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Biomarker Predicts Who Will Have Severe COVID-19
- Airway cell analyses showing an activated immune axis could pinpoint the COVID-19 patients who will most benefit from targeted therapies.-
KAIST researchers have identified key markers that could help pinpoint patients who are bound to get a severe reaction to COVID-19 infection. This would help doctors provide the right treatments at the right time, potentially saving lives. The findings were published in the journal Frontiers in Immunology on August 28.
People’s immune systems react differently to infection with SARS-CoV-2, the virus that causes COVID-19, ranging from mild to severe, life-threatening responses.
To understand the differences in responses, Professor Heung Kyu Lee and PhD candidate Jang Hyun Park from the Graduate School of Medical Science and Engineering at KAIST analysed ribonucleic acid (RNA) sequencing data extracted from individual airway cells of healthy controls and of mildly and severely ill patients with COVID-19. The data was available in a public database previously published by a group of Chinese researchers.
“Our analyses identified an association between immune cells called neutrophils and special cell receptors that bind to the steroid hormone glucocorticoid,” Professor Lee explained. “This finding could be used as a biomarker for predicting disease severity in patients and thus selecting a targeted therapy that can help treat them at an appropriate time,” he added.
Severe illness in COVID-19 is associated with an exaggerated immune response that leads to excessive airway-damaging inflammation. This condition, known as acute respiratory distress syndrome (ARDS), accounts for 70% of deaths in fatal COVID-19 infections.
Scientists already know that this excessive inflammation involves heightened neutrophil recruitment to the airways, but the detailed mechanisms of this reaction are still unclear.
Lee and Park’s analyses found that a group of immune cells called myeloid cells produced excess amounts of neutrophil-recruiting chemicals in severely ill patients, including a cytokine called tumour necrosis factor (TNF) and a chemokine called CXCL8.
Further RNA analyses of neutrophils in severely ill patients showed they were less able to recruit very important T cells needed for attacking the virus. At the same time, the neutrophils produced too many extracellular molecules that normally trap pathogens, but damage airway cells when produced in excess.
The researchers additionally found that the airway cells in severely ill patients were not expressing enough glucocorticoid receptors. This was correlated with increased CXCL8 expression and neutrophil recruitment.
Glucocorticoids, like the well-known drug dexamethasone, are anti-inflammatory agents that could play a role in treating COVID-19. However, using them in early or mild forms of the infection could suppress the necessary immune reactions to combat the virus. But if airway damage has already happened in more severe cases, glucocorticoid treatment would be ineffective.
Knowing who to give this treatment to and when is really important. COVID-19 patients showing reduced glucocorticoid receptor expression, increased CXCL8 expression, and excess neutrophil recruitment to the airways could benefit from treatment with glucocorticoids to prevent airway damage. Further research is needed, however, to confirm the relationship between glucocorticoids and neutrophil inflammation at the protein level.
“Our study could serve as a springboard towards more accurate and reliable COVID-19 treatments,” Professor Lee said.
This work was supported by the National Research Foundation of Korea, and Mobile Clinic Module Project funded by KAIST.
Figure. Low glucocorticoid receptor (GR) expression led to excessive inflammation and lung damage by neutrophils through enhancing the expression of CXCL8 and other cytokines.
Image credit: Professor Heung Kyu Lee, KAIST. Created with Biorender.com.
Image usage restrictions: News organizations may use or redistribute these figures and image, with proper attribution, as part of news coverage of this paper only.
-Publication:
Jang Hyun Park, and Heung Kyu Lee. (2020). Re-analysis of Single Cell Transcriptome Reveals That the NR3C1-CXCL8-Neutrophil Axis Determines the Severity of COVID-19. Frontiers in Immunology, Available online at https://doi.org/10.3389/fimmu.2020.02145
-Profile: Heung Kyu Lee
Associate Professor
heungkyu.lee@kaist.ac.kr
https://www.heungkyulee.kaist.ac.kr/
Laboratory of Host Defenses
Graduate School of Medical Science and Engineering (GSMSE)
The Center for Epidemic Preparedness at KAIST Institute
http://kaist.ac.kr
Korea Advanced Institute of Science and Technology (KAIST)
Daejeon, Republic of Korea
Profile: Jang Hyun Park
PhD Candidate
janghyun.park@kaist.ac.kr
GSMSE, KAIST
2020.09.17 View 15628 -
‘Mole-bot’ Optimized for Underground and Space Exploration
Biomimetic drilling robot provides new insights into the development of efficient drilling technologies
Mole-bot, a drilling biomimetic robot designed by KAIST, boasts a stout scapula, a waist inclinable on all sides, and powerful forelimbs. Most of all, the powerful torque from the expandable drilling bit mimicking the chiseling ability of a mole’s front teeth highlights the best feature of the drilling robot.
