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KAIST proposes alternatives to chemical factories through “iBridge”
- A computer simulation program “iBridge” was developed at KAIST that can put together microbial cell factories quickly and efficiently to produce cosmetics and food additives, and raw materials for nylons - Eco-friendly and sustainable fermentation process to establish an alternative to chemical plants As climate change and environmental concerns intensify, sustainable microbial cell factories garner significant attention as candidates to replace chemical plants. To develop microorganisms to be used in the microbial cell factories, it is crucial to modify their metabolic processes to induce efficient target chemical production by modulating its gene expressions. Yet, the challenge persists in determining which gene expressions to amplify and suppress, and the experimental verification of these modification targets is a time- and resource-intensive process even for experts. The challenges were addressed by a team of researchers at KAIST (President Kwang-Hyung Lee) led by Distinguished Professor Sang Yup Lee. It was announced on the 9th by the school that a method for building a microbial factory at low cost, quickly and efficiently, was presented by a novel computer simulation program developed by the team under Professor Lee’s guidance, which is named “iBridge”. This innovative system is designed to predict gene targets to either overexpress or downregulate in the goal of producing a desired compound to enable the cost-effective and efficient construction of microbial cell factories specifically tailored for producing the chemical compound in demand from renewable biomass. Systems metabolic engineering is a field of research and engineering pioneered by KAIST’s Distinguished Professor Sang Yup Lee that seeks to produce valuable compounds in industrial demands using microorganisms that are re-configured by a combination of methods including, but not limited to, metabolic engineering, synthetic biology, systems biology, and fermentation engineering. In order to improve microorganisms’ capability to produce useful compounds, it is essential to delete, suppress, or overexpress microbial genes. However, it is difficult even for the experts to identify the gene targets to modify without experimental confirmations for each of them, which can take up immeasurable amount of time and resources. The newly developed iBridge identifies positive and negative metabolites within cells, which exert positive and/or negative impact on formation of the products, by calculating the sum of covariances of their outgoing (consuming) reaction fluxes for a target chemical. Subsequently, it pinpoints "bridge" reactions responsible for converting negative metabolites into positive ones as candidates for overexpression, while identifying the opposites as targets for downregulation. The research team successfully utilized the iBridge simulation to establish E. coli microbial cell factories each capable of producing three of the compounds that are in high demands at a production capacity that has not been reported around the world. They developed E. coli strains that can each produce panthenol, a moisturizing agent found in many cosmetics, putrescine, which is one of the key components in nylon production, and 4-hydroxyphenyllactic acid, an anti-bacterial food additive. In addition to these three compounds, the study presents predictions for overexpression and suppression genes to construct microbial factories for 298 other industrially valuable compounds. Dr. Youngjoon Lee, the co-first author of this paper from KAIST, emphasized the accelerated construction of various microbial factories the newly developed simulation enabled. He stated, "With the use of this simulation, multiple microbial cell factories have been established significantly faster than it would have been using the conventional methods. Microbial cell factories producing a wider range of valuable compounds can now be constructed quickly using this technology." Professor Sang Yup Lee said, "Systems metabolic engineering is a crucial technology for addressing the current climate change issues." He added, "This simulation could significantly expedite the transition from resorting to conventional chemical factories to utilizing environmentally friendly microbial factories." < Figure. Conceptual diagram of the flow of iBridge simulation > The team’s work on iBridge is described in a paper titled "Genome-Wide Identification of Overexpression and Downregulation Gene Targets Based on the Sum of Covariances of the Outgoing Reaction Fluxes" written by Dr. Won Jun Kim, and Dr. Youngjoon Lee of the Bioprocess Research Center and Professors Hyun Uk Kim and Sang Yup Lee of the Department of Chemical and Biomolecular Engineering of KAIST. The paper was published via peer-review on the 6th of November on “Cell Systems” by Cell Press. This research was conducted with the support from the Development of Platform Technologies of Microbial Cell Factories for the Next-generation Biorefineries Project (Project Leader: Distinguished Professor Sang Yup Lee, KAIST) and Development of Platform Technology for the Production of Novel Aromatic Bioplastic using Microbial Cell Factories Project (Project Leader: Research Professor So Young Choi, KAIST) of the Korean Ministry of Science and ICT.
