THE
-
Professor Jeong-Ho Lee Named the KAISTian of 2018
(Professor Jeong-Ho Lee (right) poses with President Sung-Chul Shin)
Professor Jeong-Ho Lee from the Graduate School of Medical Science and Engineering was selected as the KAISTian of the Year of 2018. The award was established in 2001 and recognizes the most outstanding scholars who have made significant research and scholastic achievements during the year. Professor Lee was awarded during the New Year ceremony held in the auditorium on January 2.
Professor Lee has investigated mutations arising in the brain for decades and has published in renowned journals such as Nature, Nature Medicine, and Cell. Last August, Professor Lee reported breakthrough research on glioblastoma in Nature, giving insight into understanding how the mutation causing glioblastoma starts and suggested novel ways to treat glioblastoma, which was thought to be incurable. (Click for more)
Professor Lee’s Translational Neurogenetics Laboratory lab is investigating innovative diagnostics and therapeutics for untreatable brain disorders including intractable epilepsy and glioblastoma. To commercialize his technology, he established the tech-startup SoVarGen and now works as its CTO.
Professor Lee credited all his lab colleagues and staff. “I know all of this research would not have possible without their sweat and effort. I am happy to receive this honorable award on behalf of them.”
Remembering the beginning of his career at KAIST in 2012, Professor Lee said “KAIST seemed to be a very high and formidable barrier for me, after completing my medical education in Korea. I thank my department professors and colleagues who led me to focus on the research path that I really wanted. They provided everything for my research environment to help make good results.”
“I will continue to strive for promoting the well-being of humanity by addressing various incurable diseases as well as developing novel therapeutics. That will be the way to promote the stature of KAIST at home and abroad,” he added.
2019.01.02 View 4925 -
Professor Baik Awarded Sangsan Young Mathematician Prize
(Professor Hyungryul Baik)
Professor Hyungryul Baik from the Department of Mathematical Sciences was honored as the recipient of the 2018 Sangsan Prize for Young Mathematicians by the Korean Mathematical Society (KMS).
The Sangsan Prize recognizes young mathematicians who finished their degree within the previous five years and have begun an outstanding research career. Professor Baik was recognized for his studies in the fields of low-dimensional topology, geophysical mathematics, and geometric theory. In particular, his Ph.D. dissertation presented a new criterion that completely identifies the hyperbolic surface group, making an inference about the nature of the hyperbolic manifold group.
Recently, Professor Baik co-published a paper entitled Spaces of Invariant Circular Orders of Groups with Professor Eric Samperton at the University of California Santa Barbara in the renowned academic journal Groups, Geometry, and Dynamics in 2018.
Professor Baik earned his BS at KAIST and finished his MS and Ph.D. in mathematics in 2014 at Cornell University. He joined KAIST as a faculty member last year.
2018.10.30 View 5307 -
A Novel Biosensor to Advance Diverse High-Level Production of Microbial Cell Factories
A research group at KAIST presented a novel biosensor which can produce diverse, high-level microbial cell factories. The biosensor monitors the concentration of products and even intermediates when new strains are being developed. This strategy provides a new platform for manufacturing diverse natural products from renewable resources. The team succeeded in creating four natural products of high-level pharmaceutical importance with this strategy.
Malonyl-CoA is a major building block for many value-added chemicals including diverse natural products with pharmaceutical importance. However, due to the low availability of malonyl-CoA in bacteria, many malonyl-CoA-derived natural products have been produced by chemical synthesis or extraction from natural resources that are harmful to the environment and are unsustainable. For the sustainable biological production of malonyl-CoA-derived natural products, increasing the intracellular malonyl-CoA pool is necessary. To this end, the development of a robust and efficient malonyl-CoA biosensor was required to monitor the concentration of intracellular malonyl-CoA abundance as new strains are developed.
Metabolic engineering researchers at KAIST addressed this issue. This research reports the development of a simple and robust malonyl-CoA biosensor by repurposing a type III polyketide synthase (also known as RppA), which produces flaviolin, a colorimetric indicator of malonyl-CoA. Subsequently, the RppA biosensor was used for the rapid and efficient colorimetric screening of gene manipulation targets enabling enhanced malonyl-CoA abundance. The screened beneficial gene targets were employed for the high-level production of four representative natural products derived from malonyl-CoA. Compared with the previous strategies, which were expensive and time-consuming, the new biosensor could be easily applied to industrially relevant bacteria including Escherichia coli, Pseudomonas putida, and Corynebacterium glutamicum to enable a one-step process.
