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Mystery Solved with Math: Cytoplasmic Traffic Jam Disrupts Sleep-Wake Cycles
KAIST mathematicians and their collaborators at Florida State University have identified the principle of how aging and diseases like dementia and obesity cause sleep disorders. A combination of mathematical modelling and experiments demonstrated that the cytoplasmic congestion caused by aging, dementia, and/or obesity disrupts the circadian rhythms in the human body and leads to irregular sleep-wake cycles. This finding suggests new treatment strategies for addressing unstable sleep-wake cycles.
Human bodies adjust sleep schedules in accordance with the ‘circadian rhythms’, which are regulated by our time keeping system, the ‘circadian clock’. This clock tells our body when to rest by generating the 24-hour rhythms of a protein called PERIOD (PER) (See Figure 1).
The amount of the PER protein increases for half of the day and then decreases for the remaining half. The principle is that the PER protein accumulating in the cytoplasm for several hours enters the cell nucleus all at once, hindering the transcription of PER genes and thereby reducing the amount of PER.
However, it has remained a mystery how thousands of PER molecules can simultaneously enter into the nucleus in a complex cell environment where a variety of materials co-exist and can interfere with the motion of PER. This would be like finding a way for thousands of employees from all over New York City to enter an office building at the same time every day.
A group of researchers led by Professor Jae Kyoung Kim from the KAIST Department of Mathematical Sciences solved the mystery by developing a spatiotemporal and probabilistic model that describes the motion of PER molecules in a cell environment.
This study was conducted in collaboration with Professor Choogon Lee’s group from Florida State University, where the experiments were carried out, and the results were published in the Proceedings of the National Academy of Sciences (PNAS) last month.
The joint research team’s spatial stochastic model (See Figure 2) described the motion of PER molecules in cells and demonstrated that the PER molecule should be sufficiently condensed around the cell nucleus to be phosphorylated simultaneously and enter the nucleus together (See Figure 3 Left). Thanks to this phosphorylation synchronization switch, thousands of PER molecules can enter the nucleus at the same time every day and maintain stable circadian rhythms.
However, when aging and/or diseases including dementia and obesity cause the cytoplasm to become congested with increased cytoplasmic obstacles such as protein aggregates and fat vacuoles, it hinders the timely condensation of PER molecules around the cell nucleus (See Figure 3 Right). As a result, the phosphorylation synchronization switch does not work and PER proteins enter into the nucleus at irregular times, making the circadian rhythms and sleep-wake cycles unstable, the study revealed.
Professor Kim said, “As a mathematician, I am excited to help enable the advancement of new treatment strategies that can improve the lives of so many patients who suffer from irregular sleep-wake cycles. Taking these findings as an opportunity, I hope to see more active interchanges of ideas and collaboration between mathematical and biological sciences.”
This work was supported by the National Institutes of Health and the National Science Foundation in the US, and the International Human Frontiers Science Program Organization and the National Research Foundation of Korea.
Publication:
Beesley, S. and Kim, D. W, et al. (2020) Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis. Proceedings of the National Academy of Sciences (PNAS), Vol. 117, No. 45, 28402-28411. Available online at https://doi.org/10.1073/pnas.2003524117
Profile:
Jae Kyoung Kim, Ph.D.
Associate Professor
jaekkim@kaist.ac.kr
http://mathsci.kaist.ac.kr/~jaekkim
@umichkim on Twitter
Department of Mathematical Sciences
Korea Advanced Institute of Science and Technology (KAIST)
Daejeon, Republic of Korea
Profile:
Choogon Lee, Ph.D.
Associate Professor
clee@neuro.fsu.edu
https://med.fsu.edu/biosci/lee-lab
Department of Biomedical Sciences
Florida State University
Florida, USA
(END)
2020.12.11 View 8406 -
A Comprehensive Review of Biosynthesis of Inorganic Nanomaterials Using Microorganisms and Bacteriophages
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.
-ProfileDistinguished Professor Sang Yup Lee leesy@kaist.ac.krMetabolic &Biomolecular Engineering National Research Laboratoryhttp://mbel.kaist.ac.krDepartment of Chemical and Biomolecular EngineeringKAIST
2020.12.07 View 8939 -
Team USRG’s Winning Streak Continues at the AI Grand Challenge
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.
