Expanding the Biosynthetic Pathway via Retrobiosyn..
- Researchers reports a new strategy for the microbial production of multiple short-chain primary amines via retrobiosynthesis. - KAIST metabolic engineers presented the bio-based production of multiple short-chain primary amines that have a wide range of applications in chemical industries for the first time. The research team led by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering designed the novel biosynthetic pathways for short-chain primary amines by combining retrobiosynthesis and a precursor selection step. The research team verified the newly designed pathways by confirming the in vivo production of 10 short-chain primary amines by supplying the precursors. Furthermore, the platform Escherichia coli strains were metabolically engineered to produce three proof-of-concept short-chain primary amines from glucose, demonstrating the possibility of the bio-based production of diverse short-chain primary amines from renewable resources. The research team said this study expands the strategy of systematically designing biosynthetic pathways for the production of a group of related chemicals as demonstrated by multiple short-chain primary amines as examples. Currently, most of the industrial chemicals used in our daily lives are produced with petroleum-based products. However, there are several serious issues with the petroleum industry such as the depletion of fossil fuel reserves and environmental problems including global warming. To solve these problems, the sustainable production of industrial chemicals and materials is being explored with microorganisms as cell factories and renewable non-food biomass as raw materials for alternative to petroleum-based products. The engineering of these microorganisms has increasingly become more efficient and effective with the help of systems metabolic engineering – a practice of engineering the metabolism of a living organism toward the production of a desired metabolite. In this regard, the number of chemicals produced using biomass as a raw material has substantially increased. Although the scope of chemicals that are producible using microorganisms continues to expand through advances in systems metabolic engineering, the biological production of short-chain primary amines has not yet been reported despite their industrial importance. Short-chain primary amines are the chemicals that have an alkyl or aryl group in the place of a hydrogen atom in ammonia with carbon chain lengths ranging from C1 to C7. Short-chain primary amines have a wide range of applications in chemical industries, for example, as a precursor for pharmaceuticals (e.g., antidiabetic and antihypertensive drugs), agrochemicals (e.g., herbicides, fungicides and insecticides), solvents, and vulcanization accelerators for rubber and plasticizers. The market size of short-chain primary amines was estimated to be more than 4 billion US dollars in 2014. The main reason why the bio-based production of short-chain primary amines was not yet possible was due to their unknown biosynthetic pathways. Therefore, the team designed synthetic biosynthetic pathways for short-chain primary amines by combining retrobiosynthesis and a precursor selection step. The retrobiosynthesis allowed the systematic design of a biosynthetic pathway for short-chain primary amines by using a set of biochemical reaction rules that describe chemical transformation patterns between a substrate and product molecules at an atomic level. These multiple precursors predicted for the possible biosynthesis of each short-chain primary amine were sequentially narrowed down by using the precursor selection step for efficient metabolic engineering experiments. “Our research demonstrates the possibility of the renewable production of short-chain primary amines for the first time. We are planning to increase production efficiencies of short-chain primary amines. We believe that our study will play an important role in the development of sustainable and eco-friendly bio-based industries and the reorganization of the chemical industry, which is mandatory for solving the environmental problems threating the survival of mankind,” said Professor Lee. This paper titled “Microbial production of multiple short-chain primary amines via retrobiosynthesis” was published in Nature Communications. 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 (NRF) of Korea. < Biosynthetic reactions constructed in E. coli for the in vivo production of 12 SCPAs. These 12 SCPAs were the ones shown to be produced by valine decarboxylase (VlmD) in vitro (dotted boxes). Amine and carboxylic groups shown in each dotted box are presented with yellow and green circles, respectively. Reaction center carbon atoms that are subject to chemical transformations are marked with asterisks. Glycolysis is indicated with a red background, which leads to the biosynthesis of 12 amino acid precursors. Multiple reactions are presented with two or more arrows. > -Publication Dong In Kim, Tong Un Chae, Hyun Uk Kim, Woo Dae Jang, and Sang Yup Lee. Microbial production of multiple short-chain primary amines via retrobiosynthesis. Nature Communications ( https://www.nature.com/articles/s41467-020-20423-6) -Profile Distinguished Professor Sang Yup Lee leesy＠kaist.ac.kr Metabolic &Biomolecular Engineering National Research Laboratory http://mbel.kaist.ac.kr Department of Chemical and Biomolecular Engineering KAIST
KAIST Mobile Clinic Module to Fill Negative Pressu..