The study employs synthetic small regulatory RNA (sRNA) technology to rapidly and efficiently reduce endogenous target gene expression for improved malonyl-CoA production. The researchers constructed an E. coli genome-scale synthetic sRNA library targeting 1,858 genes covering all major metabolic genes in E. coli. This library was employed with the RppA biosensor to screen for gene targets which are believed to be beneficial for enhancing malonyl-CoA accumulation upon their expression knockdown.
From this colorimetric screening, 14 gene targets were selected, all of which were successful at significantly increasing the production of four natural products (6-methylsalicylic acid, aloesone, resveratrol, and naringenin). Although specific examples are demonstrated in E. coli as a host, the researchers showed that the biosensor is also functional in P. putida and C. glutamicum, industrially important representative gram-negative and gram-positive bacteria, respectively. The malonyl-CoA biosensor developed in this research will serve as an efficient platform for the rapid development of strains capable of producing natural products crucial for the pharmaceutical, chemical, cosmetics, and food industries.
An important aspect of this work is that the high-performance strains constructed in this research were developed rapidly and easily by utilizing the simple approach of colorimetric screening, without involving extensive metabolic engineering approaches. 6-Methylsalicylic acid (an antibiotic) could be produced to the highest titer reported for E. coli, and the microbial production of aloesone (a precursor of aloesin, an anti-inflammatory agent/whitening agent) was achieved for the first time.
“A sustainable process for producing diverse natural products using renewable resources is of great interest. This study represents the development of a robust and efficient malonyl-CoA biosensor generally applicable to a wide range of industrially important bacteria. The capability of this biosensor for screening a large library was demonstrated to show that the rapid and efficient construction of high-performance strains is feasible. This research will be useful for further accelerating the development process of strains capable of producing valuable chemicals to industrially relevant levels,” said Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering, who led the research.
This study entitled “Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria,” was published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) on October 02.
PhD students Dongsoo Yang and Won Jun Kim, MS student Shin Hee Ha, research staff Mun Hee Lee, Research Professor Seung Min Yoo, and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering and Dr. Jong Hyun Choi of the Applied Microbiology Research Center at the Korea Research Institute of Bioscience and Biotechnology (KRIBB) participated in this research.
Figure: Type III polyketide synthase (RppA) as a malonyl-CoA biosensor. RppA converts five molecules of malonyl-CoA into one molecule of red-colored flaviolin. This schematic diagram shows the overall conceptualization of the malonyl-CoA biosensor by indicating that higher malonyl-CoA abundance leads to higher production and secretion of flaviolin, resulting in a deeper red color of the culture. This system was employed for the enhanced production of four representative natural products (6-methylsalicylic acid, aloesone, resveratrol, and naringenin) from engineered E. coli strains.
2018.10.11 View 8497 -
President Shin Presents Opportunities & Challenges of the 4IR at the Summer Davos Forum
(President Shin makes a keynote speech at the 2018 Summer Davos Forum in China on Sept.20.)
KAIST co-hosted the Asia Session with the World Economic Forum during the 2018 Summer Davos Forum in Tianjin, China from September 18 through 20. The session highlighted regional collaboration in Asia to promote inclusive growth in the Fourth Industrial Revolution.
KAIST is working closely with the WEF to take the lead in the Fourth Industrial Revolution. Last July, KAIST established the Fourth Industrial Revolution Information Center (FIRIC) at the KAIST Institute and signed an MOU with the Center for the Fourth Industrial Revolution (C4IR) at the WEF in October. The session is a follow-up event KAIST and the C4IR agreed to last year during the Roundtable Session held in Seoul.
Many experts in new emerging industries as well as many project directors, including Director Murat Sonmez of the C4IR, attended the session KAIST hosted. Director Chizuru Suga at the C4IR in Japan, Director Danil Kerimi in China, and Director Shailesh Sharda in India also attended the session and discussed ways to expand collaboration and networks among the countries.
In his keynote speech at the session on September 20, President Sung-Chul Shin presented how the Korean government is trying to drive the economy by strategically investing in focused industries in the new global industrial environment. President Shin introduced the government’s strategic roadmap to build the competitiveness of emerging technologies such as AI, blockchain, and precision medicine.
