemical companies such as S-Oil, Lotte Chemicals, SK Innovation, and STX attended the event. Kyung-Wook Paik, Vice President of Research at KAIST, said, “In order to help find solutions to carbon management, KAIST and Saudi Aramco will facilitate to exchange each party’s complementary technical expertise, gain insight into new research fields, and have access to key sources of talent, while promoting innovation for technology solutions and contributing to the lifelong learning agenda of both organizations.” Samir Al-Tubayyeb, Vice President of Engineering Services at Saudi Aramco, added that “As a world-leading oil and gas company, Saudi Aramco’s mission is to promote the continued use of safe, environmentally-friendly petroleum products with a vision to becoming a global leader in research and technology. Building a strong and cooperative relationship with KAIST in our endeavor to search for alternative ways to better utilization of fossil fuels will expedite the creation of opportunities to make the world environmentally safer and sustainable.” KAIST and Saudi Aramco will each chip in a maximum of USD 5 million annually for the establishment and operation of the Saudi Aramco-KAIST CO2 Management Center during the initial term of the Master Research and Collaboration Agreement, which starts in 2013 and continues through 2018.
2013.03.19
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Prof. Jong Chul Ye Appointed as the Editor of IEEE TIP
Professor Jong Chul Ye KAIST Bio & brain engineering department’s Professor Jong Chul Ye has been appointed as the editor of the "IEEE image processing transactions (IEEE TIP, IEEE Transaction on Image Processing)’, a prominent journal in the sector of imaging and medical image processing. Professor Ye will act as the editor in the field of medical imaging from February 2013 to January 2016, during which he will participate in examining thesis, establishing the direction of the journal and more. Professor Jong Chul Ye was recognized for his notable work in the field of medical imaging research using compressed sensing for the development of a high resolution medical image reconstruction techniques. This technique has pioneered a new area that is applicable in magnetic resonance imaging (MRI), computed tomography (CT), positron emission Camcorder (PET) and brain imaging. On the other hand, “IEEE TIP” was first published in 1992 and is currently the world’s leading authority in the field of image processing, medical imaging, image acquisition, compression and output.
2013.02.21
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Professor Hwang Kyu Young and Professor Yang Dong Yeol Receives Engineer of Korea Award
Emeritus Professor Hwang Kyu Young (Department of Computer Sciences) and Professor Yang Dong Yeol (Department of Mechanical Engineering) were named as the 2012 Engineer of Korea by the Ministry of Education, Science, and Technology and Korea Science Foundation. The Engineer of Korea Award is awarded biannually to scientists and engineers that have contributed to the development of Korea’s science and technology and national economy. Professor Hwang’s work with DBMS and close coupling architecture of information search and overall new theories and application technology development in the field of database system has aided the opening and expansion of IT software industry development and the advent of internet information culture era. Professor Yang is a word renowned scholar in the field of net shape manufacturing and is considered to have opened a new page in the field of nano-molding technique. In addition, Professor Eum Sang Il (Department of Mathematical Science) has been selected as the 2012 Young Scientist Award.
2013.01.22
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KAIST Professors win 2012 Korea Engineering Award
Distinguished Professor Hwang Gyu Young (Department of Computer Science) and Professor Yang Dong Yol (Department of Mechanical Engineering) from KAIST received the 2012 ‘Korea Engineering Award’ hosted by the Ministry of Education, Science and Technology and the Korea Research Foundation. The ‘Korea Engineering Award’ is given biennially to researchers who have accomplished world class research and have contributed greatly to Korea’s development in the field of Science and Technology. The award started in 1994 and a total of 24 recipients were recognized in various fields such as electronics, mechanics, chemistry, construction, etc. The recipients of the award areawarded the Presidential award as well as 50million won as prize money. Professor Hwang was recognized for his research on DBMS close-coupling architecture as well as other new data base system theories, contributing to the development of the IT software industry in Korea. Professor Yang was praised for his work in precision shape creation and manufacturing, especially for his work in the nano-stereolithography process. In addition, Professor Oum Sang-il from the Deparment of Mathematical Science received the 2012 ‘Young Scientist Award’ hosted by the Ministry of Education, Science and Technology and the Korean Academy of Science and Technology. The ceremony for ‘Korea Engineering Award’ and the ‘Young Scientist Award’ was held in Seoul Press Center Press Club on the 21st of December.
2012.12.26
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Ph.D. students Hyowon Park and Won Ma receive Grand Prizes in Mathematics and Biology respectively.