Efficient versatile ready-for-rapid building system of MCM will serve as both a triage unit and bridge center in emergency medical situations < The view of ready-for-rapid-production negative pressure room called a Mobile Clinic Module (MCM) developed by KAIST. > A team from KAIST has developed a low-cost and ready-for-rapid-production negative pressure room called a Mobile Clinic Module (MCM). The MCM is expandable, moveable, and easy to store through a combination of negative pressure frames, air tents, and multi-function panels. The MCM expects to quickly meet the high demand for negative pressure beds in the nation and eventually many other countries where the third wave of COVID-19 is raging. The module is now ready to be rolled out after a three-week test period at the Korea Cancer Center Hospital. Professor Tek-Jin Nam’s team swung into action, rapidly working together with researchers, engineers with expertise in mechanical design, and a team of clinical doctors to complete the MCM as one of KAIST’s New Deal R&D initiatives launched last July. Professor Nam cites ‘expandability’ as the key feature of the MCM. Eventually, it will serve as both a triage unit and bridge center in emergency medical situations. “The module is a very efficient and versatile unit building system. It takes approximately two hours to build the basic MCM unit, which comprises four negative pressure bed rooms, nurse’s station, locker room, and treatment room. We believe this will significantly contribute to relieving the drastic need for negative pressure beds and provide a place for monitoring patients with moderate symptoms,” said Professor Nam. “It will also be helpful for managing less-severe patients who need to be monitored daily in quarantined rooms or as bridge stations where on-site medical staff can provide treatment and daily monitoring before hospitalization. These wards can be efficiently deployed either inside or outside existing hospitals.” The research team specially designed the negative pressure frame to ensure safety level A for the negative pressure room, which is made of a multi-function panel wall and roofed with an air tent. The multi-function panels can hold medical appliances such as ventilators, oxygen and bio-signal monitors. Positive air pressure devices supply fresh air from outside the tent. An air pump and controller maintain air beam pressure, while filtering exhausted air. An internal air information monitoring system efficiently controls room air pressure and purifies the air. While a conventional negative pressure bed is reported to cost approximately 3.5 billion KRW (50 billion won for a ward), this module is estimated to cost 0.75 billion won each (10 billion won for a ward), cutting the costs by approximately 80％. The MCM is designed to be easily transported and relocated due to its volume, weight, and maintainability. This module requires only one-fourth of the volume of existing wards and takes up approximately 40％ of their weight. The unit can be transported in a 40-foot container truck. “We believe this will significantly contribute to relieving the drastic need for negative pressure beds and provide a place for monitoring patients with moderate symptoms. We look forward to the MCM upgrading epidemic management resources around the world.” Professor Nam’s team is also developing antiviral solutions and devices such as protective gear, sterilizers, and test kits under the KAIST New Deal R&D Initiative that was launched to promptly and proactively respond to the epidemic. More than 45 faculty members and researchers at KAIST are collaborating with industry and clinical hospitals to develop the antiviral technology that will improve preventive measures, diagnoses, and treatment.
A Biological Strategy Reveals How Efficient Brain ..