He also stressed that the three components of innovation, collaboration, and speed should be prioritized in all sectors for the successful realization of the Fourth Industrial Revolution. For instance, innovation in education, research, and technology commercialization, expansive domestic and international collaboration beyond the private and public sectors, speedy deregulation, and efficient governance will all be critical.
He also said that KAIST will launch new pilot collaboration projects along with the WEF soon. “We paved the way for leading the network with major countries including Japan and India for advancing the Fourth Industrial Revolution through this session,” President Shin said.
2018.09.21 View 6963 -
Engineered E. coli Using Formic Acid and CO2 As a C1-Refinery Platform Strain
(Figure: Formic acid and CO2 assimilation pathways consisting of the reconstructed THF cycle and reverse glycine cleavage reaction. This schematic diagram shows the formic acid and CO2 assimilation procedure through the pathway. Plasmids used in this study and the genetic engineering performed in this study are illustrated.)
A research group at KAIST has developed an engineered E. coli strain that converts formic acid and CO2 to pyruvate and produces cellular energy from formic acid through reconstructed one-carbon pathways. The strategy described in this study provides a new platform for producing value-added chemicals from one-carbon sources.
Formic acid is a carboxylic acid composed of one carbon. Formic acid was produced from CO2 by the chemical method. Recently, the C1 Gas Refinery R&D Center has successfully developed a biological process that produces formic acid from carbon monoxide for the first time. Formic acid is in a liquid state when at room temperature and atmospheric pressure. In addition, it is chemically stable and less toxic, thus, easy to store and transport. Therefore, it can be used as an alternative carbon source in the microbial fermentation process. In order to produce value-added chemicals using formic acid, a metabolic pathway that converts formic acid into cellular molecules composed of multiple carbons is required. However, a metabolic pathway that can efficiently convert formic acid into cellular molecules has not been developed. This acted as an obstacle for the production of value-added chemicals using formic acid
A research group of Ph.D. student Junho Bang and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering addressed this issue. This study, entitled “Assimilation of Formic Acid and CO2 by Engineered Escherichia coli Equipped with Reconstructed One-Carbon Assimilation Pathways”, has been published online in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) on September 18.
There has been increasing interest in utilizing formic acid as an alternative carbon source for the production of value-added chemicals. This research reports the development of an engineered E. coli strain that can convert formic acid and CO2 to pyruvate and produce cellular energy from formic acid through the reconstructed one-carbon pathways.
The metabolic pathway that efficiently converts formic acid and CO2 into pyruvate was constructed by the combined use of the tetrahydrofolate cycle and reverse glycine cleavage reaction. The tetrahydrofolate cycle was reconstructed by utilizing Methylobacterium extorquens formate-THF ligase, methenyl-THF cyclohydrolase, and methylene-THF dehydrogenase. The glycine cleavage reaction was reversed by knocking out the repressor gene (gcvR) and overexpressing the gcvTHP genes that encode enzymes related with the glycine cleavage reaction. Formic acid and CO2 conversion to pyruvate was increased via metabolic engineering of the E. coli strain equipped with the one-carbon assimilation pathway.
In addition, in order to reduce glucose consumption and increase formic acid consumption, Candida boidnii formate dehydrogenase was additionally introduced to construct a cellular energy producing pathway from formic acid. This reduces glucose consumption and increases formic acid consumption.
The reconstructed one-carbon pathways can supply cellular molecules and cellular energies from the formic acid and CO2. Thus, the engineered E. coli strain equipped with the formic acid and CO2 assimilation pathway and cellular energy producing pathway from formic acid showed cell growth from formic acid and CO2 without glucose. Cell growth was monitored and 13C isotope analysis was performed to confirm E. coli growth from the formic acid and CO2. It was found that the engineered E. coli strain sustained cell growth from the formic acid and CO2 without glucose.
Professor Lee said, “To construct the C1-refinery system, a platform strain that can convert one-carbon materials to higher carbon materials needs to be developed. In this report, a one-carbon pathway that can efficiently convert formic acid and CO2 to pyruvate was developed and a cellular energy producing pathway from formic acid was introduced. This resulted in an engineered E. coli strain that can efficiently utilize formic acid as a carbon source while glucose consumption was reduced. The reconstructed one-carbon pathways in this research will be useful for the construction of the C1-refinery system.”