2020.12.01 View 7445 -
Three Professors Named to Highly Cited Researchers 2020 List
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.
2020.11.30 View 7778 -
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.
-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
2020.11.26 View 11016 -
Feel the Force with ElaStick
ElaStick, a handheld variable stiffness display, renders the dynamic haptic response of a flexible object
Haptic controllers play an important role in providing rich and immersive virtual reality experiences. Professor Andrea Bianchi’s team in the Department of Industrial Design recreated the haptic response of flexible objects made of different materials and with different shapes by changing the stiffness of a custom-controller – ElaStick.
ElaStick is a portable hand-held force-feedback controller that is capable of rendering the illusion of how flexible and deformable objects feel when held in the hand. This VR haptic controller can change its stiffness in two directions independently and continuously. Since providing haptic feedback enhances the VR experience, researchers have suggested numerous approaches for rendering the physical properties of virtual objects - such as weights, the movement of mass, impacts, and damped oscillations.
The research team designed a new mechanism based on a quaternion joint and four variable-stiffness tendons. The quaternion joint is a two-DoF bending joint that enables ElaStick to bend and oscillate in any direction using a pair of tendons with varying stiffness. In fact, each tendon around the joint is made of a series of elastic rubber bands and inelastic fishing lines and can vary its stiffness by changing the proportion of the two materials. Thanks to these structures, each pair of tendons can behave independently, controlling the anisotropic characteristics of the entire device.
“The main challenge was to implement the mechanism to control the stiffness while maintaining independence between deformations in two perpendicular directions,” said Professor Bianchi.
The research team successfully measured the relative threshold of human perception on the stiffness of a handheld object. The results showed that the just-noticeable difference (JND) of human perception of stiffness is at most about 30% of the change from the initial value. It also found that appropriate haptic responses significantly enhance the quality of the VR experience. The research team surveyed the perceived realism, immersion, and enjoyment of participants after they played with various flexible objects in VR.
“It is meaningful that the haptic feedback of a flexible object was mechanically reproduced and its effectiveness in VR was proven. ElaStick has succeeded in implementing a novel mechanism to recreate the dynamic response of flexible objects that mimic real ones, suggesting a new category of haptic feedback that can be provided in VR,” explained Professor Bianchi.
The team plans to extend the ElaStick’s applications, from being used merely as a game controller to driving simulations, medical training, and many other digital contexts. This research, led by MS candidate Neung Ryu, won the Best Paper Award at the ACM UIST 2020 (the ACM Symposium on User Interface Software & Technology) last month.
-ProfileProfessor Andrea BianchiMakinteract.kaist.ac.krDepartment of Industrial DesignKAIST
2020.11.23 View 5509 -
Researchers Control Multiple Wavelengths of Light from a Single Source
KAIST researchers have synthesized a collection of nanoparticles, known as carbon dots, capable of emitting multiple wavelengths of light from a single particle. Additionally, the team discovered that the dispersion of the carbon dots, or the interparticle distance between each dot, influences the properties of the light the carbon dots emit. The discovery will allow researchers to understand how to control these carbon dots and create new, environmentally responsible displays, lighting, and sensing technology.
Research into nanoparticles capable of emitting light, such as quantum dots, has been an active area of interest for the last decade and a half. These particles, or phosphors, are nanoparticles made out of various materials that are capable of emitting light at specific wavelengths by leveraging quantum mechanical properties of the materials. This provides new ways to develop lighting and display solutions as well as more precise detection and sensing in instruments.
As technology becomes smaller and more sophisticated, the usage of fluorescent nanoparticles has seen a dramatic increase in many applications due to the purity of the colors emitting from the dots as well as their tunability to meet desired optical properties.
Carbon dots, a type of fluorescent nanoparticles, have seen an increase in interest from researchers as a candidate to replace non-carbon dots, the construction of which requires heavy metals that are toxic to the environment. Since they are made up of mostly carbon, the low toxicity is an extremely attractive quality when coupled with the tunability of their inherent optical properties.
Another striking feature of carbon dots is their capability to emit multiple wavelengths of light from a single nanoparticle. This multi-wavelength emission can be stimulated under a single excitation source, enabling the simple and robust generation of white light from a single particle by emitting multiple wavelengths simultaneously.
