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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
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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
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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
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Chemical Scissors Snip 2D Transition Metal Dichalcogenides into Nanoribbon
New ‘nanoribbon’ catalyst should slash cost of hydrogen production for clean fuels Researchers have identified a potential catalyst alternative – and an innovative way to produce them using chemical ‘scissors’ – that could make hydrogen production more economical. The research team led by Professor Sang Ouk Kim at the Department of Materials Science and Engineering published their work in Nature Communications. Hydrogen is likely to play a key role in the clean transition away from fossil fuels and other processes that produce greenhouse gas emissions. There is a raft of transportation sectors such as long-haul shipping and aviation that are difficult to electrify and so will require cleanly produced hydrogen as a fuel or as a feedstock for other carbon-neutral synthetic fuels. Likewise, fertilizer production and the steel sector are unlikely to be “de-carbonized” without cheap and clean hydrogen. The problem is that the cheapest methods by far of producing hydrogen gas is currently from natural gas, a process that itself produces the greenhouse gas carbon dioxide–which defeats the purpose. Alternative techniques of hydrogen production, such as electrolysis using an electric current between two electrodes plunged into water to overcome the chemical bonds holding water together, thereby splitting it into its constituent elements, oxygen and hydrogen are very well established. But one of the factors contributing to the high cost, beyond being extremely energy-intensive, is the need for the very expensive precious and relatively rare metal platinum. The platinum is used as a catalyst–a substance that kicks off or speeds up a chemical reaction–in the hydrogen production process. As a result, researchers have long been on the hunt for a substitution for platinum -- another catalyst that is abundant in the earth and thus much cheaper. Transition metal dichalcogenides, or TMDs, in a nanomaterial form, have for some time been considered a good candidate as a catalyst replacement for platinum. These are substances composed of one atom of a transition metal (the elements in the middle part of the periodic table) and two atoms of a chalcogen element (the elements in the third-to-last column in the periodic table, specifically sulfur, selenium and tellurium). What makes TMDs a good bet as a platinum replacement is not just that they are much more abundant, but also their electrons are structured in a way that gives the electrodes a boost. In addition, a TMD that is a nanomaterial is essentially a two-dimensional super-thin sheet only a few atoms thick, just like graphene. The ultrathin nature of a 2-D TMD nanosheet allows for a great many more TMD molecules to be exposed during the catalysis process than would be the case in a block of the stuff, thus kicking off and speeding up the hydrogen-making chemical reaction that much more. However, even here the TMD molecules are only reactive at the four edges of a nanosheet. In the flat interior, not much is going on. In order to increase the chemical reaction rate in the production of hydrogen, the nanosheet would need to be cut into very thin – almost one-dimensional strips, thereby creating many edges. In response, the research team developed what are in essence a pair of chemical scissors that can snip TMD into tiny strips. “Up to now, the only substances that anyone has been able to turn into these ‘nano-ribbons’ are graphene and phosphorene,” said Sang Professor Kim, one of the researchers involved in devising the process. “But they’re both made up of just one element, so it’s pretty straightforward. Figuring out how to do it for TMD, which is made of two elements was going to be much harder.” The ‘scissors’ involve a two-step process involving first inserting lithium ions into the layered structure of the TMD sheets, and then using ultrasound to cause a spontaneous ‘unzipping’ in straight lines. “It works sort of like how when you split a plank of plywood: it breaks easily in one direction along the grain,” Professor Kim continued. “It’s actually really simple.” The researchers then tried it with various types of TMDs, including those made of molybdenum, selenium, sulfur, tellurium and tungsten. All worked just as well, with a catalytic efficiency as effective as platinum’s. Because of the simplicity of the procedure, this method should be able to be used not just in the large-scale production of TMD nanoribbons, but also to make similar nanoribbons from other multi-elemental 2D materials for purposes beyond just hydrogen production. -ProfileProfessor Sang Ouk KimSoft Nanomaterials Laboratory (http://snml.kaist.ac.kr)Department of Materials Science and EngineeringKAIST