This work was supported by the C1 Gas Refinery Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (NRF-2016M3D3A1A01913250). For further information: Sang Yup Lee, Distinguished Professor of Chemical and Biomolecular Engineering, KAIST (leesy@kaist.ac.kr, Tel: +82-42-350-3930)
2018.09.18 View 5906 -
Photonic Capsules for Injectable Laser Resonators
A KAIST research group presented photonic capsules for injectable laser resonators using microfluidic technology. The capsule’s diameter is comparable to a human hair and stable in gas and liquid media, so it is injectable into any target volume.
The research group headed by Professor Shin-Hyun Kim in the Department of Chemical and Biomolecular Engineering applied an interesting optical property from nature. Professor Kim, who has dived deep into photonic materials research inspired from nature such as the Morpho butterfly, used a trait of beetles this time.
Chrysina gloriosa, commonly known as the glorious beetle, shows a green color similar to leaves when illuminated by left-handed, circularly-polarized light while showing no color with right-handed, circularly-polarized light. This unique optical feature helps the beetles communicate with each other and protects them from predators.
The principle behind this interesting optical property of the beetles relies on helical nanostructures with left-handedness that are present on the shell of the beetles. The helical structures reflect a circularly-polarized light with the same handedness of the helix at the wavelength selected by the helical pitch through optical interference.
Such helical nanostructures can be artificially created using liquid crystals (LCs). LCs with a helical arrangement are referred to as cholesteric LCs (CLCs). The CLCs exhibit the polarization-dependent reflection of light in the same manner as the beetles and have been used for various photonic applications.
In particular, CLCs have been cast to a film format that serves as mirrorless laser resonators, unlike conventional lasing systems. However, the film-type CLCs are large in size and show unidirectional emission, which restricts the use of CLC resonators in microenvironments.
To overcome these limitations, Professor Kim’s group has encapsulated the CLCs with dual shells using microfluidic technology. The inner shell is a water layer that promotes the alignment of LC molecules and the outer shell is an elastic polymer layer that secures capsule stability and enables reversible mechanical deformation. The spherical symmetry of the capsules enables omnidirectional laser emissions. Moreover, laser intensity and lasing direction can be further controlled by deforming the capsules, while its wavelength remains tunable. This new type of CLC laser resonator is promising for laser treatments in various biomedical applications.
Professor Kim said, “The helical nanostructure used in the laser resonator resembles that of the shell of chrysina gloriosa. Humans learn from nature and engineer materials to create something unprecedented.”
This research was led by graduate student Sang Seok Lee and an article entitled “Wavelength-tunable and shape-reconfigurable photonic capsule resonators containing cholesteric liquid crystals” was published online on June 22, in Science Advances.
Figure 1. Chrysina gloriosa illuminated by left-handed (left panel) and right-handed (right panel) circularly-polarized lights.
(Image source: https://doi.org/10.1016/j.cub.2010.05.036 , permitted for reuse in news media)
Figure 2. Composition (left panel) and optical microscopy image (right panel) of the capsule-type laser resonator
2018.07.05 View 8561 -
KAIST Team Reaching Out with Appropriate Technology
(The gold prize winning team of KATT)
The KAIST Appropriate Technology Team (KATT) consisting of international students at KAIST won the gold and silver prizes at ‘The 10th Creative Design Competition for the Other 90 Percent.’
More than 218 students from 50 teams nationwide participated in the competition hosted by the Ministry of Science and ICT last month.
The competition was created to discover appropriate technology and sustainable design items to enhance the quality of life for those with no or few accessible technologies.
A team led by Juan Luis Gonzalez Bello, graduate student from the School of Electrical Engineering received the gold prize for presenting a prosthetic arm. Their artificial arm was highly recognized for its affordability and good manageability. The team said that it cost less than 10 US dollars to construct from materials available in underprivileged regions and was easy to assemble.
Sophomore Hutomo Calvin from the Department of Materials Science & Engineering also worked on the prosthetic arm project with freshmen Bella Godiva, Stephanie Tan, and Koptieuov Yearbola.
Alexandra Tran, senior from the School of Electrical Engineering led the silver prize winning team. Her team developed a portable weather monitor, ‘Breathe Easy’. She worked with Alisher Tortay, senior from the School of Computing, Ashar Alam, senior from the Department of Mechanical Engineering, Bereket Eshete, junior from the School of Computing, and Marthens Hakzimana, sophomore from the Department of Mechanical Engineering.
