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Bioengineers develop a new strategy for accurate prediction of cellular metabolic fluxes A team of pioneering South Korean scientists has developed a new strategy for accurately predicting cellular metabolic fluxes under various genotypic and environmental conditions. This groundbreaking research is published in the journal Proceedings of the National Academy of Sciences of the USA (PNAS) on August 2, 2010. To understand cellular metabolism and predict its metabolic capability at systems-level, systems biological analysis by modeling and simulation of metabolic network plays an important role. The team from the Korea Advanced Institute of Science and Technology (KAIST), led by Distinguished Professor Sang Yup Lee, focused their research on the development of a new strategy for more accurate prediction of cellular metabolism. “For strain improvement, biologists have made every effort to understand the global picture of biological systems and investigate the changes of all metabolic fluxes of the system under changing genotypic and environmental conditions,” said Lee. The accumulation of omics data, including genome, transcriptome, proteome, metabolome, and fluxome, provides an opportunity to understand the cellular physiology and metabolic characteristics at systems-level. With the availability of the fully annotated genome sequence, the genome-scale in silico (means “performed on computer or via computer simulation.”) metabolic models for a number of organisms have been successfully developed to improve our understanding on these biological systems. With these advances, the development of new simulation methods to analyze and integrate systematically large amounts of biological data and predict cellular metabolic capability for systems biological analysis is important. Information used to reconstruct the genome-scale in silico cell is not yet complete, which can make the simulation results different from the physiological performances of the real cell. Thus, additional information and procedures, such as providing additional constraints (constraint: a term to exclude incorrect metabolic fluxes by restricting the solution space of in silico cell) to the model, are often incorporated to improve the accuracy of the in silico cell. By employing information generated from the genome sequence and annotation, the KAIST team developed a new set of constraints, called Grouping Reaction (GR) constraints, to accurately predict metabolic fluxes. Based on the genomic information, functionally related reactions were organized into different groups. These groups were considered for the generation of GR constraints, as condition- and objective function- independent constraints. Since the method developed in this study does not require complex information but only the genome sequence and annotation, this strategy can be applied to any organism with a completely annotated genome sequence. “As we become increasingly concerned with environmental problems and the limits of fossil resources, bio-based production of chemicals from renewable biomass has been receiving great attention. Systems biological analysis by modeling and simulation of biological systems, to understand cellular metabolism and identify the targets for the strain improvement, has provided a new paradigm for developing successful bioprocesses,” concluded Lee. This new strategy for predicting cellular metabolism is expected to contribute to more accurate determination of cellular metabolic characteristics, and consequently to the development of metabolic engineering strategies for the efficient production of important industrial products and identification of new drug targets in pathogens.”
2010.08.05 View 12362
Native-like Spider Silk Produced in Metabolically Engineered Bacterium Microscopic picture of 285 kilodalton recombinant spider silk fiber Researchers have long envied spiders’ ability to manufacture silk that is light-weighted while as strong and tough as steel or Kevlar. Indeed, finer than human hair, five times stronger by weight than steel, and three times tougher than the top quality man-made fiber Kevlar, spider dragline silk is an ideal material for numerous applications. Suggested industrial applications have ranged from parachute cords and protective clothing to composite materials in aircrafts. Also, many biomedical applications are envisioned due to its biocompatibility and biodegradability. Unfortunately, natural dragline silk cannot be conveniently obtained by farming spiders because they are highly territorial and aggressive. To develop a more sustainable process, can scientists mass-produce artificial silk while maintaining the amazing properties of native silk? That is something Sang Yup Lee at the Korea Advanced Institute of Science and Technology (KAIST) in Daejeon, the Republic of Korea, and his collaborators, Professor Young Hwan Park at Seoul National University and Professor David Kaplan at Tufts University, wanted to figure out. Their method is very similar to what spiders essentially do: first, expression of recombinant silk proteins; second, making the soluble silk proteins into water-insoluble fibers through spinning. For the successful expression of high