Carbon dots also exhibit a concentration-dependent photoluminescence. In other words, the distance between individual carbon dots affects the light that the carbon dots subsequently emit under an excitation source. These combined properties make carbon dots a unique source that will result in extremely accurate detection and sensing.
This concentration-dependency, however, had not been fully understood. In order to fully utilize the capabilities of carbon dots, the mechanisms that govern the seemingly variable optical properties must first be uncovered. It was previously theorized that the concentration-dependency of carbon dots was due to a hydrogen bonding effect.
Now, a KAIST research team, led by Professor Do Hyun Kim of the Department of Chemical and Biomolecular Engineering has posited and demonstrated that the dual-color-emissiveness is instead due to the interparticle distances between each carbon dot. This study was made available online in June 2020 ahead of final publication in the 36th Issue of Physical Chemistry Chemical Physics on September 28, 2020.
First author of the paper, PhD candidate Hyo Jeong Yoo, along with Professor Kim and researcher Byeong Eun Kwak, examined how the relative light intensity of the red and blue colors changed when varying the interparticle distances, or concentration, of the carbon dots. They found that as the concentration was adjusted, the light emitted from the carbon dots would transform. By varying the concentration, the team was able to control the relative intensity of the colors, as well as emit them simultaneously to generate a white light from a single source (See Figure).
“The concentration-dependence of the photoluminescence of carbon dots on the change of the emissive origins for different interparticle distances has been overlooked in previous research. With the analysis of the dual-color-emission phenomenon of carbon dots, we believe that this result may provide a new perspective to investigate their photoluminescence mechanism,” Yoo explained.
The newly analyzed ability to control the photoluminescence of carbon dots will likely be heavily utilized in the continued development of solid-state lighting applications and sensing.
Publication:
Yoo, H. J., Kwak, B. E., and Kim. D. H. (2020) Interparticle distance as a key factor for controlling the dual-emission properties of carbon dots. Physical Chemistry Chemical Physics, Issue 36, Pages 20227-20237. Available online at https://doi.org/10.1039/d0cp02120b
Profile:
Do Hyun Kim, Sc.D.
Professor
dokim@kaist.ac.kr
http://procal.kaist.ac.kr/
Process Analysis Laboratory
Department of Chemical and Biomolecular Engineering
https://www.kaist.ac.kr
Korea Advanced Institute of Science and Technology (KAIST)Daejeon, Republic of Korea
(END)
2020.11.23 View 9306 -
‘WalkON Suit 4’ Releases Paraplegics from Wheelchairs
- KAIST Athletes in ‘WalkON Suit 4’ Dominated the Cybathlon 2020 Global Edition. -
Paraplegic athletes Byeong-Uk Kim and Joohyun Lee from KAIST’s Team Angel Robotics won a gold and a bronze medal respectively at the Cybathlon 2020 Global Edition last week. ‘WalkON Suit 4,’ a wearable robot developed by the Professor Kyoungchul Kong’s team from the Department of Mechanical Engineering topped the standings at the event with double medal success.
Kim, the former bronze medallist, clinched his gold medal by finishing all six tasks in 3 minutes and 47 seconds, whereas Lee came in third with a time of 5 minutes and 51 seconds. TWIICE, a Swiss team, lagged 53 seconds behind Kim’s winning time to be the runner-up.
Cybathlon is a global championship, organized by ETH Zurich, which brings together people with physical disabilities to compete using state-of-the-art assistive technologies to perform everyday tasks. The first championship was held in 2016 in Zurich, Switzerland.
Due to the COVID-19 pandemic, the second championship was postponed twice and held in a new format in a decentralized setting. A total of 51 teams from 20 countries across the world performed the events in their home bases in different time zones instead of traveling to Zurich. Under the supervision of a referee and timekeeper, all races were filmed and then reviewed by judges.
KAIST’s Team Angel Robotics participated in the Powered Exoskeleton Race category, where nine pilots representing five nations including Korea, Switzerland, the US, Russia, and France competed against each other.
The team installed their own arena and raced at the KAIST Main Campus in Daejeon according to the framework, tasks, and rules defined by the competition committee. The two paraplegic pilots were each equipped with exoskeletal devices, the WalkON Suit 4, and undertook six tasks related to daily activities.
The WalkON Suit 4 recorded the fastest walking speed for a complete paraplegic ever reported. For a continuous walk, it achieved a maximum speed of 40 meters per minute. This is comparable to the average walking pace of a non-disabled person, which is around two to four kilometers per hour.