- A KAIST team’s mathematical modelling shows that the topographic tiling of cortical maps originates from bottom-up projections from the periphery. - Researchers have explained how the regularly structured topographic maps in the visual cortex of the brain could arise spontaneously to efficiently process visual information. This research provides a new framework for understanding functional architectures in the visual cortex during early developmental stages. A KAIST research team led by Professor Se-Bum Paik from the Department of Bio and Brain Engineering has demonstrated that the orthogonal organization of retinal mosaics in the periphery is mirrored onto the primary visual cortex and initiates the clustered topography of higher visual areas in the brain. This new finding provides advanced insights into the mechanisms underlying a biological strategy of brain circuitry for the efficient tiling of sensory modules. The study was published in Cell Reports on January 5. In higher mammals, the primary visual cortex is organized into various functional maps for neural tuning such as ocular dominance, orientation selectivity, and spatial frequency selectivity. Correlations between the topographies of different maps have been observed, implying their systematic organizations for the efficient tiling of sensory modules across cortical areas. These observations have suggested that a common principle for developing individual functional maps may exist. However, it has remained unclear how such topographical organizations could arise spontaneously in the primary visual cortex of various species. The research team found that the orthogonal organization in the primary visual cortex of the brain originates from the spatial organization in bottom-up feedforward projections. The team showed that an orthogonal relationship among sensory modules already exists in the retinal mosaics, and that this is mirrored onto the primary visual cortex to initiate the clustered topography. By analyzing the retinal ganglion cell mosaics data in cats and monkeys, the researchers found that the structure of ON-OFF feedforward afferents is organized into a topographic tiling, analogous to the orthogonal intersection of cortical tuning maps. Furthermore, the team’s analysis of previously published data collected on cats also showed that the ocular dominance, orientation selectivity, and spatial frequency selectivity in the primary visual cortex are correlated with the spatial profiles of the retinal inputs, implying that efficient tiling of cortical domains can originate from the regularly structured retinal patterns. Professor Paik said, “Our study suggests that the structure of the periphery with simple feedforward wiring can provide the basis for a mechanism by which the early visual circuitry is assembled.” He continued, “This is the first report that spatially organized retinal inputs from the periphery provide a common blueprint for multi-modal sensory modules in the visual cortex during the early developmental stages. Our findings would make a significant impact on our understanding the developmental strategy of brain circuitry for efficient sensory information processing.” This work was supported by the National Research Foundation of Korea (NRF). < Figure 1. The image depicts the retinal origin of functional maps of neural tuning in visual cortex. > < Figure 2. The image depicts the orthogonal intersection of cortical tuning maps that are initiated by the topographic tiling of retinal ganglion cell mosaics. > < Figure 3. The regularly structured retinal circuits provide a blueprint of the clustered topography of multiple tuning maps in the primary visual cortex. > Image credit: Professor Se-Bum Paik, KAIST Image usage restrictions: News organizations may use or redistribute this image, with proper attribution, as part of news coverage of this paper only. Publication: Song, M, et al. (2021) Projection of orthogonal tiling from the retina to the visual cortex. Cell Reports 34, 108581. Available online at https://doi.org/10.1016/j.celrep.2020.108581 Profile: Se-Bum Paik, Ph.D Assistant Professor sbpaik＠kaist.ac.kr http://vs.kaist.ac.kr/ VSNN Laboratory Department of Bio and Brain Engineering Program of Brain and Cognitive Engineering http://kaist.ac.kr Korea Advanced Institute of Science and Technology (KAIST) Daejeon, Republic of Korea Profile: Min Song Ph.D. Candidate night＠kaist.ac.kr Program of Brain and Cognitive Engineering Profile: Jaeson Jang, Ph.D. Researcher jaesonjang＠kaist.ac.kr Department of Bio and Brain Engineering, KAIST (END)
Professor Poong Hyun Seong Elected INSC Chair
< Professor Emeritus Poong Hyun Seong > Professor Emeritus Poong Hyun Seong from the Department of Nuclear and Quantum Engineering was elected as the Chairman of the International Nuclear Societies Council (INSC). His two-year term began on January 1. The INSC is an organization made up of nuclear societies all over the world, representing more than 80,000 nuclear professionals. The INSC founded in 1990 acts as a global forum to establish common goals of nuclear power usage, delivering the views and ideas of professionals throughout their regional societies. The INSC has advocated for nuclear power to be deemed an indispensable clean energy resources that can mitigate the climate change. The council has engaged in public awareness and publicity activities promoting the advantages of nuclear energy for developing next-generation power plants such as small nuclear reactors, local heating system, seawater desalination, and fair production of energy. Professor Seong is a globally renowned scholar in the fields of nuclear instrumentation control and human factor engineering. He retired last year after 30-year career at KAIST. He took on leadership roles in the Korea Nuclear Society and served as a member of the Korea Nuclear Safety and Security Commission as well as Atomic Energy Commission. A fellow at the America Nuclear Society, Professor Seong served as the first vice chair of the INSC and he received the Don Miller Award in 2019. The award established in 2009 by the American Nuclear Society in honor of former ANS President Don Miller is given to an individual who has made a significant contribution to the advancement of nuclear instrumentation and control of human-machine interfaces. He led the leadership role to help the Korean government steered into efficient and reasonable energy policymaking. More recently, as the Korean government decided to abandon nuclear energy, he actively opposed the government’s pivot. Professor Seong said, “Advanced countries like the US, UK, France, and Japan push forward the production of renewable energy by driving nuclear power plant under their pledges toward carbon neutrality by 2050. However, we are very concerned about the government’s policy shift to decrease the number of nuclear power plants while increasing the fossil fuel usage. I don’t think we can realize carbon neutrality by 2050 with the current policy.” (END)
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. < Figure: The network architecture of DeepTFactor. An input protein sequence is processed using three parallel subnetworks. > -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 leesy＠kaist.ac.kr Metabolic &Biomolecular Engineering National Research Laboratory http://mbel.kaist.ac.kr Department of Chemical and Biomolecular Engineering KAIST
Extremely Stable Perovskite Nanoparticles Films fo..