molecular weight spider silk protein, Professor Lee and his colleagues pieced together the silk gene from chemically synthesized oligonucleotides, and then inserted it into the expression host (in this case, an industrially safe bacterium Escherichia coli which is normally found in our gut). Initially, the bacterium refused to the challenging task of producing high molecular weight spider silk protein due to the unique characteristics of the protein, such as extremely large size, repetitive nature of the protein structure, and biased abundance of a particular amino acid glycine. “To make E. coli synthesize this ultra high molecular weight (as big as 285 kilodalton) spider silk protein having highly repetitive amino acid sequence, we helped E. coli overcome the difficulties by systems metabolic engineering,” says Sang Yup Lee, Distinguished Professor of KAIST, who led this project. His team boosted the pool of glycyl-tRNA, the major building block of spider silk protein synthesis. “We could obtain appreciable expression of the 285 kilodalton spider silk protein, which is the largest recombinant silk protein ever produced in E. coli. That was really incredible.” says Dr. Xia. But this was only step one. The KAIST team performed high-cell-density cultures for mass production of the recombinant spider silk protein. Then, the team developed a simple, easy to scale-up purification process for the recombinant spider silk protein. The purified spider silk protein could be spun into beautiful silk fiber. To study the mechanical properties of the artificial spider silk, the researchers determined tenacity, elongation, and Young’s modulus, the three critical mechanical parameters that represent a fiber’s strength, extensibility, and stiffness. Importantly, the artificial fiber displayed the tenacity, elongation, and Young’s modulus of 508 MPa, 15%, and 21 GPa, respectively, which are comparable to those of the native spider silk. “We have offered an overall platform for mass production of native-like spider dragline silk. This platform would enable us to have broader industrial and biomedical applications for spider silk. Moreover, many other silk-like biomaterials such as elastin, collagen, byssus, resilin, and other repetitive proteins have similar features to spider silk protein. Thus, our platform should also be useful for their efficient bio-based production and applications,” concludes Professor Lee. This work is published on July 26 in the Proceedings of the National Academy of Sciences (PNAS) online.
2010.07.28 View 16761
A new facility at KAIST opened on July 6, 2010. Ryu Geun-Chul Sports Complelx will allow students, faculty and staff to pause a moment and exhale in the hustle and bustle of their daily lives. An opening ceremony celebrating the completion of a new facility for the KAIST family was held on July 6, 2010 at the campus. Had it not been for contributions of many people and organizations throughout the nation, among others, Dr. Geun-Chul Ryu, POSCO, Woori Bank, members of KAIST community, parents, and other citizens, it would be impossible to build the facility, said the university. The Complex, a three-story building with a basement, has an indoor court for basketball and volleyball with 3,000 individual seats, 200 meters of running track, indoor golf range, a fitness center, and other convenient facilities. Any members of KAIST community can visit the building and relax their body and mind stressed with work and study. It also provides a large space for ceremonial and cultural gatherings such as 2010 KAIST commencement ceremony. The official name of the building is “Ryu Geun-Chul Sports Complelx,” which was created in appreciation of Dr. Geun-Chul Ryu’s generous act who had donated 57.8 billion won worth of real estate to KAIST in August 2008.
2010.07.07 View 11963
KAIST's Mobile Harbor Program Attracts Two Corporate Investments KAIST-developed Mobile Harbor Program has attracted investments from Korea"s two big-name industrial corporations, university authorities said on Monday (Oct. 19). KAIST has recently signed an agreement with Hyundai Wia Corp., a machine parts supplier, to collaborate in the researches of the mobile harbor programs and commercialization. Under the agreement, Hyundai WIA will invest a total of 7.5 billion won in the program for two years starting from January 2010. KAIST has also received a letter of intent from the Daewoo Shipbuilding & Marine Engineering Co. on investing 20 billion won in the commercialization of the project. The Mobile Harbor Program is designed to create mobile units that can go out to the ship which are anchored off-shore and unload the cargo and take it to where it is needed. It is aimed at overcoming the shortcomings of the current maritime container transportation systems. Container ships are getting larger and larger, requiring deep waters, large and complex loading and unloading systems, and major investments in facilities. Prof. Byung-Man Kwak, leader of the program"s R&D team, said: "With the investment from two global industrial companies, the program has gained a crucial momentum. The development of the program is expected to help Korea to become a global leader in marine transportation and maintain its supremacy in shipbuilding."