The Mole-bot is expected to be used for space exploration and mining for underground resources such as coalbed methane and Rare Earth Elements (REE), which require highly advanced drilling technologies in complex environments.
The research team, led by Professor Hyun Myung from the School of Electrical Engineering, found inspiration for their drilling bot from two striking features of the African mole-rat and European mole.
“The crushing power of the African mole-rat’s teeth is so powerful that they can dig a hole with 48 times more power than their body weight. We used this characteristic for building the main excavation tool. And its expandable drill is designed not to collide with its forelimbs,” said Professor Myung.
The 25-cm wide and 84-cm long Mole-bot can excavate three times faster with six times higher directional accuracy than conventional models. The Mole-bot weighs 26 kg.
After digging, the robot removes the excavated soil and debris using its forelimbs. This embedded muscle feature, inspired by the European mole’s scapula, converts linear motion into a powerful rotational force. For directional drilling, the robot’s elongated waist changes its direction 360° like living mammals.
For exploring underground environments, the research team developed and applied new sensor systems and algorithms to identify the robot’s position and orientation using graph-based 3D Simultaneous Localization and Mapping (SLAM) technology that matches the Earth’s magnetic field sequence, which enables 3D autonomous navigation underground.
According to Market & Market’s survey, the directional drilling market in 2016 is estimated to be 83.3 billion USD and is expected to grow to 103 billion USD in 2021. The growth of the drilling market, starting with the Shale Revolution, is likely to expand into the future development of space and polar resources. As initiated by Space X recently, more attention for planetary exploration will be on the rise and its related technology and equipment market will also increase.
The Mole-bot is a huge step forward for efficient underground drilling and exploration technologies. Unlike conventional drilling processes that use environmentally unfriendly mud compounds for cleaning debris, Mole-bot can mitigate environmental destruction. The researchers said their system saves on cost and labor and does not require additional pipelines or other ancillary equipment.
“We look forward to a more efficient resource exploration with this type of drilling robot. We also hope Mole-bot will have a very positive impact on the robotics market in terms of its extensive application spectra and economic feasibility,” said Professor Myung.
This research, made in collaboration with Professor Jung-Wuk Hong and Professor Tae-Hyuk Kwon’s team in the Department of Civil and Environmental Engineering for robot structure analysis and geotechnical experiments, was supported by the Ministry of Trade, Industry and Energy’s Industrial Technology Innovation Project.
Profile
Professor Hyun Myung
Urban Robotics Lab
http://urobot.kaist.ac.kr/
School of Electrical Engineering
KAIST
2020.06.05 View 10732 -
Professor Dongsu Han Named Program Chair for ACM CoNEXT 2020
Professor Dongsu Han from the School of Electrical Engineering has been appointed as the program chair for the 16th Association for Computing Machinery’s International Conference on emerging Networking EXperiments and Technologies (ACM CoNEXT 2020). Professor Han is the first program chair to be appointed from an Asian institution.
ACM CoNEXT is hosted by ACM SIGCOMM, ACM's Special Interest Group on Data Communications, which specializes in the field of communication and computer networks.
Professor Han will serve as program co-chair along with Professor Anja Feldmann from the Max Planck Institute for Informatics. Together, they have appointed 40 world-leading researchers as program committee members for this conference, including Professor Song Min Kim from KAIST School of Electrical Engineering.
Paper submissions for the conference can be made by the end of June, and the event itself is to take place from the 1st to 4th of December.
Conference Website: https://conferences2.sigcomm.org/co-next/2020/#!/home
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2020.06.02 View 10219 -
KAIST Elected to Universities Space Research Association Membership
KAIST joined the Universities Space Research Association (USRA) on May 4, and brought the Association to a total of 113 member universities. The expertise KAIST brings will broaden the Association’s collective strength in space-related science, technology, and engineering worldwide. Professor Hyosang Yoon from the Department of Aerospace Engineering will serve as the representative of KAIST to USRA.
KAIST was selected by USRA’s current university members, in recognition of its significant commitment in, and contributions to, the fields of space and aerospace research. Especially, KAIST have developed Korea's first satellite, KITSAT-1 in 1992, which paved the way for space research in Korea and helped the nation strengthen technological competitiveness in that field.