2020.10.29
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'Mini-Lungs' Reveal Early Stages of SARS-CoV-2 Infection
Researchers in Korea and the UK have successfully grown miniature models of critical lung structures called alveoli, and used them to study how the coronavirus that causes COVID-19 infects the lungs. To date, there have been more than 40 million cases of COVID-19 and almost 1.13 million deaths worldwide. The main target tissues of SARS-CoV-2, the virus that causes COVID-19, especially in patients that develop pneumonia, appear to be alveoli – tiny air sacs in the lungs that take up the oxygen we breathe and exchange it with carbon dioxide to exhale. To better understand how SARS-CoV-2 infects the lungs and causes disease, a team of Professor Young Seok Ju from the Graduate School of Medical Science and Engineering at KAIST in collaboration with the Wellcome-MRC Cambridge Stem Cell Institute at the University of Cambridge turned to organoids – ‘mini-organs’ grown in three dimensions to mimic the behaviour of tissue and organs. The team used tissue donated to tissue banks at the Royal Papworth Hospital NHS Foundation Trust and Addenbrooke’s Hospital, Cambridge University NHS Foundations Trust, UK, and Seoul National University Hospital to extract a type of lung cell known as human lung alveolar type 2 cells. By reprogramming these cells back to their earlier ‘stem cell’ stage, they were able to grow self-organizing alveolar-like 3D structures that mimic the behaviour of key lung tissue. “The research community now has a powerful new platform to study precisely how the virus infects the lungs, as well as explore possible treatments,” said Professor Ju, co-senior author of the research. Dr. Joo-Hyeon Lee, another co-senior author at the Wellcome-MRC Cambridge Stem Cell Institute, said: “We still know surprisingly little about how SARS-CoV-2 infects the lungs and causes disease. Our approach has allowed us to grow 3D models of key lung tissue – in a sense, ‘mini-lungs’ – in the lab and study what happens when they become infected.” The team infected the organoids with a strain of SARS-CoV-2 taken from a patient in Korea who was diagnosed with COVID-19 on January 26 after traveling to Wuhan, China. Using a combination of fluorescence imaging and single cell genetic analysis, they were able to study how the cells responded to the virus. When the 3D models were exposed to SARS-CoV-2, the virus began to replicate rapidly, reaching full cellular infection just six hours after infection. Replication enables the virus to spread throughout the body, infecting other cells and tissue. Around the same time, the cells began to produce interferons – proteins that act as warning signals to neighbouring cells, telling them to activate their antiviral defences. After 48 hours, the interferons triggered the innate immune response – its first line of defence – and the cells started fighting back against infection. Sixty hours after infection, a subset of alveolar cells began to disintegrate, leading to cell death and damage to the lung tissue. Although the researchers observed changes to the lung cells within three days of infection, clinical symptoms of COVID-19 rarely occur so quickly and can sometimes take more than ten days after exposure to appear. The team say there are several possible reasons for this. It may take several days from the virus first infiltrating the upper respiratory tract to it reaching the alveoli. It may also require a substantial proportion of alveolar cells to be infected or for further interactions with immune cells resulting in inflammation before a patient displays symptoms. “Based on our model we can tackle many unanswered key questions, such as understanding genetic susceptibility to SARS-CoV-2, assessing relative infectivity of viral mutants, and revealing the damage processes of the virus in human alveolar cells,” said Professor Ju. “Most importantly, it provides the opportunity to develop and screen potential therapeutic agents against SARS-CoV-2 infection.” “We hope to use our technique to grow these 3D models from cells of patients who are particularly vulnerable to infection, such as the elderly or people with diseased lungs, and find out what happens to their tissue,” added Dr. Lee. The research was a collaboration involving scientists from KAIST, the University of Cambridge, Korea National Institute of Health, Institute for Basic Science (IBS), Seoul National University Hospital and Genome Insight in Korea. - ProfileProfessor Young Seok JuLaboratory of Cancer Genomics https://julab.kaist.ac.kr the Graduate School of Medical Science and EngineeringKAIST
2020.10.26
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Professor Won-Ki Cho Selected as the 2020 SUHF Young Investigator