2009.10.20 View 14392
KAIST Secures Top Ranking of Korean Universities KAIST won the No. 1 position for the second year in a row in the daily JoongAng Ilbo"s university rankings for 2009. Seoul National University took back the No. 2 spot, followed in order by POSTECH, Korea and Yonsei universities. The survey was conducted in the four categories, educational environment/finance, professors" research, general reputation/social advancement and globalization. KAIST scored 293 points out of possible 400 this year, while the second-ranking SNU and third-ranking POSTECH earned 234 and 226 points, respectively. The daily noted that KAIST particularly excelled in the category of educational environment/finance. It observed that donations to KAIST surged almost 100 times for the past three years since 2006 when President Suh took office. In specific rankings of universities by academic disciplines, SNU came in first overall. KAIST topped in the science and engineering field, while Korea University ranked first in liberal arts studies. This year, 88 four-year universities participated in the survey. The daily JoongAng Ilbo started its annual evaluation of Koran universities in 1994 to stimulate productive competition among institutions of higher learning and to provide objective standards for students and their parents to select schools for application. For more information, news.joins.com/article/391/3789391.html
2009.09.24 View 13663
Scaling Laws between Population and Facility Densities Found A research team led by Prof. Ha-Woong Jeong of the Department of Physics, KAIST, has found a positive correlation between facilities and population densities, university authorities said on Tuesday (Sept. 2). The research was conducted in the cooperation with a research team of Prof. Beom-Jun Kim at Sungkyunkwan University. The researchers investigated the ideal relation between the population and the facilities within the framework of an economic mechanism governing microdynamics. In previous studies based on the global optimization of facility positions in minimizing the overall travel distance between people and facilities, the relation between population and facilities should follow a simple law. The new empirical analysis, however, determined that the law is not a fixed value but spreads in a broad range depending on facility types. To explain this discrepancy, the researchers proposed a model based on economic mechanism that mimics the competitive balance between the profit of the facilities and the social opportunity cost for population. The results were published in the Proceedings of the National Academy of Sciences of the United States on Aug. 25.
2009.09.04 View 11978
KAIST Professor Whang Turns VLDB Journal Into One of the Best in Its Field Kyu-Young Whang, a Distinguished Professor at KAIST’s Computer Science Department, has developed The VLDB Journal into one of the world’s best journals on database technology. Professor Whang, Editor-in-Chief of The VLDB Journal, is credited for the journal’s remarkable success evidenced by the rise of the publication’s Science Citation Index (SCI) impact factor from 3.818 to 6.8 in the period of one year. This placed the VLDB in the first place amongst 99 information systems journals and 44 hardware and architecture-related journals registered with the SCI. With only the exception of the Survey Journal, this makes The VLDB Journal the best in computer science. The VLDB Journal is a quarterly journal published on behalf of the VLDB Endowment. The journal, launched in 1992, is dedicated to the publication of scholarly contributions to the advancement of information system architectures, the impact of technological advancements on information systems, and the development of novel database applications. The VLDB Journal’s closest competitors in database technology, IEEE Transactions on Knowledge and Data Engineering and ACM Transactions on Database Systems, received an impact factor of 2.236 and 1.613 respectively. Comparatively, Professor Whang’s journal retains an impact factor nearly 3 to 4 times greater. During Professor Whang’s six-year term as Editor-in-Chief, he has actively pursued the use of innovative ideas, strengthened the board of editors, standardized the length of review time, and made the journal much more accessible through the Internet. Furthermore, he drastically reduced publication time and sought a policy that focused more on the journal’s readers, which led to The VLDB Journal’s SCI impact factor rising from 1.149 (2002) to 6.8 (2008). As one of The VLDB Journal’s founding members, Professor Whang has worked for the advancement of his journal tirelessly for 19 years with many accomplishments in database technology, including physical database design, determining the quality of a database, and the creation of a database management system. As a result, Professor Whang became the first IEEE fellow concerning domestic computer science. He is also a trustee of The VLDB Endowment, a fellow of the Korean Academy of Science and Technology, and of course, a Distinguished Professor at KAIST.