This weather monitor is a low-cost but efficient air quality monitor. The team said it just cost less than seven US dollars to construct the monitor.KAIST students have now won the gold prize for two consecutive years.
2018.06.19 View 9087 -
Recombinant E. Coli As a Biofactory for the Biosynthesis of Diverse Nanomaterials
(Distinguished Professor Lee and PhD candidate Choi)
A metabolic research group at KAIST and Chung-Ang University in Korea has developed a recombinant E. coli strain that biosynthesizes 60 different nanomaterials covering 35 elements on the periodic table. Among the elements, the team could biosynthesize 33 novel nanomaterials for the first time, advancing the forward design of nanomaterials through the biosynthesis of various single and multi-elements.
The study analyzed the nanomaterial biosynthesis conditions using a Pourbaix diagram to predict the producibility and crystallinity. Researchers studied a Pourbaix diagram to predict the stable chemical species of each element for nanomaterial biosynthesis at varying levels of reduction potential (Eh) and pH. Based on the Pourbaix diagram analyses, the initial pH of the reaction was changed from 6.5 to 7.5, resulting in the biosynthesis of various crystalline nanomaterials that were previously amorphous or not synthesized.
This strategy was extended to biosynthesize multi-element nanomaterials. Various single and multi-element nanomaterials biosynthesized in this research can potentially serve as new and novel nanomaterials for industrial applications such as catalysts, chemical sensors, biosensors, bioimaging, drug delivery, and cancer therapy.
A research group consisting of PhD candidate Yoojin Choi, Associate Professor Doh Chang Lee, and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at KAIST and Associate Professor Tae Jung Park of the Department of Chemistry at Chung-Ang University reported the synthesis. This study, entitled “Recombinant Escherichia coli as a biofactory for various single- and multi-element nanomaterials,” was published online in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) on May 21.
A recent successful biosynthesis of nanomaterials under mild conditions without requiring physical and chemical treatments has triggered the exploration of the full biosynthesis capacity of a biological system for producing a diverse range of nanomaterials as well as for understanding biosynthesis mechanisms for crystalline versus amorphous nanomaterials.
There has been increased interest in synthesizing various nanomaterials that have not yet been synthesized for various applications including semiconducting materials, enhanced solar cells, biomedical materials, and many others. This research reports the construction of a recombinant E. coli strain that co-expresses metallothionein, a metal binding protein, and phytochelatin synthase that synthesizes the metal-binding peptide phytochelatin for the biosynthesis of various nanomaterials. Subsequently, an E. coli strain was engineered to produce a diverse range of nanomaterials, including those never biosynthesized before, by using 35 individual elements from the periodic table and also by combining multi-elements.
Distinguished Professor Lee said, “An environmentally-friendly and sustainable process is of much interest for producing nanomaterials by not only chemical and physical methods but biological synthesis. Moreover, there has been much attention paid to producing diverse and novel nanomaterials for new industrial applications. This is the first report to predict the biosynthesis of various nanomaterials, by far the largest number of various single- and multi-elements nanomaterials. The strategies used for nanomaterial biosynthesis in this research will be useful for further diversifying the portfolio of nanomaterials that can be manufactured.”
Figure: The biosynthesis of diverse nanomaterials using recombinant E. coli. This schematic diagram shows the overall conceptualization of the biosynthesis of various single and multi-element nanomaterials using recombinant E. coli under incubation with corresponding elemental precursors. The 35 elements that were tested to biosynthesize nanomaterials are shown in black circles on the periodic table.
2018.05.23 View 10293 -
Professor Hee-Sung Park Named Scientist of May
(Professor Hee-Sung Park)
Professor Hee-Sung Park from the Department of Chemistry was named ‘Scientist of May’ sponsored by the Ministry of Science and ICT and the National Research Foundation of Korea. Professor Park was honored in recognition of his developing a tool to engineer designer proteins via diverse chemical modifications. This approach provides a novel platform for investigating numerous diseases such as cancer and dementia.
His research focuses on the production of synthetic proteins and the generation of diverse protein functions as well as the designing and engineering of new translation machinery for genetic code expansion, and the application of synthetic biology techniques for basic cell biology and applied medical science.
Post-translational modifications (PTMs) are constantly taking place during or after protein biosynthesis. PTMs play a vital role in expanding protein functional diversity and, as a result, critically affect numerous biological processes. Abnormal PTMs have been known to trigger various diseases including cancer and dementia. Therefore, this technology enables proteins to reproduce with specific modifications at selected residues and will significantly help establish experimental strategies to investigate fundamental biological mechanisms including the development of targeted cancer therapies.