< Figure 1:Photographs of large-area siloxane-encapsulated perovskite nanoparticle films. The left one indicates the perfect color converting property on commercial mobile phone screens. The right one presents color converted films under versatile bending states. > Researchers have reported an extremely stable cross-linked perovskite nanoparticle that maintains a high photoluminescence quantum yield (PLQY) for 1.5 years in air and harsh liquid environments. This stable material’s design strategies, which addressed one of the most critical problems limiting their practical application, provide a breakthrough for the commercialization of perovskite nanoparticles in next-generation displays and bio-related applications. According to the research team led by Professor Byeong-Soo Bae, their development can survive in severe environments such as water, various polar solvents, and high temperature with high humidity without additional encapsulation. This development is expected to enable perovskite nanoparticles to be applied to high color purity display applications as a practical color converting material. This result was published as the inside front cover article in Advanced Materials. Perovskites, which consist of organics, metals, and halogen elements, have emerged as key elements in various optoelectronic applications. The power conversion efficiency of photovoltaic cells based on perovskites light absorbers has been rapidly increased. Perovskites are also great promise as a light emitter in display applications because of their low material cost, facile wavelength tunability, high (PLQY), very narrow emission band width, and wider color gamut than inorganic semiconducting nanocrystals and organic emitters. Thanks to these advantages, perovskites have been identified as a key color-converting material for next-generation high color-purity displays. In particular, perovskites are the only luminescence material that meets Rec. 2020 which is a new color standard in display industry. However, perovskites are very unstable against heat, moisture, and light, which makes them almost impossible to use in practical applications. To solve these problems, many researchers have attempted to physically prevent perovskites from coming into contact with water molecules by passivating the perovskite grain and nanoparticle surfaces with organic ligands or inorganic shell materials, or by fabricating perovskite-polymer nanocomposites. These methods require complex processes and have limited stability in ambient air and water. Furthermore, stable perovskite nanoparticles in the various chemical environments and high temperatures with high humidity have not been reported yet. The research team in collaboration with Seoul National University develops siloxane-encapsulated perovskite nanoparticle composite films. Here, perovskite nanoparticles are chemically crosslinked with thermally stable siloxane molecules, thereby significantly improving the stability of the perovskite nanoparticles without the need for any additional protecting layer. Siloxane-encapsulated perovskite nanoparticle composite films exhibited a high PLQY (> 70％) value, which can be maintained over 600 days in water, various chemicals (alcohol, strong acidic and basic solutions), and high temperatures with high humidity (85℃/85％). The research team investigated the mechanisms impacting the chemical crosslinking and water molecule-induced stabilization of perovskite nanoparticles through various photo-physical analysis and density-functional theory calculation. The research team confirmed that displays based on their siloxane-perovskite nanoparticle composite films exhibited higher PLQY and a wider color gamut than those of Cd-based quantum dots and demonstrated perfect color converting properties on commercial mobile phone screens. Unlike what was commonly believed in the halide perovskite field, the composite films showed excellent bio-compatibility because the siloxane matrix prevents the toxicity of Pb in perovskite nanoparticle. By using this technology, the instability of perovskite materials, which is the biggest challenge for practical applications, is greatly improved through simple encapsulation method. “Perovskite nanoparticle is the only photoluminescent material that can meet the next generation display color standard. Nevertheless, there has been reluctant to commercialize it due to its moisture vulnerability. The newly developed siloxane encapsulation technology will trigger more research on perovskite nanoparticles as color conversion materials and will accelerate early commercialization,” Professor Bae said. This work was supported by the Wearable Platform Materials Technology Center (WMC) of the Engineering Research Center (ERC) Project, and the Leadership Research Program funded by the National Research Foundation of Korea. < Figure 2. Schematic illustration of the water-induced stabilization of siloxane-encapsulated perovskite nanoparticles. > -Publication: Junho Jang, Young-Hoon Kim, Sunjoon Park, Dongsuk Yoo, Hyunjin Cho, Jinhyeong Jang, Han Beom Jeong, Hyunhwan Lee, Jong Min Yuk, Chan Beum Park, Duk Young Jeon, Yong-Hyun Kim, Byeong-Soo Bae, and Tae-Woo Lee. “Extremely Stable Luminescent Crosslinked Perovskite Nanoparticles under Harsh Environments over 1.5 Years” Advanced Materials, 2020, 2005255. https://doi.org/10.1002/adma.202005255. Link to download the full-text paper: https://onlinelibrary.wiley.com/doi/10.1002/adma.202005255 -Profile: Prof. Byeong-Soo Bae (Corresponding author) bsbae＠kaist.ac.kr Lab. of Optical Materials & Coating Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST)
A Comprehensive Review of Biosynthesis of Inorgani..