The research team raised the functionality of the robot by adding technology that can observe the user’s level of anxiety and external factors like the state of the walking surface, so it can control itself intelligently. The assistive functions a robot should provide vary greatly with the environment, and the WalkON Suit 4 made it possible to analyze the pace of the user within 30 steps and provide a personally optimized walking pattern, enabling a high walking speed.
The six tasks that Kim and Lee had to complete were:1) sitting and standing back up, 2) navigating around obstacles while avoiding collisions, 3) stepping over obstacles on the ground, 4) going up and down stairs, 5) walking across a tilted path, and 6) climbing a steep slope, opening and closing a door, and descending a steep slope.
Points were given based on the accuracy of each completed task, and the final scores were calculated by adding all of the points that were gained in each attempt, which lasted 10 minutes. Each pilot was given three opportunities and used his/her highest score. Should pilots have the same final score, the pilot who completed the race in the shortest amount of time would win.
Kim said in his victory speech that he was so thrilled to see all his and fellow researchers’ years of hard work paying off. “This will be a good opportunity to show how outstanding Korean wearable robot technologies are,” he added.
Lee, who participated in the competition for the first time, said, “By showing that I can overcome my physical disabilities with robot technology, I’d like to send out a message of hope to everyone who is tired because of COVID-19”.
Professor Kong’s team collaborated in technology development and pilot training with their colleagues from Angel Robotics Co., Ltd., Severance Rehabilitation Hospital, Yeungnam University, Stalks, and the Institute of Rehabilitation Technology.
Footage from the competition is available at the Cybathlon’s official website.
(END)
2020.11.20 View 7657 -
In Memory of Professor Dong-Soo Kim
Pioneering geotechnical engineer Dong-Soo Kim dies at 59
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.
2020.11.19 View 6592 -
Engineered C. glutamicum Strain Capable of Producing High-Level Glutaric Acid from Glucose
An engineered C. glutamicum strain that can produce the world’s highest titer of glutaric acid was developed by employing systems metabolic engineering strategies
A metabolic engineering research group at KAIST has developed an engineered Corynebacterium glutamicum strain capable of producing high-level glutaric acid without byproducts from glucose. This new strategy will be useful for developing engineered micro-organisms for the bio-based production of value-added chemicals.
Glutaric acid, also known as pentanedioic acid, is a carboxylic acid that is widely used for various applications including the production of polyesters, polyamides, polyurethanes, glutaric anhydride, 1,5-pentanediol, and 5-hydroxyvaleric acid. Glutaric acid has been produced using various petroleum-based chemical methods, relying on non-renewable and toxic starting materials. Thus, various approaches have been taken to biologically produce glutaric acid from renewable resources. Previously, the development of the first glutaric acid producing Escherichia coli by introducing Pseudomonas putida genes was reported by a research group from KAIST, but the titer was low. Glutaric acid production by metabolically engineered Corynebacterium glutamicum has also been reported in several studies, but further improvements in glutaric acid production seemed possible since C. glutamicum has the capability of producing more than 130 g/L of L-lysine.
A research group comprised of Taehee Han, Gi Bae Kim, and Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering addressed this issue. Their research paper “Glutaric acid production by systems metabolic engineering of an L-lysine-overproducing Corynebacterium glutamicum” was published online in PNAS on November 16, 2020.
This research reports the development of a metabolically engineered C. glutamicum strain capable of efficiently producing glutaric acid, starting from an L-lysine overproducer. The following novel strategies and approaches to achieve high-level glutaric acid production were employed. First, metabolic pathways in C. glutamicum were reconstituted for glutaric acid production by introducing P. putida genes. Then, multi-omics analyses including genome, transcriptome, and fluxome were conducted to understand the phenotype of the L-lysine overproducer strain. In addition to systematic understanding of the host strain, gene manipulation targets were predicted by omics analyses and applied for engineering C. glutamicum, which resulted in the development of an engineered strain capable of efficiently producing glutaric acid. Furthermore, the new glutaric acid exporter was discovered for the first time, which was used to further increase glutaric acid production through enhancing product excretion. Last but not least, culture conditions were optimized for high-level glutaric acid production. As a result, the final engineered strain was able to produce 105.3 g/L glutaric acid, the highest titer ever reported, in 69 hours by fed-batch fermentation.