NYU-KAIST Global AI & Digital Governance Conference Held
< Photo 1. Opening of NYU-KAIST Global AI & Digital Governance Conference > In attendance of the Minister of Science and ICT Jong-ho Lee, NYU President Linda G. Mills, and KAIST President Kwang Hyung Lee, KAIST co-hosted the NYU-KAIST Global AI & Digital Governance Conference at the Paulson Center of New York University (NYU) in New York City, USA on September 21st, 9:30 pm. At the conference, KAIST and NYU discussed the direction and policies for ‘global AI and digital governance’ with participants of upto 300 people which includes scholars, professors, and students involved in the academic field of AI and digitalization from both Korea and the United States and other international backgrounds. This conference was a forum of an international discussion that sought new directions for AI and digital technology take in the future and gathered consensus on regulations. Following a welcoming address by KAIST President, Kwang Hyung Lee and a congratulatory message from the Minister of Science and ICT, Jong-ho Lee, a panel discussion was held, moderated by Professor Matthew Liao, a graduate of Princeton and Oxford University, currently serving as a professor at NYU and the director at the Center for Bioethics of the NYU School of Global Public Health. Six prominent scholars took part in the panel discussion. Prof. Kyung-hyun Cho of NYU Applied Mathematics and Data Science Center, a KAIST graduate who has joined the ranks of the world-class in AI language models and Professor Jong Chul Ye, the Director of Promotion Council for Digital Health at KAIST, who is leading innovative research in the field of medical AI working in collaboration with major hospitals at home and abroad was on the panel. Additionally, Professor Luciano Floridi, a founding member of the Yale University Center for Digital Ethics, Professor Shannon Vallor, the Baillie Gifford Professor in the Ethics of Data and Artificial Intelligence at the University of Edinburgh of the UK, Professor Stefaan Verhulst, a Co-Founder and the DIrector of GovLab‘s Data Program at NYU’s Tandon School of Engineering, and Professor Urs Gasser, who is in charge of public policy, governance and innovative technology at the Technical University of Munich, also participated. Professor Matthew Liao from NYU led the discussion on various topics such as the ways to to regulate AI and digital technologies; the concerns about how deep learning technology being developed in medicinal purposes could be used in warfare; the scope of responsibilities Al scientists' responsibility should carry in ensuring the usage of AI are limited to benign purposes only; the effects of external regulation on the AI model developers and the research they pursue; and on the lessons that can be learned from the regulations in other fields. During the panel discussion, there was an exchange of ideas about a system of standards that could harmonize digital development and regulatory and social ethics in today’s situation in which digital transformation accelerates technological development at a global level, there is a looming concern that while such advancements are bringing economic vitality it may create digital divides and probles like manipulation of public opinion. Professor Jong-cheol Ye of KAIST (Director of the Promotion Council for Digital Health), in particular, emphasized that it is important to find a point of balance that does not hinder the advancements rather than opting to enforcing strict regulations. < Photo 2. Panel Discussion in Session at NYU-KAIST Global AI & Digital Governance Conference > KAIST President Kwang Hyung Lee explained, “At the Digital Governance Forum we had last October, we focused on exploring new governance to solve digital challenges in the time of global digital transition, and this year’s main focus was on regulations.” “This conference served as an opportunity of immense value as we came to understand that appropriate regulations can be a motivation to spur further developments rather than a hurdle when it comes to technological advancements, and that it is important for us to clearly understand artificial intelligence and consider what should and can be regulated when we are to set regulations on artificial intelligence,” he continued. Earlier, KAIST signed a cooperation agreement with NYU to build a joint campus, June last year and held a plaque presentation ceremony for the KAIST NYU Joint Campus last September to promote joint research between the two universities. KAIST is currently conducting joint research with NYU in nine fields, including AI and digital research. The KAIST-NYU Joint Campus was conceived with the goal of building an innovative sandbox campus centering aroung science, technology, engineering, and mathematics (STEM) combining NYU's excellent humanities and arts as well as basic science and convergence research capabilities with KAIST's science and technology. KAIST has contributed to the development of Korea's industry and economy through technological innovation aiding in the nation’s transformation into an innovative nation with scientific and technological prowess. KAIST will now pursue an anchor/base strategy to raise KAIST's awareness in New York through the NYU Joint Campus by establishing a KAIST campus within the campus of NYU, the heart of New York.
President-Elect Suk-Yeol Yoon Meets and Talks with KAIST Students
President-Elect Yoon stresses science and technology-powered economic growth during his visit to KAIST Korean President-elect Suk-Yeol Yoon stressed that semiconductors are the key strategical industry that will take the lead during the fourth industrial revolution powered by AI and data during a meeting with KAIST graduate students on April 29. President-elect Yoon promised systemic policy support for making science and technology breakthroughs possible and better rewarding young researchers who are devoted to advances in R&D during his meeting at KAIST. Before he met with the students, he toured the National Nanofab Center, which is affiliated with KAIST, and was briefed on the center’s role and responsibilities. President-elect Yoon, who will take office on May 10, said that the best way to ensure prompt growth in Korea’s aging society hinges on advances in science and technology. “All-out investments in science and technology will help us move forward to improve people’s quality of life and lessen the social divide,” he explained. Eight Master’s and PhD candidates majoring in nuclear engineering, AI robotics, semiconductors, electrical engineering, aerospace, and bioengineering attended the meeting with President-elect Yoon. The students asked for help dealing with the challenges they are experiencing while researching and called for deregulation in the process of forming startups. PhD candidate Jae Wan Cho from the Department Nuclear and Quantum Engineering stressed the importance of energy security. He asked for the prompt development of new types of nuclear reactors such as small modular reactors, adding, “Korea has very excellent technologies in nuclear plant construction and parts manufacturing, but lags behind in the new types of nuclear reactors. This sector will develop new energy markets and create synergy along with the shipbuilding industry, which will emerge as new pillars of our export.” Student entrepreneurs such as PhD candidate Kwang Min Kim from the Department of Bio and Brain Engineering and PhD candidate Dong Yoon Shin from the Department of Mechanical and Aerospace Engineering asked for more deregulation in the process of creating startups. PhD candidate Dong Hon Lee from the School of Electrical Engineering pointed out the insecure future caused by the ‘special research fellow system,’ where the number of fellows who have been designated alternative military service has drastically decreased.