< Distinguished Professor Lee and Dr. Yoojin Choi > There are diverse methods for producing numerous inorganic nanomaterials involving many experimental variables. Among the numerous possible matches, finding the best pair for synthesizing in an environmentally friendly way has been a longstanding challenge for researchers and industries. A KAIST bioprocess engineering research team led by Distinguished Professor Sang Yup Lee conducted a summary of 146 biosynthesized single and multi-element inorganic nanomaterials covering 55 elements in the periodic table synthesized using wild-type and genetically engineered microorganisms. Their research highlights the diverse applications of biogenic nanomaterials and gives strategies for improving the biosynthesis of nanomaterials in terms of their producibility, crystallinity, size, and shape. The research team described a 10-step flow chart for developing the biosynthesis of inorganic nanomaterials using microorganisms and bacteriophages. The research was published at Nature Review Chemistry as a cover and hero paper on December 3. “We suggest general strategies for microbial nanomaterial biosynthesis via a step-by-step flow chart and give our perspectives on the future of nanomaterial biosynthesis and applications. This flow chart will serve as a general guide for those wishing to prepare biosynthetic inorganic nanomaterials using microbial cells,” explained Dr.Yoojin Choi, a co-author of this research. Most inorganic nanomaterials are produced using physical and chemical methods and biological synthesis has been gaining more and more attention. However, conventional synthesis processes have drawbacks in terms of high energy consumption and non-environmentally friendly processes. Meanwhile, microorganisms such as microalgae, yeasts, fungi, bacteria, and even viruses can be utilized as biofactories to produce single and multi-element inorganic nanomaterials under mild conditions. After conducting a massive survey, the research team summed up that the development of genetically engineered microorganisms with increased inorganic-ion-binding affinity, inorganic-ion-reduction ability, and nanomaterial biosynthetic efficiency has enabled the synthesis of many inorganic nanomaterials. Among the strategies, the team introduced their analysis of a Pourbaix diagram for controlling the size and morphology of a product. The research team said this Pourbaix diagram analysis can be widely employed for biosynthesizing new nanomaterials with industrial applications.Professor Sang Yup Lee added, “This research provides extensive information and perspectives on the biosynthesis of diverse inorganic nanomaterials using microorganisms and bacteriophages and their applications. We expect that biosynthetic inorganic nanomaterials will find more diverse and innovative applications across diverse fields of science and technology.” Dr. Choi started this research in 2018 and her interview about completing this extensive research was featured in an article at Nature Career article on December 4. < Single- and two-element map of inorganic nanomaterials biosynthesized using microbial cells and bacteriophages. Fifty-one elements (excluding H, C, N and O) have been used in inorganic nanomaterial synthesis using microbial cells and bacteriophages. White spaces indicate that biosynthesis of inorganic nanomaterials comprising the corresponding elements has not yet been reported. Red denotes unary or binary metal/non-metal nanomaterials that have been biosynthesized. Dark blue denotes metal/non-metal oxides that have been biosynthesized. Light blue indicates biosynthesized metal hydroxides. Light purple indicates that metal/non-metal phosphates have been biosynthesized. Orange indicates that metal carbonates have been biosynthesized. All inorganic nanomaterials biosynthesized using microbial cells and bacteriophages are listed in the paper. > -Profile Distinguished Professor Sang Yup Lee leesy＠kaist.ac.kr Metabolic &Biomolecular Engineering National Research Laboratory http://mbel.kaist.ac.kr Department of Chemical and Biomolecular Engineering KAIST
Three Professors Named to Highly Cited Researchers..