Professor Won-Ki Cho from the Department of Biological Sciences was named one of three recipients of the 2020 Suh Kyung-Bae Science Foundation (SUHF) Young Investigator Award. The SUHF is a non-profit organization established in 2016 and funded by a personal donation of 300 billion KRW in shares from Chairman and CEO Kyung-Bae Suh of the Amorepacific Group. The primary purpose of the foundation is to serve as a platform to nurture and provide comprehensive long-term support for creative and passionate young Korean scientists committed to pursuing research in the field of life sciences. The SUHF selects three to five scientists through an open recruiting process every year and grants each scientist a maximum of 2.5 billion KRW over a period of up to five years. Since January this year, the foundation received 67 research proposals from scientists across the nation, especially from those who had less than five years of experience as professors, and selected the three recipients. Professor Cho proposed research on how to observe the interactions between nuclear structures and constantly-changing chromatin monomers in four dimensions through ultra-high-resolution imaging of single living cells. This proposal was recognized as one that could help us better understand the process of transcription regulation, which remains a long-standing question in biology. The other awards were given to Professor Soung-hun Roh of Seoul National University and Professor Joo-Hyeon Lee of the University of Cambridge. With these three new awardees, a total of 17 scientists have been named SUHF Young Investigators to date, and the funding to support these scientists now totals 42.5 billion KRW. Professor Inkyung Jung and Professor Ki-Jun Yoon from the Department of Biological Sciences, and Professor Young Seok Ju and Professor Jeong Ho Lee from the Graduate School of Medical Science and Engineering are the four previous winners from KAIST in the years 2017 through 2019. (END)
2020.10.15
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Big Ideas on Emerging Materials Explored at EMS
Renowned scholars and editors from academic journals joined the Emerging Materials e-Symposium (EMS) held at KAIST and shared the latest breakthroughs and big ideas in new material development last month. This e-symposium was organized by Professor Il-Doo Kim from the KAIST Department of Materials Sciences and Engineering over five days from September 21 through 25 via Zoom and YouTube. Professor Kim also serves as an associate editor of ACS Nano. Esteemed scholars and editors of academic journals including ACS Nano, Nano Energy, and Energy Storage Materials made Zoom presentations in three main categories: 1) nanostructures for next-generation applications, 2) chemistry and biotechnology for applications in the fields of environment and industry, and 3) material innovation for technological applications. During Session I, speakers including Professor John A. Rogers of Northwestern University and Professor Zhenan Bao of Stanford University led the session on Emerging Soft Electronics and 3D printing. In later sessions, other globally recognized scholars gave talks titled Advanced Nanostructuring for Emerging Materials, Frontiers in Emerging Materials Research, Advanced Energy Materials and Functional Nanomaterials, and Latest Advances in Nanomaterials Research. These included 2010 Nobel Prize laureate and professor at Manchester University Andre Geim, editor-in-chief of ACS Nano and professor at UCLA Paul S. Weiss, Professor Paul Alivisatos of UC Berkeley, Professor William Chueh of Stanford University, and Professor Mircea Dinca of MIT. KAIST President Sung-Chul Shin, who is also a materials physicist, said in his opening address, “Innovation in materials science will become an important driving force to change our way of life. All the breakthroughs in materials have extended a new paradigm that has transformed our lives.” “Creative research projects alongside global collaborators like all of you will allow the breakthroughs that will deliver us from these crises,” he added. (END)
2020.10.06
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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
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Life After COVID-19: Big Questions on Medical and Bio-Engineering
KAIST GSI forum explores big questions in the medical and bio-engineering revolution caused by the COVID-19 in fight against infectious diseases and life quality On September 9, the Global Strategy Institute at KAIST will delve into innovative future strategies for the medical and bio-engineering sectors that have been disrupted by COVID-19. The forum will live stream via YouTube, KTV, and Naver TV from 9:00 am Korean time. The online forum features a speaker lineup of world-renowned scholars who will discuss an array of bio-engineering technologies that will improve our quality of life and even extend our life span. This is the GSI’s third online forum since the first one in April that covered the socio-economic implications of the global pandemic and the second one in June focusing on the education sector. In hosting the third round of the GSI Forum series, KAIST President Sung-Chul Shin stressed the power of science and technology saying, “In this world full of uncertainties, one thing for sure