2009.07.16 View 13133
KAIST Ranks 95th among World Universities Oct. 13, 2008 --KAIST is ranked 95th among Top 200 Universities of the World this year, scoring a notable increase from last year"s ranking of 132nd. KAIST, Seoul National University which was placed 50th, and POSTECH ranked 188th became the only three institutions of higher education in Korea to make it to the list, called "The Times Higher Education -- QS World University Rankings." KAIST"s advancement was more conspicuous in specific area evaluations. In the area of Engineering and Information Technology, it is ranked 34th (49th last year), in Natural Sciences 46th (86th last year), and in Biological Sciences and Biotechnology 134th (166th last year). While North America dominates the ranking with 42 universities on the list, Europe and Asia Pacific are also well represented with 36 and 22 institutions, respectively. The list, compiled by The Times (of London) newspaper annually, is topped by Harvard University (USA), followed by Yale University (USA) and University of Cambridge (United Kingdom). Last year, only KAIST and SNU were included in the top 200 list. This year, Yonsei University raised its ranking to 203rd from last year"s 223rd while Korea University improved from 243rd to 236th, showing overall improvement of universities in Korea. Again this year, Japan and China had most of the top ranked universities in Asia, each sharing three in the top 50. University of Tokyo, ranked 19th, led all Japanese universities; Kyoto University was placed 25th and Osaka University 44th. University of Hong Kong was listed 26th, followed by Hong Kong University of Science and Technology on 39th and the Chinese University of Hong Kong on 42nd. The Times Higher Education--QS World University Rankings evaluates four main categories: quality of research, globalization, and quality of education and work of graduates in society. The evaluation also considers academic peer review, citations per faculty, recruiter review, international faculty, international students and faculty-student ratio. QS Top 100 Universities 2008 Source: QS Quacquarelli Symonds (www.topuniversities.com) Copyright?004-2008QSQuacquarelliSymondsLtd. 1 HARVARD University United States 2 YALE University United States 3 University of CAMBRIDGE United Kingdom 4 University of OXFORD United Kingdom 5 CALIFORNIA Institute of Technology (Calt... United States 6 IMPERIAL College London United Kingdom 7 UCL (University College London) United Kingdom 8 University of CHICAGO United States 9 MASSACHUSETTS Institute of Technology (M... United States 10 COLUMBIA University United States 11 University of PENNSYLVANIA United States 12 PRINCETON University United States 13= DUKE University United States 13= JOHNS HOPKINS University United States 15 CORNELL University United States 16 AUSTRALIAN National University Australia 17 STANFORD University United States 18 University of MICHIGAN United States 19 University of TOKYO Japan 20 MCGILL University Canada 21 CARNEGIE MELLON University United States 22 KING"S College London United Kingdom 23 University of EDINBURGH United Kingdom 24 ETH Zurich (Swiss Federal Institute of T... Switzerland 25 KYOTO University Japan 26 University of HONG KONG Hong Kong 27 BROWN University United States 28 ?ole Normale Sup?ieure, PARIS France 29 University of MANCHESTER United Kingdom 30= National University of SINGAPORE(NUS) Singapore 30= University of CALIFORNIA, Los Angeles (U... United States 32 University of BRISTOL United Kingdom 33 NORTHWESTERN University United States 34= ?OLE POLYTECHNIQUE France 34= University of BRITISH COLUMBIA Canada 36 University of California, BERKELEY United States 37 The University of SYDNEY Australia 38 The University of MELBOURNE Australia 39 HONG KONG University of Science & Techno... Hong Kong 40 NEW YORK University (NYU) United States 41 University of TORONTO Canada 42 The CHINESE University of Hong Kong Hong Kong 43 University of QUEENSLAND Australia 44 OSAKA University Japan 45 University of NEW SOUTH