< Distinguished Professor Chang, Distinguished Professor Lee, and Professor Eom (from left) > Distinguished Professor Sukbok Chang from the Department of Chemistry, Distinguished Professor Sang-Yup Lee from the Department of Chemical & Biomolecular Engineering, and Professor Jiyong Eom from the College of Business were named to Clarivate’s Highly Cited Researchers 2020 list. Clarivate announced the researchers who rank in the top 1％ of citations by field and publication year in the Web of Science citation index. A total of 6,167 researchers from more than 60 countries were listed this year and 37 Korean scholars made the list. The methodology that determines the “Who’s Who” of influential researchers draws on data and analyses performed by bibliometric experts and data scientists at the Institute for Scientific Information at Clarivate. It also uses the tallies to identify the countries and research institutions where these scientific elite are based. More than 6,000 researchers from 21 fields in the sciences, social sciences, and cross field categories were selected based on the number of highly cited papers they produced over an 11-year period from January 2009 to December 2019. Professor Chang made the list six years in a row, while Professor Lee made it for four consecutive years, and Professor Eom for the last two years. Professor Chang’s group (http://sbchang.kaist.ac.kr) investigates catalytic hydrocarbon functionalization. Professor Lee (http://mbel.kaist.ac.kr) is a pioneering scholar in the field of metabolic engineering, systems, and synthetic biology. Professor Eom’s (https://kaistceps.quv.kr) research extends to energy and environmental economics and management, energy big data, and green information systems.
Simulations Open a New Way to Reverse Cell Aging
Turning off a newly identified enzyme could reverse a natural aging process in cells. Research findings by a KAIST team provide insight into the complex mechanism of cellular senescence and present a potential therapeutic strategy for reducing age-related diseases associated with the accumulation of senescent cells. Simulations that model molecular interactions have identified an enzyme that could be targeted to reverse a natural aging process called cellular senescence. The findings were validated with laboratory experiments on skin cells and skin equivalent tissues, and published in the Proceedings of the National Academy of Sciences (PNAS). “Our research opens the door for a new generation that perceives aging as a reversible biological phenomenon,” says Professor Kwang-Hyun Cho of the Department of Bio and Brain engineering at the Korea Advanced Institute of Science and Technology (KAIST), who led the research with colleagues from KAIST and Amorepacific Corporation in Korea. Cells respond to a variety of factors, such as oxidative stress, DNA damage, and shortening of the telomeres capping the ends of chromosomes, by entering a stable and persistent exit from the cell cycle. This process, called cellular senescence, is important, as it prevents damaged cells from proliferating and turning into cancer cells. But it is also a natural process that contributes to aging and age-related diseases. Recent research has shown that cellular senescence can be reversed. But the laboratory approaches used thus far also impair tissue regeneration or have the potential to trigger malignant transformations. Professor Cho and his colleagues used an innovative strategy to identify molecules that could be targeted for reversing cellular senescence. The team pooled together information from the literature and databases about the molecular processes involved in cellular senescence. To this, they added results from their own research on the molecular processes involved in the proliferation, quiescence (a non-dividing cell that can re-enter the cell cycle) and senescence of skin fibroblasts, a cell type well known for repairing wounds. Using algorithms, they developed a model that simulates the interactions between these molecules. Their analyses allowed them to predict which molecules could be targeted to reverse cell senescence. They then investigated one of the molecules, an enzyme called PDK1, in incubated senescent skin fibroblasts and three-dimensional skin equivalent tissue models. They found that blocking PDK1 led to the inhibition of two downstream signalling molecules, which in turn restored the cells’ ability to enter back into the cell cycle. Notably, the cells retained their capacity to regenerate wounded skin without proliferating in a way that could lead to malignant transformation. The scientists recommend investigations are next done in organs and organisms to determine the full effect of PDK1 inhibition. Since the gene that codes for PDK1 is overexpressed in some cancers, the scientists expect that inhibiting it will have both anti-aging and anti-cancer effects. < Figure: The scientists conducted what is known as an ensemble model simulation to identify molecules that could be targeted to reverse cell senescence. They then used the model to predict the effects of inhibiting PDK1 in senescent cells, and confirmed the results in lab-cultured cells and skin equivalent tissue models. > -Profile Professor Kwang-Hyun Cho Laboratory for Systems Biology and Bio-Inspired Engineering http://sbie.kaist.ac.kr Department of Bio and Brain Engineering KAIST
Chairman Soo-Young Lee Named Among the Heroes of P..