Researchers in KAIST received best paper awards in two out of three fields at this year’s award ceremony for the “Second Annual Best Thesis Paper Award” held collectively by the Korea University Presidents’ Federation (with Chairman DaeSoon Lee) and the Korean Academy of Science and Technology (with Director GilSang Jung). Two researchers from KAIST, Hyowon Park (Department of Mathematics) and Won Ma (Department of Biology) received best paper awards. This prize, given by the both the Korea University Presidents’ Federation and the Korean Academy of Science and Technology since last year, is awarded to researchers and assistant professors who write the most outstanding thesis papers in the field of basic sciences. Park, who received the best paper award this year, did research on graph braid groups. He was supervised by Professor Kihyung Ko, who received the best supervisor reward. Ma, who received the best paper award in the field of biological science, researched about the Attention Deficit/Hyperactivity Disorder due to deficiency of the GIT1 synapse protein. His supervising professor also received the supervisor award. The award ceremony was held in the auditorium of the S-OIL headquarters in Seoul on November 30. Meanwhile, NASA researcher Jaehwa Lee received the best paper award in the field of earth science, and his supervising professor, Professor Jun Kim from Yonsei University who studies atmospheric science, received the best supervisor award.
2012.12.21
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KAIST International Students Organize KAIST ONE Program
International Students at KAIST are running a program called “KAIST ONE” (Overseas Networking Exchange) in order to promote an active exchange between students and to present their cultures. Originally an international cultural activity at the ICU (then the Information and Communications University) in 2007, the program changed its name to “KAIST ONE” and was continued after the merging of the university with KAIST. Students of about 40 different countries have participated to date, and each annual event attracts more than 150 students. Over 700 international students from 70 different countries around the world spontaneously organize and manage the KAIST ONE program, which is run five times this semester, every other Thursday from 7p.m. to 9p.m. at the KAIST International Center. The 11th of last month and the 1st of this month witnessed an enthusiastic response from about 150 participants who joined the Columbian and the Saudi Arabian students in introducing their cultures, presenting traditional cultural performances, and sharing traditional foods. The next in line are Danish, Ugandan, and Cameroonian students who are set to have their turns on this month’s 15th, 29th, and next month’s 6th, respectively. Also notable is the active attention and support from foreign embassies such as the participation of Tunisian, Brazilian, Pakistani, Azerbaijani, Thai, and German ambassadors in the program since last year to provide food and introductory guides to cultures. The director of this year’s program, Karim Charfi (Tunisian, 3rd year Electrical Engineering) said, “During the selection stage of each semester, everyone competes for the chance to present their country,” and “KAIST ONE has established itself as a unique and exotic cultural event at KAIST since it networks about 40 of the relatively less known countries such as Uganda, Cameroon, Tunisia, and Chile and the people with diverse cultures.” The supervisor of the program, Chang Dong Yoo of the Office of Special Projects and Institutional Relations said, “KAIST ONE is an opportunity for international students to acquaint people with their cultures, and it is also a site of cultural exchange and of building friendships among KAIST students and international students,” and “we plan to extend the event such that not only the KAIST members but also the local residents can join in.” The program welcomes KAIST students as well as the general public.
2012.12.21
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KAIST shocks the world with its creativity
Researchers at KAIST yielded great results at the world’s leading international Human Computer Interaction Society. Professor Lee Gi Hyuk’s (Department of Computer Sciences) and Professor Bae Seok Hyung’ (Department of Industrial Design) respective teams received awards in two criteria in student innovation contest and was the only domestic university that presented their thesis at the ACM Symposium on User Interface Software. The ACM UIST holds a student innovation contest prior to its opening. This year’s topic was the pressure sensing multi touch pad of Synaptics and involved 27 prestigious universities including MIT and CMU. The KAIST team (Ki Son Joon Ph.D. candidate, Son Jeong Min M.A. candidate of Department of Computer Sciences and Woo Soo Jin M.A. candidate of Department of Industrial Design) designed a system that allows modulated control by attaching a simple structure to the pressure sensing multi touch pad. The second KAIST team (Huh Seong Guk Ph.D. candidate, Han Jae Hyun Ph.D. candidate, Koo Ji Sung Ph.D. candidate at the Department of Computer Sciences, and Choi Ha Yan M.A. candidate at Department of Industrial Design) designed a system that utilizes a highly elastic fiber to allow the sensing of lateral forces. They also created a slingshot game application which was the second most popular system. In the thesis session Professor Bae’s team (Lee DaWhee Ph.D. candidate, Son Kyung Hee Ph.D. candidate, Lee Joon Hyup M.A. candidate at Department of Industrial Design) presented a thesis that dealt with the technology that innovated the table pen for displays. The new ‘phantom pen’ solved the issue arising from the hiding effect of the pen’s contact point and the display error due to the thickness of the display. In addition the ‘phantom pen’ has the ability to show the same effects as crayons or markers in a digital environment.
2012.11.29
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'KAIST ONE" program run by international students
International Students at KAIST are currently running the ‘KAIST ONE (Overseas Networking Exchange)’ program which promotes cultural exchange with other students. The program started in 2007 at ICU and continues on as the ‘KAIST ONE’ event, after the school was integrated into KAIST. Students from over 40 different nationalities have participated in the program and an average of 150 students participates in each event. The ‘KAIST ONE’ event is held every other Thursday at the KAIST international center from 7 to 9pm. Columbian and Saudi Arabian students hosted the event in October and November respectively and displayed their traditional culture and food. Students from Denmark, Uganda and Cameroon will host the event on November 15th, 19th and on December 6th respectively. Since last year, the event has received great interest from many different embassies, with foreign ambassadors participating in the events. Karim Charfi (Tunisia, Junior at the Department of Electrical Engineering), who planned the event, said that “KAIST ONE is a great opportunity to introduce foreign to other students” and that “it has become a unique event that can only be experienced at KAIST”. Anyone can participate in the program, from KAIST students to outsiders.