Professor Sang Yup Lee said, “It is meaningful that we were able to develop a highly efficient glutaric acid producer capable of producing glutaric acid at the world’s highest titer without any byproducts from renewable carbon sources. This will further accelerate the bio-based production of valuable chemicals in pharmaceutical/medical/chemical industries.” This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation and funded by the Ministry of Science and ICT.
-Profile
Distinguished Professor Sang Yup Lee
leesy@kaist.ac.kr
http://mbel.kaist.ac.kr
Department of Chemical and Biomolecular Engineering
KAIST
2020.11.17 View 6247 -
Chairman Soo-Young Lee Named Among the Heroes of Philanthropy in 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.
2020.11.13 View 5476 -
Drawing the Line to Answer Art’s Big Questions
- KAIST scientists show how statistical physics can reveal art trends across time and culture. -
Algorithms have shown that the compositional structure of Western landscape paintings changed “suspiciously” smoothly between 1500 and 2000 AD, potentially indicating a selection bias by art curators or in art historical literature, physicists from the Korea Advanced Institute of Science and Technology (KAIST) and colleagues report in the Proceedings of the National Academy of Sciences (PNAS).
KAIST statistical physicist Hawoong Jeong worked with statisticians, digital analysts and art historians in Korea, Estonia and the US to clarify whether computer algorithms could help resolve long-standing questions about design principles used in landscape paintings, such as the placement of the horizon and other primary features.
“A foundational question among art historians is whether artwork contains organizing principles that transcend culture and time and, if yes, how these principles evolved over time,” explains Jeong. “We developed an information-theoretic approach that can capture compositional proportion in landscape paintings and found that the preferred compositional proportion systematically evolved over time.”
Digital versions of almost 15,000 canonical landscape paintings from the Western renaissance in the 1500s to the more recent contemporary art period were run through a computer algorithm. The algorithm progressively divides artwork into horizontal and vertical lines depending on the amount of information in each subsequent partition. It allows scientists to evaluate how artists and various art styles compose landscape artwork, in terms of placement of a piece’s most important components, in addition to how high or low the landscape’s horizon is placed.
The scientists started by analysing the first two partitioning lines identified by the algorithm in the paintings and found they could be categorized into four groups: an initial horizontal line followed by a second horizontal line (H-H); an initial horizontal line followed by a second vertical line (H-V); a vertical followed by horizontal line (V-H); or a vertical followed by a vertical line (V-V) (see image 1 and 2). They then looked at the categorizations over time.
They found that before the mid-nineteenth century, H-V was the dominant composition type, followed by H-H, V-H, and V-V. The mid-nineteenth century then brought change, with the H-V composition style decreasing in popularity with a rise in the H-H composition style. The other two styles remained relatively stable.
The scientists also looked at how the horizon line, which separates sky from land, changed over time. In the 16th century, the dominant horizon line of the painting was above the middle of the canvas, but it gradually descended to the lower middle of the canvas by the 17th century, where it remained until the mid-nineteenth century. After that, the horizon line began gradually rising again.
Interestingly, the algorithm showed that these findings were similar across cultures and artistic periods, even through periods dominated by a diversity in art styles. This similarity may well be a function, then, of a bias in the dataset.
“In recent decades, art historians have prioritized the argument that there is great diversity in the evolution of artistic expression rather than offering a relatively smoother consensus story in Western art,” Jeong says. “This study serves as a reminder that the available large-scale datasets might be perpetuating severe biases.”
The scientists next aim to broaden their analyses to include more diverse artwork, as this particular dataset was ultimately Western and male biased. Future analyses should also consider diagonal compositions in paintings, they say.
This work was supported by the National Research Foundation (NRF) of Korea.
Publication:
Lee, B, et al. (2020) Dissecting landscape art history with information theory. Proceedings of the National Academy of Sciences (PNAS), Vol. 117, No. 43, 26580-26590. Available online at https://doi.org/10.1073/pnas.2011927117
Profile:
Hawoong Jeong, Ph.D.
Professor
hjeong@kaist.ac.kr
https://www.kaist.ac.kr
Department of Physics
Korea Advanced Institute of Science and Technology (KAIST)
Daejeon, Republic of Korea
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2020.11.13 View 9536