DeepTFactor Predicts Transcription Factors
A deep learning-based tool predicts transcription factors using protein sequences as inputs A joint research team from KAIST and UCSD has developed a deep neural network named DeepTFactor that predicts transcription factors from protein sequences. DeepTFactor will serve as a useful tool for understanding the regulatory systems of organisms, accelerating the use of deep learning for solving biological problems. A transcription factor is a protein that specifically binds to DNA sequences to control the transcription initiation. Analyzing transcriptional regulation enables the understanding of how organisms control gene expression in response to genetic or environmental changes. In this regard, finding the transcription factor of an organism is the first step in the analysis of the transcriptional regulatory system of an organism. Previously, transcription factors have been predicted by analyzing sequence homology with already characterized transcription factors or by data-driven approaches such as machine learning. Conventional machine learning models require a rigorous feature selection process that relies on domain expertise such as calculating the physicochemical properties of molecules or analyzing the homology of biological sequences. Meanwhile, deep learning can inherently learn latent features for the specific task. A joint research team comprised of Ph.D. candidate Gi Bae Kim and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at KAIST, and Ye Gao and Professor Bernhard O. Palsson of the Department of Biochemical Engineering at UCSD reported a deep learning-based tool for the prediction of transcription factors. Their research paper “DeepTFactor: A deep learning-based tool for the prediction of transcription factors” was published online in PNAS. Their article reports the development of DeepTFactor, a deep learning-based tool that predicts whether a given protein sequence is a transcription factor using three parallel convolutional neural networks. The joint research team predicted 332 transcription factors of Escherichia coli K-12 MG1655 using DeepTFactor and the performance of DeepTFactor by experimentally confirming the genome-wide binding sites of three predicted transcription factors (YqhC, YiaU, and YahB). The joint research team further used a saliency method to understand the reasoning process of DeepTFactor. The researchers confirmed that even though information on the DNA binding domains of the transcription factor was not explicitly given the training process, DeepTFactor implicitly learned and used them for prediction. Unlike previous transcription factor prediction tools that were developed only for protein sequences of specific organisms, DeepTFactor is expected to be used in the analysis of the transcription systems of all organisms at a high level of performance. Distinguished Professor Sang Yup Lee said, “DeepTFactor can be used to discover unknown transcription factors from numerous protein sequences that have not yet been characterized. It is expected that DeepTFactor will serve as an important tool for analyzing the regulatory systems of organisms of interest.” This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries from the Ministry of Science and ICT through the National Research Foundation of Korea. -Publication Gi Bae Kim, Ye Gao, Bernhard O. Palsson, and Sang Yup Lee. DeepTFactor: A deep learning-based tool for the prediction of transcription factors. (https://doi.org/10.1073/pnas202117118) -Profile Distinguished Professor Sang Yup Lee firstname.lastname@example.org Metabolic &Biomolecular Engineering National Research Laboratory http://mbel.kaist.ac.kr Department of Chemical and Biomolecular Engineering KAIST
Professor Won-Ki Cho Selected as the 2020 SUHF Young Investigator
Professor Won-Ki Cho from the Department of Biological Sciences was named one of three recipients of the 2020 Suh Kyung-Bae Science Foundation (SUHF) Young Investigator Award. The SUHF is a non-profit organization established in 2016 and funded by a personal donation of 300 billion KRW in shares from Chairman and CEO Kyung-Bae Suh of the Amorepacific Group. The primary purpose of the foundation is to serve as a platform to nurture and provide comprehensive long-term support for creative and passionate young Korean scientists committed to pursuing research in the field of life sciences. The SUHF selects three to five scientists through an open recruiting process every year and grants each scientist a maximum of 2.5 billion KRW over a period of up to five years. Since January this year, the foundation received 67 research proposals from scientists across the nation, especially from those who had less than five years of experience as professors, and selected the three recipients. Professor Cho proposed research on how to observe the interactions between nuclear structures and constantly-changing chromatin monomers in four dimensions through ultra-high-resolution imaging of single living cells. This proposal was recognized as one that could help us better understand the process of transcription regulation, which remains a long-standing question in biology. The other awards were given to Professor Soung-hun Roh of Seoul National University and Professor Joo-Hyeon Lee of the University of Cambridge. With these three new awardees, a total of 17 scientists have been named SUHF Young Investigators to date, and the funding to support these scientists now totals 42.5 billion KRW. Professor Inkyung Jung and Professor Ki-Jun Yoon from the Department of Biological Sciences, and Professor Young Seok Ju and Professor Jeong Ho Lee from the Graduate School of Medical Science and Engineering are the four previous winners from KAIST in the years 2017 through 2019. (END)