USRA was established in 1969 under the auspices of the National Academy of Sciences (NAS) of the United States. It is a non-profit corporation chartered to advance space-related science, technology, and engineering. USRA operates scientific institutes and facilities, and conducts other major research and educational programs, using federal funding. USRA also engages the university community and employs in-house scientific leadership, innovative research and development, and project management expertise.
USRA’s President and CEO Dr. Jeffrey A. Isaacson said in his announcement, “We are delighted to welcome these two renowned universities as members. We look forward to their active engagement with, and contributions to, our Association.” President Isaacson visited KAIST on December 10 last year to discuss possible collaborations between two organizations.
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2020.05.29 View 7290 -
Professor Sung Yong Kim Elected as the Chair of PICES MONITOR
< Professor Sung Yong Kim >
Professor Sung Yong Kim from the Department of Mechanical Engineering was elected as the chair of the Technical Committee on Monitoring (MONITOR) of the North Pacific Marine Science Organization (PICES).
PICES is an intergovernmental marine science organization that was established in 1992 through a collaboration between six North Pacific nations including South Korea, Russia, the United States, Japan, China, and Canada to exchange and discuss research on the Pacific waters. Its headquarters is located in Canada and the organization consists of seven affiliated maritime science and marine technology committees.
Professor Kim was elected as the chair of the technical committee that focuses on monitoring and will be part of the Science Board as an ex-officio member. His term will last three years from November 2019.
Professor Kim was recognized for his academic excellence, expertise, and leadership among oceanographers both domestically and internationally.
Professor Kim will also participate as an academia civilian committee member of the Maritime and Fisheries Science and Technology Committee under the Korean Ministry of Oceans and Fisheries for two years from December 18, 2019.
He stated, “I will give my full efforts to broaden Korean oceanography research by participating in maritime leadership positions at home and abroad, and help South Korea become a maritime powerhouse.”
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2019.12.22 View 9464 -
Two Professors Receive Awards from the Korea Robotics Society
< Professor Jee-Hwan Ryu and Professor Ayoung Kim >
The Korea Robotics Society (KROS) conferred awards onto two KAIST professors from the Department of Civil and Environmental Engineering in recognition of their achievements and contributions to the development of the robotics industry in 2019. Professor Jee-Hwan Ryu has been actively engaged in researching the field of teleoperation, and this led him to win the KROS Robotics Innovation (KRI) Award. The KRI Award was newly established in 2019 by the KROS, in order to encourage researchers who have made innovative achievements in robotics. Professor Ryu shared the honor of being the first winner of this award with Professor Jaeheung Park of Seoul National University. Professor Ayoung Kim, from the same department, received the Young Investigator Award presented to emerging robitics researchers under 40 years of age. (END)
2019.12.19 View 10029 -
Image Analysis to Automatically Quantify Gender Bias in Movies
Many commercial films worldwide continue to express womanhood in a stereotypical manner, a recent study using image analysis showed. A KAIST research team developed a novel image analysis method for automatically quantifying the degree of gender bias in films.
The ‘Bechdel Test’ has been the most representative and general method of evaluating gender bias in films. This test indicates the degree of gender bias in a film by measuring how active the presence of women is in a film. A film passes the Bechdel Test if the film (1) has at least two female characters, (2) who talk to each other, and (3) their conversation is not related to the male characters.
However, the Bechdel Test has fundamental limitations regarding the accuracy and practicality of the evaluation. Firstly, the Bechdel Test requires considerable human resources, as it is performed subjectively by a person. More importantly, the Bechdel Test analyzes only a single aspect of the film, the dialogues between characters in the script, and provides only a dichotomous result of passing the test, neglecting the fact that a film is a visual art form reflecting multi-layered and complicated gender bias phenomena. It is also difficult to fully represent today’s various discourse on gender bias, which is much more diverse than in 1985 when the Bechdel Test was first presented.
Inspired by these limitations, a KAIST research team led by Professor Byungjoo Lee from the Graduate School of Culture Technology proposed an advanced system that uses computer vision technology to automatically analyzes the visual information of each frame of the film. This allows the system to more accurately and practically evaluate the degree to which female and male characters are discriminatingly depicted in a film in quantitative terms, and further enables the revealing of gender bias that conventional analysis methods could not yet detect.
Professor Lee and his researchers Ji Yoon Jang and Sangyoon Lee analyzed 40 films from Hollywood and South Korea released between 2017 and 2018. They downsampled the films from 24 to 3 frames per second, and used Microsoft’s Face API facial recognition technology and object detection technology YOLO9000 to verify the details of the characters and their surrounding objects in the scenes.