2012.11.22
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College of Cultural Sciences Announces Results for 6th Best Paper Award
The College of Cultural Sciences cohosts with the EFL Program the Best Paper Award each semester. The Best Paper Awards went to Jo Hyeong Chan and Oh Shin Ah undergraduate students. The Best Paper Award was established in 2009 in order to encourage and improve the English writing skills of undergraduate students. The College of Humanities and Social Sciences opened up 69 English courses in Spring of 2012 and 14 papers were recommended by the respective professors as ‘best papers’. Out of these papers 2 were selected for First Prize and 4 were selected as Honorable Mentions. The two recipients’ papers were recommended by Professor Park Woo Seok (Topics in Philosophy).
2012.10.16
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Commercialization of Carbon Capture and Storage Technology Speeds up
KAIST research team successfully developed the ideal method for carbon dioxide transportation, which is crucial in the capturing and underground storage of carbon dioxide technology. Professor Jang Dae Joon of the department of Ocean Systems Engineering developed a carbon dioxide transportation that minimizes evaporative gases. The new technology is the final piece of the three part carbon capture storage which involves capture, transportation, and storage of carbon dioxide. The completion of the three part technology will allow for commercialization in the near future. Carbon Capture and Storage technology is regarded as the technology that will reduce carbon dioxide levels. It captures the carbon dioxide emitted from power plants and factories and storing them permanently in empty oil fields underground. If the post Kyoto Protocol was to be implemented from 2013, Korea will not be able to shirk from the need to reduce carbon emissions. Therefore the Korean government set out to reduce 32 million tons of carbon dioxide (10% of predicted carbon reduction) until 2030. In response to the government’s efforts to reduce carbon dioxide emissions, Korean research teams like KAIST have responded. Professor Jang’s team succeeded in developing the core technology for underground storage in the 2009 ‘Carbon dioxide Transport and Injection Terminal Project’. And as the final piece of the puzzle the team developed an optimization solution that addressed the evaporating gases emitted from carbon dioxide during transportation. Professor Jang’s team focused on the required low temperature and high pressure conditions in liquid carbon dioxide transport. The problem lies in the temperature gradient which can cause the transport canister to explode. The solution developed by the team is to evaporate carbon dioxide in a pressurized contained which is then re-liquidated. External variables like price of oil, carbon taxation, etc. have been considered and the process was optimized accordingly. The result of Professor Jang’s team’s solution to Carbon Capture and Storage was stored in the online edition of International Journal of Greenhouse Gas Control.
2012.07.26
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Successful Development of Excavation System of Biomarkers containing Protein Decomposition Control Enzyme Information
A Korean team of researchers successfully developed a biomarker excavation system named E3Net that excavates biomarkers containing information of the enzymes that control the decomposition of proteins. The development of the system paved the possibility of development of new high quality biomarkers. *Biomarker: Molecular information of unique patterns derived from genes and proteins that allow the monitoring of physical changes from genetic or environmental causes. Professor Lee Kwan Soo’s team (Department of Biological Sciences) composed of Doctorate candidate Han Young Woong, Lee Ho Dong Ph.D. and Professor Park Jong Chul published a dissertation in the April edition of Molecular and Cellular Proteomics. (Dissertation Title: A system for exploring E3-mediated regulatory networks of cellular functions). Professor Lee’s team compiled all available information of the enzyme that controls protein decomposition (E3 enzyme) and successfully compiled the inter-substrate network by extracting information from 20,000 biology related data base dissertations. The result was the development of the E3Net system that analyzes the related cell function and disease. Cells have a system that produces, destroys, and recycles proteins in response to the ever changing environmental conditions. Error in these processes leads to disease. Therefore finding the relationship between E3 enzymes that control the decomposition of proteins and the substrates will allow disease curing and prevention to become much easier. E3 enzyme is responsible for 80% of the protein decomposition and is therefore predicted to be related to various diseases. However the information on E3 enzyme and inter-substrate behavior are spread out among numerous dissertations and data bases which prevented methodological analysis of the role of the related cells and characteristics of the disease itself. Professor Lee’s team was successful in creating the E3Net that compiled 2,201 pieces of E3 substrate information, 4,896 pieces of substrate information, and 1,671 pieces of inter-substrate relationship information. This compilation allows for the systematic analysis of cells and diseases. The newly created network is 10 times larger than the existing network and is the first case where it is possible to accurately find the cell function and related diseases. It is anticipated that the use of the E3Net will allow the excavation of new biomarkers for the development of personalized drug systems. The research team applied the E3Net to find tens of new candidate biomarkers related to the major modern diseases like diabetes and cancer.
2012.05.30
View 10630
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