< Chairman Soo-Young Lee at the KAIST Development Foundation (far left) was selected as one of 15 philanthropists in Asia by Forbes Asia. (Photo by Forbes Asia) > Chairman Soo-Young Lee from the KAIST Development Foundation was named one of 15 philanthropists who made the biggest donations in the Asia-Pacific region by Forbes Asia on November 11. The annual Heroes of Philanthropy list features the 15 the most generous individual philanthropists who are donating from their personal fortunes, not through companies. This year, the biggest philanthropies donated to make a difference in wide arrays of sectors such as Covid-19 relief to education and the arts. Chairman Lee donated totaling 68 billion KRW to KAIST in July. Her donation marked the largest donation KAIST has ever received. She is one of two Korean philanthropists that Forbes selected. Honorary Chairman of GS Caltex Dong-Soo Huh also made the list. Her donation will establish the Soo-Young Lee Science Education Foundation to support ‘the Singularity Professor program’ that KAIST is launching. She expressed confidence that her donation will fund KAIST researchers to make breakthroughs that will lead to a Nobel Prize. “Without the advancement of science and technology, Korea cannot be one of the top countries in the world. I believe KAIST can make it with our all supports,” she frequently said when asked why she selected KAIST for her donation. Chairman Lee previously made generous donations in 2012 and 2016 and said she plans to make another gift to KAIST in the very near future.
In Memory of Professor Dong-Soo Kim
Pioneering geotechnical engineer Dong-Soo Kim dies at 59 < The late Professor Dong-Soo Kim at the Department of Civil and Environmental Engineering. > The Department of Civil and Environmental Engineering lost a pioneering scholar in geotechnical engineering, Professor Dong-Soo Kim. Professor Kim died on November 3, after a one-and-a-half-year battle with a brain tumor. He was 59. Known for his piercing insight and infectious enthusiasm for the deepest questions in geotechnical science and engineering, Professor Kim built an extraordinary academic career while working at KAIST for 26 years. Professor Kim paved the way for establishing the geo-centrifuge experiment facilities at KAIST as part of the KOCED (Korea Construction Engineering Development Collaboratory Management Institute) Projects funded by the Ministry of Land, Infrastructure and Transport. He also served as director of the KOCED Geo-Centrifuge Center. “He made significant contributions to the growth of the department since his joining and he was at the forefront of the globalization of the department. He passed away so early leaving behind so many projects,” lamented Professor Emeritus Chung-Bang Yun. “Professor Kim insisted on lecturing despite his serious illness. He wanted to play his part so gracefully for his students until his last days,” said Professor Hyo-Gyong Kwak, the head of the department who was also a close colleague of 25 years. “His captivating warm smile and unwavering mentorship and guidance will be missed by students and faculty alike. We lost an exemplary leader, mentor, colleague, and friend.” One of his colleagues, Professor Gye-Chun Cho said, “We have lost a great professor and colleague in civil engineering worldwide. His impact and legacy will be remembered forever.” Joining the KAIST faculty in 1994, he began his academic career at the Polytechnique University, New York for three years after earning his PhD at the University of Texas at Austin in 1991. He finished his BS and MS at Seoul National University in 1983 and 1985 respectively. While at KAIST, he led the Soil Dynamics Lab in 1994 and researched on site characterization via field and lab tests. He also conducted geotechnical centrifuge tests on earthquake and offshore geotechnical problems. His research team studied the seismic design of geotechnical structures and explored the non-destructive testing and evaluation of civil structures. Professor Kim made profound contributions to understanding fundamental geotechnical engineering problems. More recently, his lab investigated physical modeling using the geo-centrifuge testing machine that could simulate field geotechnical problems on small-scale models. Professor Kim’s perseverance, deep curiosity, and enthusiasm for discovery served him well in his roles as a teacher, mentor, and colleague in the department and beyond. “I thought of him as an elder brother who fully understand everything with generous mind,” said Professor Haeng-Ki Lee, former head of the department. “I will never forget the hiking trip to Halla Mountain in Jeju last summer. He continuously cheered on the junior professors. Without him, we could not have made it to the summit. His support and encouragement always led us to produce good results and achievement in the labs,” remembered Professor Youngchul Kim. Taking great delight in helping young scientists, he inspired colleagues and students to find their own eureka moments. To professors like Jong-In Han and Ayoung Kim, he was the role model they