Using the new system, the team computed eight quantitative indices that describe the representation of a particular gender in the films. They are: emotional diversity, spatial staticity, spatial occupancy, temporal occupancy, mean age, intellectual image, emphasis on appearance, and type and frequency of surrounding objects.
Figure 1. System Diagram
Figure 2. 40 Hollywood and Korean Films Analyzed in the Study
According to the emotional diversity index, the depicted women were found to be more prone to expressing passive emotions, such as sadness, fear, and surprise. In contrast, male characters in the same films were more likely to demonstrate active emotions, such as anger and hatred.
Figure 3. Difference in Emotional Diversity between Female and Male Characters
The type and frequency of surrounding objects index revealed that female characters and automobiles were tracked together only 55.7 % as much as that of male characters, while they were more likely to appear with furniture and in a household, with 123.9% probability.
In cases of temporal occupancy and mean age, female characters appeared less frequently in films than males at the rate of 56%, and were on average younger in 79.1% of the cases. These two indices were especially conspicuous in Korean films.
Professor Lee said, “Our research confirmed that many commercial films depict women from a stereotypical perspective. I hope this result promotes public awareness of the importance of taking prudence when filmmakers create characters in films.”
This study was supported by KAIST College of Liberal Arts and Convergence Science as part of the Venture Research Program for Master’s and PhD Students, and will be presented at the 22nd ACM Conference on Computer-Supported Cooperative Work and Social Computing (CSCW) on November 11 to be held in Austin, Texas.
Publication:
Ji Yoon Jang, Sangyoon Lee, and Byungjoo Lee. 2019. Quantification of Gender Representation Bias in Commercial Films based on Image Analysis. In Proceedings of the 22nd ACM Conference on Computer-Supported Cooperative Work and Social Computing (CSCW). ACM, New York, NY, USA, Article 198, 29 pages. https://doi.org/10.1145/3359300
Link to download the full-text paper:
https://files.cargocollective.com/611692/cscw198-jangA--1-.pdf
Profile: Prof. Byungjoo Lee, MD, PhD
byungjoo.lee@kaist.ac.kr
http://kiml.org/
Assistant Professor
Graduate School of Culture Technology (CT)
Korea Advanced Institute of Science and Technology (KAIST)
https://www.kaist.ac.kr Daejeon 34141, Korea
Profile: Ji Yoon Jang, M.S.
yoone3422@kaist.ac.kr
Interactive Media Lab
Graduate School of Culture Technology (CT)
Korea Advanced Institute of Science and Technology (KAIST)
https://www.kaist.ac.kr Daejeon 34141, Korea
Profile: Sangyoon Lee, M.S. Candidate
sl2820@kaist.ac.kr
Interactive Media Lab
Graduate School of Culture Technology (CT)
Korea Advanced Institute of Science and Technology (KAIST)
https://www.kaist.ac.kr Daejeon 34141, Korea
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2019.10.17 View 25109 -
Distinguished Professor Sukbok Chang Donates His Prize Money
The honoree of the 2019 Korea Best Scientist and Technologist Award, Distinguished Professor Sukbok Chang donated his prize money of one hundred million KRW to the Chemistry Department Scholarship Fund and the Lyu Keun-Chul Sports Complex Management Fund during a donation ceremony last week.
Professor Chang won the award last month in recognition of his pioneering achievements and lifetime contributions to the development of carbon-hydrogen activation strategies, especially for carbon-carbon, carbon-nitrogen, and carbon-oxygen formations. Professor Chang, a world renowned chemist, has been recognized for his highly selective catalytic systems, allowing the controlled defunctionalization of bio-derived platform substrates under mild conditions and opening a new avenue for the utilization of biomass-derived platform chemicals.
“All my achievements are the results of my students’ hard work and dedication. I feel very fortunate to have such talented team members. I want to express my sincere gratitude for such a great research environment that we have worked together in so far,” said Professor Chang at the ceremony.
KAIST President Sung-Chul Shin said, “Not only will Professor Chang’s donation make a significant contribution to the Department of Chemistry, but also to the improvement of the Lyu Keun-Chul Sports Complex’s management, which directly links to the health and welfare of the KAIST community.”
Professor Chang currently holds the position of distinguished professor at KAIST and director of the Center for Catalytic Hydrocarbon Functionalizations in the Institute for Basic Science (IBS). He previously received the Kyung-Ahm Academic Award in 2013 and the Korea Toray Science Award in 2018. All these prize money also went to the school.