is that only the advancement of science and technology will deliver us from this crisis.” Korean Prime Minister Sye-Kyun Chung will also deliver a speech explaining the government’s response to COVID-19 and vaccine development strategies. The President of the National Academy of Medicine in the US will share ideal policies to back up the bio-engineering and medical sectors and Futurist Thomas Frey from the Davinci Institute will present his distinct perspectives on our future lives after COVID-19. His thought-provoking insights on advancements in the bioengineering sector will examine whether humanity can put an end to infectious diseases and find new ways to lengthen our lives. Two distinguished professors in the field of genetic engineering technology will share their latest breakthroughs. Professor George McDonald Church from Harvard Medical School who developed genome sequencing will deliver a keynote speech on how the advancement of gene editing and genome technology will overcome diseases and contribute to extending human life spans. Professor Kwang-Soo Kim, a KAIST alumnus from Harvard Medical School who recently reported new discoveries for Parkinson’s disease treatment by reprogramming a patient’s own skin cells to replace cells in the brain, will introduce the latest clinical cell treatment technologies based on personalized therapeutics. Senior Vice President and Chief Product Officer of Illumina Susan Tousi, a leading genome sequencing solution provider, will describe genome analysis technology and explore the potential for disease prevention. KAIST medical scientist Jeong Ho Lee, who was the first to identify the causes of intractable epilepsies and has identified the genes responsible for several developmental brain disorders. Professor Jin-Hyung Lee from Stanford University and Dr. David B. Resnik from the National Institute of Environmental Health Science will also join the speaker lineup to discuss genetics-based personalized solutions to extend human life spans. The forum will also invite about 50 young scientists and medical researchers from around the world to participate in an online panel session. They will engage in a Q&A session and a discussion with the speakers. (END)
2020.09.04
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Advanced NVMe Controller Technology for Next Generation Memory Devices
KAIST researchers advanced non-volatile memory express (NVMe) controller technology for next generation information storage devices, and made this new technology named ‘OpenExpress’ freely available to all universities and research institutes around the world to help reduce the research cost in related fields. NVMe is a communication protocol made for high-performance storage devices based on a peripheral component interconnect-express (PCI-E) interface. NVMe has been developed to take the place of the Serial AT Attachment (SATA) protocol, which was developed to process data on hard disk drives (HDDs) and did not perform well in solid state drives (SSDs). Unlike HDDs that use magnetic spinning disks, SSDs use semiconductor memory, allowing the rapid reading and writing of data. SSDs also generate less heat and noise, and are much more compact and lightweight. Since data processing in SSDs using NVMe is up to six times faster than when SATA is used, NVMe has become the standard protocol for ultra-high speed and volume data processing, and is currently used in many flash-based information storage devices. Studies on NVMe continue at both the academic and industrial levels, however, its poor accessibility is a drawback. Major information and communications technology (ICT) companies around the world expend astronomical costs to procure intellectual property (IP) related to hardware NVMe controllers, necessary for the use of NVMe. However, such IP is not publicly disclosed, making it difficult to be used by universities and research institutes for research purposes. Although a small number of U.S. Silicon Valley startups provide parts of their independently developed IP for research, the cost of usage is around 34,000 USD per month. The costs skyrocket even further because each copy of single-use source code purchased for IP modification costs approximately 84,000 USD. In order to address these issues, a group of researchers led by Professor Myoungsoo Jung from the School of Electrical Engineering at KAIST developed a next generation NVMe controller technology that achieved parallel data input/output processing for SSDs in a fully hardware automated form. The researchers presented their work at the 2020 USENIX Annual Technical Conference (USENIX ATC ’20) in July, and released it as an open research framework named ‘OpenExpress.’ This NVMe controller technology developed by Professor Jung’s team comprises a wide range of basic hardware IP and key NVMe IP cores. To examine its actual performance, the team made an NVMe hardware controller prototype using OpenExpress, and designed all logics provided by OpenExpress to operate at high frequency. The field-programmable gate array (FPGA) memory card prototype developed using OpenExpress demonstrated increased input/output data processing capacity per second, supporting up to 7 gigabit per second (GB/s) bandwidth. This makes it suitable for ultra-high speed and volume next generation memory device research. In a test comparing various storage server loads on devices, the team’s FPGA also showed 76% higher bandwidth and 68% lower input/output delay compared to Intel’s new high performance SSD (Optane SSD), which is sufficient for many researchers studying systems employing future memory devices. Depending on user needs, silicon devices can be synthesized as well, which is expected to further enhance performance. The NVMe controller technology of Professor Jung’s team can be freely used and modified under the OpenExpress open-source end-user agreement for non-commercial use by all universities and research institutes. This makes it extremely useful for research on next-generation memory compatible NVMe controllers and software stacks. “With the product of this study being disclosed to the world, universities and research institutes can now use controllers that used to be exclusive for only the world’s biggest companies, at no cost,ˮ said Professor Jung. He went on to stress, “This is a meaningful first step in research of information storage device systems such as high-speed and volume next generation memory.” This work was supported by a grant from MemRay, a company specializing in next generation memory development and distribution. More details about the study can be found at http://camelab.org. Image credit: Professor Myoungsoo Jung, KAIST 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: Myoungsoo Jung. (2020). OpenExpress: Fully Hardware Automated Open Research Framework for Future Fast NVMe Devices. Presented in the Proceedings of the 2020 USENIX Annual Technical Conference (USENIX ATC ’20), Available online at https://www.usenix.org/system/files/atc20-jung.pdf -Profile: Myoungsoo Jung Associate Professor m.jung@kaist.ac.kr http://camelab.org Computer Architecture and Memory Systems Laboratory School of Electrical Engineering http://kaist.ac.kr Korea Advanced Institute of Science and Technology (KAIST) Daejeon, Republic of Korea (END)
2020.09.04
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KAIST Technology Value Tops in Commercialization Market
KAIST became the first Korean university to achieve 10.183 billion KRW in annual technology royalties, and was also selected as an ‘Institution of Outstanding Patent Quality Management’ and an ‘Institution of Outstanding Public Patent Technology Transfer’ for 2020. KAIST earns its technology royalties through 56 technology transfer contracts. Following KAIST in the rankings were Seoul National University (SNU) in second place with 8.8 billion KRW from 87 contracts and Korea University (KU) in the third with 5.4 billion KRW from 133 contracts. The data shows the high value of KAIST-created technology in the market. The Korean Intellectual Property Office (KIPO) started to recognize the Institution of Outstanding Patent Quality Management this year to encourage profit-driven patent management at universities and public research institutes, and KAIST was selected as one of the four first recipients of this distinction. In addition, KAIST was selected as an Institution of Outstanding Public Patent Technology Transfer, a title given by KIPO to three universities and public research institutes this year with outstanding achievements in technology transfers and commercialization to encourage patent utilization. Director of the KAIST Institute of Technology Value Creation (ITVC) Professor Kyung-cheol Choi said that KAIST’s achievement in annual technology royalties and technology transfers and commercialization were prime examples of accelerating competitiveness in intellectual property through innovative R&D investment. In April, KAIST expanded and reorganized its Industry-Academia Collaboration Team into the ITVC to support technology transfers and commercialization. Specialized organizations such as the Intellectual Property and Technology Transfer Center and Industrial Liaison Center have been established under the ITVC, and industry experts have been recruited as special professors focusing on industry-academia collaborations to enhance its specialized functions. KAIST also operates an enterprise membership system and technology consulting system, aimed at sharing its outstanding intellectual property within domestic industries. In 2019, it secured a technology transfer commercialization fund of 1.2 billion KRW available for three years under KIPO’s Intellectual Property Profit Reinvestment Support Program (formerly the Korean Patent Gap Fund Creation Project). This program was introduced to bridge the gap between the technology developed in universities and the level of technology required by industry. Under the program, bold investments are made in early-stage technologies at the research paper or experiment phase. The program encourages enterprises to take active steps for the transfer of technologies by demonstrating their commercial potential through prototype production, testing and certification, and standard patent filing. KAIST is currently funding approximately 20 new technologies under this program as of July 2020. KAIST’s outstanding intellectual property management has also received international recognition, with its selection as Asia’s leading institution in university R&D intellectual property at the Intellectual Property Business Congress (IPBC) Asia 2019 held in Tokyo, Japan last October. (END)