The World Economic Forum Invites KAIST to 2014 Davos Forum
President Steve Kang and Distinguished Professor Sang Yup Lee have been invited by the World Economic Forum (WEF) to attend its annual meeting slated for January 22-25, 2014 in Davos-Klosters, Switzerland. The president will also join the Global University Leaders Forum (GULF) to be held during the annual meeting. The GULF consists of leading research universities throughout the world, at which President Kang will address agenda related to higher education and research. From September 11th to 13th, KAIST was invited to the WEF’s 2013 Summer Davos Forum held in Dalian, China. The Summer Davos Forum is recognized as a barometer of the world economy, and KAIST hosted three sessions there. In a session titled “Smart Regulations,” Professor Sang Yup Lee hosted presentations and discussions under the topic of “How regulation models can strengthen technical innovation and expansion.” President Steve Kang, Peter Sands, CEO of Standard Chartered Bank Group, Mark Weinberger, CEO of Ernest & Young, and Peter Terium, CEO of RWE, participated in the discussions. The KAIST delegates also presented and participated in a session titled “From Trade Center to Innovative Hub” to discuss how to lead innovations in Asia, as well as “Marine Resources: Finding New Frontier” to address issues of how to develop and manage oceanic resources for potential growth. President Kang said, “The World Economic Forum allows us to introduce the results of our innovative and creative research to global leaders and to demonstrate that our global position continues to grow.” The WEF has been hosting Summer Davos Forum in China since 2007. About 1,500 participants from over 90 countries joined in this year’s summer forum under the theme of “Innovation: Inevitable Mainstream.” New strategies for innovations and solutions for global threats were suggested through presentations and discussions in 125 sessions. The World Economic Forum (WEF) is an independent, international, and non-profit organization based in Geneva, Switzerland. It is committed to improving the state of the world by engaging business, political, academic, and government leaders to shape global, regional and industry agenda. Among the meetings and forums organized by the WEF, its annual meeting held each January in Davos, a.k.a. the Davos Forum, has been the best known gathering. The Davos Forum brings together some 2,500 top business leaders, international political leaders, selected intellectuals and journalists to discuss the most pressing issues facing the world including health and environment.
18th Student Council Elected
The KAIST Herald December 3, 2003 The votes were cast and counted on November 27. Donggodongrak won the election of the 18th Undergraduage Student Council of Korea Advanced Institute of Science and Technology (KAIST). Of the 2,340 eligible voters for the 18th student council election, 1,304 votes, or about 56 percent of the total, were amassed after a full day of election on November 27. The two candidate teams, waiting to hear the result with much anxiety, were juniors Hye-min Kim and Jung-mo Kim running for the president and vice president positions, respectively, of the team "Donggodongrak" and juniors Dong-geun Kim and Yong-jae Yoon running for the same positions, respectively under the name "Woorung Chonggak." Donggodongrak secured over 58 percent of the votes, with 760 supporting ballots, while Woorung Chongak polled 503 votes, or about 39 percent of the votes. Forty-one votes, or three percent of the votes cast were spoiled votes. With more than half the voters having participated, the election was valid, and Donggodongrak was declared the new student council of KAIST. The election platform of the Donggodongrak team largely consist of four themes, composed of several smaller goals. First, they assert the "togetherness" of the student government and plan to achieve it by publishing monthly newsletters, hosting an open outdoor student council every other week, and creating various committees. Secondly, they assert under the theme of an "improving" student government that they will promote festivals and events among the sixteen departments, form an official "class" of the freshmen, and broaden the association of the student representatives. Third, Donggodongrak declares it wants to create an "open and just environment" by holding periodic meetings with the school for direct discussions of school policies; and by taking care of the welfare of the students in detail. Finally, they advocate "a student government that communicates with society"; they will support opportunities to become more aware of various issues of society. President Hye-min Kim, a graduate of Pusan Science High School, has participated in various intramural, socially active groups, and is majoring in applied mathematics. Vice-president Jung-mo Kim is a graduate of Mokpo High School and studies mechanical engineering.
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