WALES Australia 46 BOSTON University United States 47 MONASH University Australia 48 University of COPENHAGEN Denmark 49 TRINITY College Dublin Ireland 50= Ecole Polytechnique F??ale de LAUSANNE... Switzerland 50= PEKING University China 50= SEOUL National University Korea, South 53 University of AMSTERDAM Netherlands 54 DARTMOUTH College United States 55 University of WISCONSIN-Madison United States 56 TSINGHUA University China 57 HEIDELBERG Universit? Germany 58 University of CALIFORNIA, San Diego United States 59 University of WASHINGTON United States 60 WASHINGTON University in St. Louis United States 61 TOKYO Institute of Technology Japan 62 EMORY University United States 63 UPPSALA University Sweden 64 LEIDEN University Netherlands 65 The University of AUCKLAND New Zealand 66 LONDON School of Economics and Political... United Kingdom 67 UTRECHT University Netherlands 68 University of GENEVA Switzerland 69 University of WARWICK United Kingdom 70 University of TEXAS at Austin United States 71 University of ILLINOIS United States 72 Katholieke Universiteit LEUVEN Belgium 73 University of GLASGOW United Kingdom 74 University of ALBERTA Canada 75 University of BIRMINGHAM United Kingdom 76 University of SHEFFIELD United Kingdom 77 NANYANG Technological University Singapore 78= DELFT University of Technology Netherlands 78= RICE University United States 78= Technische Universit? M?CHEN Germany 81= University of AARHUS Denmark 81= University of YORK United Kingdom 83= GEORGIA Institute of Technology United States 83= The University of WESTERN AUSTRALIA Australia 83= University of ST ANDREWS United Kingdom 86 University of NOTTINGHAM United Kingdom 87 University of MINNESOTA United States 88 LUND University Sweden 89 University of CALIFORNIA, Davis United States 90 CASE WESTERN RESERVE University United States 91= Universit?de Montr?l Canada 91= University of HELSINKI Finland 93= Hebrew University of JERUSALEM Israel 93= Ludwig-Maximilians-Universit? M?chen Germany 95 KAIST - Korea Advanced Institute of Scie... Korea, South 96 University of VIRGINIA United States 97 University of PITTSBURGH United States 98 University of CALIFORNIA, Santa Barbara United States 99= PURDUE University United States 99= University of SOUTHAMPTON United Kingdom
2008.10.14 View 15925
KAIST Professor Exposes Structural Dynamics of Protein in Solution -- Dr. Hyot-Cherl Ihee"s 3-Year Research Is Valuable in Pharmaceutical Application Prof. Hyot-Cherl Ihee and his team at the Department of Chemistry, KAIST, has successfully unveiled the structural dynamics of protein in solution as a result of more than three years" research work. Nature Methods, a sister publication of the authoritative science magazine Nature, published the treatise, titled "Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering" in its Sept. 22 online edition. The research paper will be carried in the magazine"s printed version in its October edition, according to Dr. Lee who is its correspondence author. In May 2005, Prof. Ihee successfully photographed the structural dynamics of protein in solid state and his findings were published in the Proceedings of National Academy of Science of the United States. As protein normally exists in human body in solution, not in solid state, he directed his research to developing the technology to capture protein"s dynamics in resolved state. In July that year, Prof. Ihee succeeded in measuring the structural changes of simple organic molecules in real time. He further developed the technology to uncover the structural dynamics of hemoglobin, myoglobin and cytochrome C. Prof. Ihee"s research, helped with the Education-Science-Technology Ministry"s Creative Research Promotion Fund, can be applied to new pharmaceutical development projects as well as nanotechnology development, according to KAIST officials. Prof. Ihee who earned his doctorate at California Institute of Technology in 1994 began teaching at KAIST in 2003. He won the Young Scientist Award given by the Korean government in 2006.