2020.08.18
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Tinkering with Roundworm Proteins Offers Hope for Anti-aging Drugs
- The somatic nuclear protein kinase VRK-1 increases the worm’s lifespan through AMPK activation, and this mechanism can be applied to promoting human longevity, the study reveals. - KAIST researchers have been able to dial up and down creatures’ lifespans by altering the activity of proteins found in roundworm cells that tell them to convert sugar into energy when their cellular energy is running low. Humans also have these proteins, offering up the intriguing possibilities for developing longevity-promoting drugs. These new findings were published on July 1 in Science Advances. The roundworm Caenorhabditis elegans (C. elegans), a millimeter-long nematode commonly used in lab testing, enjoyed a boost in its lifespan when researchers tinkered with a couple of proteins involved in monitoring the energy use by its cells. The proteins VRK-1 and AMPK work in tandem in roundworm cells, with the former telling the latter to get to work by sticking a phosphate molecule, composed of one phosphorus and four oxygen atoms, on it. In turn, AMPK’s role is to monitor energy levels in cells, when cellular energy is running low. In essence, VRK-1 regulates AMPK, and AMPK regulates the cellular energy status. Using a range of different biological research tools, including introducing foreign genes into the worm, a group of researchers led by Professor Seung-Jae V. Lee from the Department of Biological Sciences at KAIST were able to dial up and down the activity of the gene that tells cells to produce the VRK-1 protein. This gene has remained pretty much unchanged throughout evolution. Most complex organisms have this same gene, including humans. Lead author of the study Sangsoon Park and his colleagues confirmed that the overexpression, or increased production, of the VRK-1 protein boosted the lifespan of the C. elegans, which normally lives just two to three weeks, and the inhibition of VRK-1 production reduced its lifespan. The research team found that the activity of the VRK-1-to-AMPK cellular-energy monitoring process is increased in low cellular energy status by reduced mitochondrial respiration, the set of metabolic chemical reactions that make use of the oxygen the worm breathes to convert macronutrients from food into the energy “currency” that cells spend to do everything they need to do. It is already known that mitochondria, the energy-producing engine rooms in cells, play a crucial role in aging, and declines in the functioning of mitochondria are associated with age-related diseases. At the same time, the mild inhibition of mitochondrial respiration has been shown to promote longevity in a range of species, including flies and mammals. When the research team performed similar tinkering with cultured human cells, they found they could also replicate this ramping up and down of the VRK-1-to-AMPK process that occurs in roundworms. “This raises the intriguing possibility that VRK-1 also functions as a factor in governing human longevity, and so perhaps we can start developing longevity-promoting drugs that alter the activity of VRK-1,” explained Professor Lee. At the very least, the research points us in an interesting direction for investigating new therapeutic strategies to combat metabolic disorders by targeting the modulation of VRK-1. Metabolic disorders involve the disruption of chemical reactions in the body, including diseases of the mitochondria. But before metabolic disorder therapeutics or longevity drugs can be contemplated by scientists, further research still needs to be carried out to better understand how VRK-1 works to activate AMPK, as well as figure out the precise mechanics of how AMPK controls cellular energy. This work was supported by the National Research Foundation (NRF), and the Ministry of Science and ICT (MSIT) of Korea. Image credit: Seung-Jae V. LEE, 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: Park, S., et al. (2020) ‘VRK-1 extends life span by activation of AMPK via phosphorylation’. Science Advances, Volume 6. No. 27, eaaw7824. Available online at https://doi.org/10.1126/sciadv.aaw7824 Profile: Seung-Jae V. Lee, Ph.D. Professor seungjaevlee@kaist.ac.kr https://sites.google.com/view/mgakaist Molecular Genetics of Aging Laboratory Department of Biological Sciences Korea Advanced Institute of Science and Technology (KAIST) https://www.kaist.ac.krDaejeon 34141, Korea (END)
2020.07.31
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