hope to be due to his rigorous scholarship and generous character. Upon his passing, Professor Jaewook Myung reviewed all the emails he and Professor Kim has sent starting from his undergraduate days at KAIST. “He was my guiding light. He always listened attentively to my struggles from my undergraduate days and advised me very warmly.” Professor Kim was also known for his key role in the Korean Geotechnical Society. His unmatched leadership led him to serve as the Chair of the Organizing Committee for the 19th International Conference on Soil Mechanics and Geotechnical Engineering in Seoul in 2017. He was the General Secretary of the 5th International Symposium on Deformation Characteristics of Geomaterials. He also served as a chair of the ISSSMGE TC 104 committee. Professor Kim successfully carried out numerous projects with his research team and supervised more than 60 graduate students. For current students under his supervision, it is still tough to acknowledge the loss of their professor. Master candidate Yeonjun Kim feels lost moving forward. PhD candidate Junsik Bae said that it is like a bad dream and he feels Professor Kim will still be in his lab whenever he goes inside. One of the staff members who worked with him, Byeol-Nim Cha, remembered that Professor Kim always entered the office with a big smile. “He always asked me how I am doing,” Cha added. Professor Kim’s trailblazing research was recognized with several awards and honors. Cited as a Top 100 Scientist by the International Biographical Center (IBC) in 2008, Professor Kim received the Young Presidential Research Award from the Korean Academy of Science and Technology in 2002, the Korean Presidential Award on Civil Engineer’s Day in 2011, and the Telford Premium Rewards in 2018. Throughout his career, he authored or co-authored 321 papers in international journals and conference proceedings, and 278 papers in domestic journals and conferences. President of the Korean Geotechnical Society Choong-gi Chung also eulogized him, “Above his impressive professional contributions, Professor Kim will be remembered forever for his generosity, simplicity, playfulness, and his smile.” Professor Kim is survived by his wife, son, and daughter.
Team USRG’s Winning Streak Continues at the AI Gra..
< Team USRG won the AI Grand Challenge 2020 for the second consecutive year. > Team USRG (Unmanned Systems Research Group) led by Professor Hyunchul Shim from the School of Electrical Engineering has won the AI Grand Challenge 2020 held on Nov. 23 at Kintex in Ilsan, Kyonggi-do for the second consecutive year. The team received 7.7 million KRW in research funding from the Ministry of Science and ICT, the organizer of the challenge. The team took a little over two minutes to complete the rescue operation mission of the challenge. The mission included swerving around seven obstacles, airdropping an aid package, and safely landing after identifying the landing spot. Their drone is the only one that successfully passed through a 10-meter tunnel out of five pre-qualified teams: three from universities and two from companies. The AI Grand Challenge, which began in 2017, was designed to promote AI technology and its applications for addressing high-risk technical challenges, especially for conducting complex disaster relief operations. For autonomous flying drones, swerving to avoid objects has always been an essential skill and a big challenge. For their flawless performance in the rescue operation, the team loaded an AI algorithm and upgraded their drone by improving the LiDAR-based localization system and a stronger propulsion system to carry more sensors. The drone weighs 2.4 kg and carries a small yet powerful computer with a GPU. This AI-powered drone can complete rescue missions more efficiently in complicated and disastrous environments by precisely comprehending where the drone should go without needing GPS. The team also designed an all-in-one prop guard and installed a gripper onto the bottom of the drone to hold the aid package securely. “We tried hard to improve our localization system better to resolve issues we had in the previous event,” said Professor Shim. Two PhD candidates, Han-Sob Lee and Bo-Sung Kim played a critical role in developing this drone. After their two-year winning streak, their prize money now totals 2.4 billion KRW, equivalent to the winning prize of the DARPA Challenge. As the winning team, they will collaborate with other champions at the AI track challenge to develop rescue mission technology for a more complex environment. “The importance of AI technology is continuing to grow and the government is providing large amounts of funding for research in this field. We would like to develop very competitive technology that will work in the real world,” Professor Shim added. His group is investigating a wide array of AI technologies applicable to unmanned vehicles including indoor flying drones, self-driving cars, delivery robots, and a tram that circles the campus. < Two PhD candidates, Han-Sob Lee and Bo-Sung Kim make a final touch for the competition. >