Professor Park also received 10 million KRW in prize money.
2018.05.04 View 8182 -
Escalation of Competition Leads to Conflict in Competitive Networks of F1 Drivers
(Professor Wonjae Lee at the Graduate School of Culture Technology)
A new study has revealed that people with similar social status in similar age groups are more likely to clash with each other. This rivalry could likely lead to taking more risks in fair weather conditions.
Competition, while is often seen as beneficial, can escalate into destructive conflict. This occurs, for instance, when athletes sabotage each other or when rival executives get caught up in a career-derailing fight. These escalations, which lead to conflict, are especially likely among similar-status competitors, who are fraught with discordant understandings of who is superior to whom.
A research team of KAIST, the US Treasury, INSEAD, and the European School of Management and Technology (ESMT) examined the link between status similarity and conflict as well as the conditions under which this link holds by using panel data on Formula 1 races from 1970 through 2014. For the study, the research team analyzed a total of 506 collision cases by 355 F1 drivers over 45 years.
The team found that similar-status F1 drivers are more prone to collide, especially when they are age-similar, performing well, and feeling safe. When these boundary conditions are met, structural equivalence likely triggers antagonism among interactants.
This research deepens the understanding of when violent conflict emerges and when prevention efforts are called for. Professor Lee from the Graduate School of Culture Technology at KAIST said, “People are not sure about their identity when facing competitors of a similar status. People tend to confirm their own stature by beating an opponent.”
The team investigated the factors that escalate competition into dangerous conflict. Recently, sociological theorizing claims that such escalations are particularly likely in pairs of structurally equivalent actors who have the same relations with the same third parties. Using the F1 data, the research team modeled the probability that two drivers would collide on a racetrack as a function of their structural equivalence in a dynamic network of competitive relationships.
Professor Lee added, “We fully understand that the drivers who ranked first and second are likely to have more conflict because they meet more frequently and know each other well. We also regulated all those conditions and confirmed that our hypothesis worked right throughout the data analysis.”
Professor Lee, who wrote his doctoral thesis on tennis tournaments for identifying the ideal organizational structure, said that sports tournaments would be best optimized for comprehending the nature of organizational structures. Tournaments, even those with rankings based on objective criteria, are in fact intensely social. However, most prior empirical work in this area has relied only on official information on competitors’ performance, thus failing to capture the important elements of past competitive encounters.
“It is not so easy to obtain data on rivalries and conflicts inside an organization. However, in sports, the performances of athletes are all recorded and the data can be utilized as a very objective methodology for understanding social relations and their structural affects.
Official positions in tournaments, although clearly informative, can also be reductionist –excluding the emotionally salient features of competitors’ histories and forcing competitors together on a scalar metric, even when the competitors themselves do not see each other as comparable.
The results from sample-split models are important for social networking research, which has paid scant attention to the contextual conditions in which structural equivalence is most consequential for social action – especially hostile social actions.
The study suggests that new work will benefit from examining how demographic overlap, network stability, and perceived costs of conflict “activate” a structurally equivalent relationship to the point that it is not only salient but also conducive to conflict.
Professor Lee said, “Sociology mainly investigates the positive results of social success and collaboration. This study shows that any violent activities, including homicide, also have something to do with organizational and social structural equivalence.”
This study was co-led by Professor Matthew Bothner from ESMT in Germany, Professor Henning Piezunk from INSEAD in France, and Dr. Richard Haynes from the US Treasury and was featured at the PNAS (Proceedings of the National Academy of Sciences of the USA) in March.
(Figure: Drivers' competitive network and collisions. Nodes are drivers. Nodes enricled in black are labeled by name. Edges denote joint competition in at least one race. Red edges connecting indicate that the two drivers collided at least once. Using Fruchtermna-Reingold, nodes are generally proximte to the extendt that their average structural equivalence (over all races, from 1970 to 2014) is high.)
2018.04.24 View 6639 -
Deep Learning Predicts Drug-Drug and Drug-Food Interactions
A Korean research team from KAIST developed a computational framework, DeepDDI, that accurately predicts and generates 86 types of drug-drug and drug-food interactions as outputs of human-readable sentences, which allows in-depth understanding of the drug-drug and drug-food interactions.