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2019.08.26 View 8152 -
FIRIC-EU JRC Joint Workshop on Smart Specialization
The Fourth Industrial Revolution Intelligence Center (FIRIC) at KAIST discussed ‘Smart Specialization’ for regional innovation and economic growth in the wake of the Fourth Industrial Revolution during the workshop with the EU Joint Research Center (EU-JRC) in Seville, Spain last week. The two sides also agreed to sign an MOU to expand mutual collaboration.
KAIST’s FIRIC was founded in cooperation with the World Economic Forum in July 2017 to carry out policy research for the promotion of science and technology-based inclusive growth and innovation and to lead related global efforts. The EU-JRC has committed to developing cohesive policies that aim to narrow regional gaps within the European Union. Founded in 1958 in Brussels, the EU-JRC has long been in charge of EU strategies for regional innovation based on emerging technologies.
The workshop also covered issues related to public-private partnerships and innovation clusters from the perspective of the EU and Asia, such as the global value chain and the implementation of industrial clusters policy amid the changes in the industrial ecosystem due to digitalization, automation, and the utilization of robotics during the Fourth Industrial Revolution.
In addition, the session included discussions on inclusive growth and job market changes in the era of the Fourth Industrial Revolution, addressing how Smart Specialization and the outcomes of the 4IR will shift the paradigm of current job and technology capabilities, as well as employment issues in many relevant industries. In particular, the actual case studies and their related policies and regulatory trends regarding the potential risks and ethical issues of artificial intelligence were introduced.
Regarding the financial services that utilize blockchain technologies and the establishment of public sector governance for such technologies, the participating experts noted difficulties in the diffusion of blockchain-based local currencies or public services, which call for a sophisticated analytical and practical framework for innovative and transparent governance.
Dr. Mark Boden, the Team Leader of the EU-JRC, introduced the EU’s initiatives to promote Smart Specialization, such as its policy process, governance design, vision sharing, and priority setting, with particular emphasis on targeted support for Smart Specialization in lagging regions. Professor So Young Kim, who is the dean of the Graduate School of Science and Technology Policy and FIRIC’s Deputy Director said, “KAIST’s global role regarding the Fourth Industrial Revolution will be expanded in the process of exploring and developing innovative models of technology-policy governance while working jointly with the EU-JRC.”
2019.08.02 View 7471 -
President Shin Shares Innovation Strategy at Moscow
President Sung-Chul Shin shared the recipe for success for rapid national development through university education during the Island 10-22 Conference held at the Skolov Institute of Science and Technology in Moscow on July 16.
President Shin stressed how urgent it is for higher education to rapidly embrace the new global economic environment brought about by the Fourth Industrial Revolution in his keynote address entitled ‘Roles and Responsibilities of Universities for Rapid National Development’.
The Island 10-22 Conference is a summit co-organized by the National University of Science and Technology MISIS and University of the National Technological Initiative 2035 and supported by the Ministry of Science and Higher Education of the Russian Federation. More than 30 world-renowned experts, presidents of leading technological universities including President Peretz Lavie from the Israel Institute of Technology Technion, President Scott Pulsipher from Western Governors University and specialists in big data participated in the conference as speakers and discussed a diverse spectrum of ideas for making innovations and digital transformations in universities. More than 1,600 participants joined the conference.
During his keynote speech, President Shin explained how Korea has achieved such rapid economic growth over the past half century. He cited the Korean government’s vision and innovation policies as factors leading to Korea’s phenomenal success. KAIST, one of the results of the Korean government’s innovation policy, led the nation to advanced technological breakthroughs in industries such as semiconductors. Such visionary policies and investments in science, technology, and education eventually made the Korea of today possible.
President Shin said that KAIST distinguished itself through its new vision of C3 that fosters intellectual creativity, caring for others, and a challenging mind . Under Vision 2031, a blueprint for becoming a leading global university, President Shin said the KAIST continues to strive for innovations in convergent education,research and entreprenurship.
2019.07.18 View 6656 -
High-Performance Sodium Ion Batteries Using Copper Sulfide
(Prof.Yuk and his two PhD candidates Parks)
Researchers presented a new strategy for extending sodium ion batteries’ cyclability using copper sulfide as the electrode material. This strategy has led to high-performance conversion reactions and is expected to advance the commercialization of sodium ion batteries as they emerge as an alternative to lithium ion batteries.