2008.09.22 View 12612
KAIST, GS Caltex Jointly Develop New Bacteria to Produce Biobutanol KAIST and GS Caltex, Korea"s second-largest refiner, have jointly developed a new strain of bacteria to produce biobutanol, which is regarded as a promising next-generation biofuel, KAIST authorities said on Monday (June 2). A research team led by Prof. Sang-Yup Lee of the Chemical and Biomolecular Engineering Department and researchers of GS Caltex succeeded in developing an improved strain of bacteria which enables to produce a large amount of biobutanol in the process of fermenting biomass. The research team has applied for international patent for the new technology. Biomass refers to living and recently dead biological material that can be used as fuel or for industrial production. It usually refers to plant matter grown for use as biofuel, but it also includes plant or animal matter used for production of fibers, chemicals or heat. In the 1970s and 1980s when scientists began researching the possibilities of alternative fuels, bacteria were used in the process of fermenting biomass. This ABE (acetone, butanol, ethanol) fermentation process yields butanol, acetone, and ethanol in a ratio of 6:3:1, respectively. Acetone produced in this process is not usable. The newly developed technology to produce biobutanol has an advantage of lowering production cost by eliminating the process to separate acetone from butanol. This has been made possible by improving the bacteria used for the fermentation in metabolic engineering terms, and producing butanol and ethanol only in a ratio of 6:1, while curbing the generation of acetone. In comparison with bioethanol, also a biofuel mixture which is currently under widespread use in some countries, butanol is more easily transported with gasoline and diesel through pipelines because of its lower tendency to separate from the fuel when contaminated with water. Butanol is also less corrosive than ethanol, another reason its transport through pipeline is preferable. Global interest in full utilization of biomass and development of other alternative energy including biobutanol has deepened in recent years, as crude oil prices have skyrocketed to record levels and climate changes resulting from the excessive use of fossil fuel have been causing various problems around the world.
2008.06.04 View 11771
Cooperation Agreement with Ajou Motor College Cooperation Agreement with Ajou Motor College KAIST Graduate School of Automobile Technology to sign a cooperation agreement with Ajou Motor College KAIST Graduate School of Automobile Technology (GSAT) signed a cooperation agreement with Ajou Motor College (AMC) on July 18th. Under the agreement, the both schools will share education and research facilities and promote mutual cooperation for joint education and researches. Lawmaker Geun-Chan Ryu, KAIST Vice President of Budget & Planning Ji-Won Yang, GSAT Dean Suck-Joo Na, AMC Dean Soo-Hoon Lee, etc. attended the ceremony.
2007.07.24 View 14294
Maximum Yield Amino Acid-Producing Microorganism Developed with use of System Biotechnology Maximum Yield Amino Acid-Producing Microorganism Developed with use of System Biotechnology A team led by Sang-Yup Lee, a distinguished professor of Chemical and Biomolecular Engineering and chair professor of LG Chemical, has succeeded in developing maximum yield L-valine-producing microorganism by using System Biotechnology methods. The research results will be published at the April fourth week (April 23 - 27) edition of the Proceedings of the National Academy of Sciences (PNAS) of the USA. Prof. Lee’s team has developed maximum yield amino acid-producing microorganism (target substance of L-valine, an essential amino-acid) by using microorganism E cell system and simulation methods. His team produced initial producing microorganism by selectively operating necessary parts in colon bacillus genome and excavated preliminary target gene which is to newly be operated through transcriptome analysis using DNA chips. Then they performed a great amount of gene deletion experiment on computer by using MBEL979, E-cells of colon bacillus, and excavated secondary engineering targets. And they finally succeeded in developing maximum yield valine-producing microorganism that can extract 37.8 grams of valine from 100 grams of glucose by applying experiment results to the actual development of microorganism so as to achieve the optimization of metabolic flux in cells, Prof. Lee said, “Since successfully used for the development of microorganism on a systematic system level, system biotechnology methods are expected to significantly contribute to the development of all biotechnology-relevant industries. At the beginning, we had huge obstacles in fusing IT and BT, but my team mates cleverly overcame such obstacles, hence I’m very proud of them.” The producing microorganism and its developing methods are pending international applications (PCT).
2007.04.26 View 13614

KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea T.042-350-2114 F.042-350-2210(2220)