Drug interactions, including drug-drug interactions (DDIs) and drug-food constituent interactions (DFIs), can trigger unexpected pharmacological effects, including adverse drug events (ADEs), with causal mechanisms often unknown. However, current prediction methods do not provide sufficient details beyond the chance of DDI occurrence, or require detailed drug information often unavailable for DDI prediction.
To tackle this problem, Dr. Jae Yong Ryu, Assistant Professor Hyun Uk Kim and Distinguished Professor Sang Yup Lee, all from the Department of Chemical and Biomolecular Engineering at Korea Advanced Institute of Science and Technology (KAIST), developed a computational framework, named DeepDDI, that accurately predicts 86 DDI types for a given drug pair. The research results were published online in Proceedings of the National Academy of Sciences of the United States of America (PNAS) on April 16, 2018, which is entitled “Deep learning improves prediction of drug-drug and drug-food interactions.”
DeepDDI takes structural information and names of two drugs in pair as inputs, and predicts relevant DDI types for the input drug pair. DeepDDI uses deep neural network to predict 86 DDI types with a mean accuracy of 92.4% using the DrugBank gold standard DDI dataset covering 192,284 DDIs contributed by 191,878 drug pairs. Very importantly, DDI types predicted by DeepDDI are generated in the form of human-readable sentences as outputs, which describe changes in pharmacological effects and/or the risk of ADEs as a result of the interaction between two drugs in pair. For example, DeepDDI output sentences describing potential interactions between oxycodone (opioid pain medication) and atazanavir (antiretroviral medication) were generated as follows: “The metabolism of Oxycodone can be decreased when combined with Atazanavir”; and “The risk or severity of adverse effects can be increased when Oxycodone is combined with Atazanavir”. By doing this, DeepDDI can provide more specific information on drug interactions beyond the occurrence chance of DDIs or ADEs typically reported to date.
DeepDDI was first used to predict DDI types of 2,329,561 drug pairs from all possible combinations of 2,159 approved drugs, from which DDI types of 487,632 drug pairs were newly predicted. Also, DeepDDI can be used to suggest which drug or food to avoid during medication in order to minimize the chance of adverse drug events or optimize the drug efficacy. To this end, DeepDDI was used to suggest potential causal mechanisms for the reported ADEs of 9,284 drug pairs, and also predict alternative drug candidates for 62,707 drug pairs having negative health effects to keep only the beneficial effects. Furthermore, DeepDDI was applied to 3,288,157 drug-food constituent pairs (2,159 approved drugs and 1,523 well-characterized food constituents) to predict DFIs. The effects of 256 food constituents on pharmacological effects of interacting drugs and bioactivities of 149 food constituents were also finally predicted. All these prediction results can be useful if an individual is taking medications for a specific (chronic) disease such as hypertension or diabetes mellitus type 2.
Distinguished Professor Sang Yup Lee said, “We have developed a platform technology DeepDDI that will allow precision medicine in the era of Fourth Industrial Revolution. DeepDDI can serve to provide important information on drug prescription and dietary suggestions while taking certain drugs to maximize health benefits and ultimately help maintain a healthy life in this aging society.”
Figure 1. Overall scheme of Deep DDDI and prediction of food constituents that reduce the in vivo concentration of approved drugs
2018.04.18 View 10318 -
Scientist of March, Professor Hee-Seung Lee
(Professor Hee-Seung Lee)
Professor Hee-Seung Lee from the Department of Chemistry at KAIST received the ‘Science and Technology Award of the Month’ awarded by the Ministry of ICT and Science, and the National Research Foundation of Korea for March 2018.
Professor Lee has been recognized for successfully producing peptide-based molecular machines, which used to be made of metals.
The methodology can be translated into magnetotactic behavior at the macroscopic scale, which is reminiscent of magnetosomes in magnetotactic bacteria.
The team employed foldectures, self-assembled molecular architectures of β-peptide foldamers, to develop the peptide-based molecular machines that uniformly align with respect to an applied static magnetic field.
Professor Lee said, “Molecular machines are widely used in the field of medical engineering or material science; however, there were limitations for developing the machines using magnetic fields. By developing peptide-based molecular machines, we were able to develop body-friendly molecular machines.”
Every month, the Ministry of ICT and Science and the National Research Foundation of Korea award a cash prize worth 10,000,000 KRW to a scientist who has contributed to science and technology with outstanding research and development performance.
2018.03.15 View 7819