Professor Jong Min Yuk’s team confirmed the stable sodium storage mechanism using copper sulfide, a superior electrode material that is pulverization-tolerant and induces capacity recovery. Their findings suggest that when employing copper sulfide, sodium ion batteries will have a lifetime of more than five years with one charge per a day. Even better, copper sulfide, composed of abundant natural materials such as copper and sulfur, has better cost competitiveness than lithium ion batteries, which use lithium and cobalt.
Intercalation-type materials such as graphite, which serve as commercialized anode materials in lithium ion batteries, have not been viable for high-capacity sodium storage due to their insufficient interlayer spacing. Thus, conversion and alloying reactions type materials have been explored to meet higher capacity in the anode part. However, those materials generally bring up large volume expansions and abrupt crystallographic changes, which lead to severe capacity degradation.
The team confirmed that semi-coherent phase interfaces and grain boundaries in conversion reactions played key roles in enabling pulverization-tolerant conversion reactions and capacity recovery, respectively.
Most of conversion and alloying reactions type battery materials usually experience severe capacity degradations due to having completely different crystal structures and large volume expansion before and after the reactions. However, copper sulfides underwent a gradual crystallographic change to make the semi-coherent interfaces, which eventually prevented the pulverization of particles. Based on this unique mechanism, the team confirmed that copper sulfide exhibits a high capacity and high cycling stability regardless of its size and morphology.
Professor Yuk said, “Sodium ion batteries employing copper sulfide can advance sodium ion batteries, which could contribute to the development of low-cost energy storage systems and address the micro-dust issue”
This study was posted in Advanced Science on April 26 online and selected as the inside back cover for June issue.
(Figure: Schematic model demonstrating grain boundaries and phase interfaces formations.)
2019.07.15 View 28057 -
Deep Learning-Powered 'DeepEC' Helps Accurately Understand Enzyme Functions
(Figure: Overall scheme of DeepEC)
A deep learning-powered computational framework, ‘DeepEC,’ will allow the high-quality and high-throughput prediction of enzyme commission numbers, which is essential for the accurate understanding of enzyme functions.
A team of Dr. Jae Yong Ryu, Professor Hyun Uk Kim, and Distinguished Professor Sang Yup Lee at KAIST reported the computational framework powered by deep learning that predicts enzyme commission (EC) numbers with high precision in a high-throughput manner.
DeepEC takes a protein sequence as an input and accurately predicts EC numbers as an output. Enzymes are proteins that catalyze biochemical reactions and EC numbers consisting of four level numbers (i.e., a.b.c.d) indicate biochemical reactions. Thus, the identification of EC numbers is critical for accurately understanding enzyme functions and metabolism.
EC numbers are usually given to a protein sequence encoding an enzyme during a genome annotation procedure. Because of the importance of EC numbers, several EC number prediction tools have been developed, but they have room for further improvement with respect to computation time, precision, coverage, and the total size of the files needed for the EC number prediction.
DeepEC uses three convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers if the three CNNs do not produce reliable EC numbers for a given protein sequence. DeepEC was developed by using a gold standard dataset covering 1,388,606 protein sequences and 4,669 EC numbers.
In particular, benchmarking studies of DeepEC and five other representative EC number prediction tools showed that DeepEC made the most precise and fastest predictions for EC numbers. DeepEC also required the smallest disk space for implementation, which makes it an ideal third-party software component.
Furthermore, DeepEC was the most sensitive in detecting enzymatic function loss as a result of mutations in domains/binding site residue of protein sequences; in this comparative analysis, all the domains or binding site residue were substituted with L-alanine residue in order to remove the protein function, which is known as the L-alanine scanning method.
This study was published online in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) on June 20, 2019, entitled “Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers.”
“DeepEC can be used as an independent tool and also as a third-party software component in combination with other computational platforms that examine metabolic reactions. DeepEC is freely available online,” said Professor Kim.
Distinguished Professor Lee said, “With DeepEC, it has become possible to process ever-increasing volumes of protein sequence data more efficiently and more accurately.”
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. This work was also funded by the Bio & Medical Technology Development Program of the National Research Foundation of Korea funded by the Korean government, the Ministry of Science and ICT.
Profile:
-Professor Hyun Uk Kim (ehukim@kaist.ac.kr)
https://sites.google.com/view/ehukim
Department of Chemical and Biomolecular Engineering
-Distinguished Professor Sang Yup Lee (leesy@kaist.ac.kr)
Department of Chemical and Biomolecular Engineering
http://mbel.kaist.ac.kr
2019.07.09 View 36989