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An Advanced Method of DNA Nanostructure Formation Developed
Professor Tae-Young Yoon’s research team from the Department of Physics at KAIST has developed a new method to form DNA nanostructures by using magnetic tweezers to observe and to induce the formation of the structure in real time.
Unlike traditional designs of "DNA origami" which relies on thermal or chemical annealing methods, the new technology utilizes a completely different dynamic in DNA folding. This allows the folding to be done within only ten minutes.
Developed in 2006, the "DNA origami" allows a long skeleton of DNA to be folded into an arbitrary structure by using small stapler DNA pieces. This has been a prominent method in DNA nanotechnology.
However, the traditional technology which adopts thermal processes could not control the DNA formation during the folding because every interaction among DNAs occurs simultaneously. Thus, the thermal processes, which take dozens of hours to complete, had to be repeated multiple times in order to find the optimal condition.
The research team designed a DNA folding using uni-molecular magnetic tweezers that applied force to a single DNA molecule while measuring the state of the DNA. Through this technology, they were able to induce the formation of DNA nanostructure and observe it at the same time.
During high temperature heat treatment, the first stage of conventional thermal processes, the internal structure of the long skeleton DNA untangles. To induce such state, after attaching one side of the skeleton DNA to the surface of glass and the other side to a magnetic material, the team unfolded the internal structure of the DNA by pulling the two sides apart with magnetic force.
Unlike the conventional thermal processes, this method lets the stapler DNA swiftly adhere to the skeleton DNA within a minute because the sites are revealed at room temperature.
After the stapler pieces connected to the skeleton, the team removed the magnetic force. Next, the structure folded through self-assembly as the stapler DNAs stuck to different sites on the skeleton DNA.
Professor Yoon said, “With the existing thermal methods, we could not differentiate the reactions of the DNA because the response of each DNA pieces mutually interacted with each other.” He added that “Using the magnetic tweezers, we were able to sort the process of DNA nanostructure formation into a series of reactions of DNA molecules that are well known, and shorten the time taken for formation in only ten minutes.”
He commented, “This nanostructure formation method will enable us to create more intricate and desirable DNA nanostructures by programming the folding of DNA origami structures.”
Conducted by Dr. Woori Bae under the guidance of Professor Yoon, the research findings were published online in the December 4th issue of Nature Communications.
Figure 1: Uni-molecular magnetic tweezers orchestrating the DNA nanostructure formation
Figure 2: The evolution of DNA nanostructure formation using magnetic tweezers. The DNA nanostructure with a 21-nanometer size was formed in about eight minutes.
2015.01.06 View 6952 -
The Graduate School of Green Growth at KAIST Holds a Student Conference
The Graduate School of Green Growth at KAIST hosted a student conference on December 22, 2014 at the Seoul campus of the College of Business. About 100 master’s and doctoral students joined the conference held under the theme of “Green Knowledge Hub” and presented their research papers.
At the conference, three students received awards. The author of a paper entitled “Development and Analysis of Climate Change Vulnerability Index Applicable to Developing Countries” received the grand prize. The authors of “Green IT and Its Case Study on the Reduction of Greenhouse Gas Emissions by Industry” and “Analysis of Correlation between Consumers’ Subjective Happiness and Their Green Purchasing” were selected for runner-up prizes, respectively.
Dean Jae-Kyu Lee of the Green Growth Graduate School said, “We offered the conference to our students to engage with their peers and share ideas and knowledge in their majors. I hope students become more motivated, and we will continue holding this event in the future.”
2015.01.05 View 6725 -
A Key Signal Transduction Pathway Switch in Cardiomyocyte Identified
A KAIST research team has identified the fundamental principle in deciding the fate of cardiomyocyte or heart muscle cells. They have determined that it depends on the degree of stimulus in β-adrenergic receptor signal transduction pathway in the cardiomyocyte to control cells' survival or death. The findings, the team hopes, can be used to treat various heart diseases including heart failure.
The research was led by KAIST Department of Bio and Brain Engineering Chair Professor Kwang-Hyun Cho and conducted by Dr. Sung-Young Shin (lead author) and Ph.D. candidates Ho-Sung Lee and Joon-Hyuk Kang. The research was conducted jointly with GIST (Gwangju Institute of Science and Technology) Department of Biological Sciences Professor Do-Han Kim’s team. The research was supported by the Ministry of Science, ICT and Future Planning, Republic of Korea, and the National Research Foundation of Korea. The paper was published in Nature Communications on December 17, 2014 with the title, “The switching role of β-adrenergic receptor signalling in cell survival or death decision of cardiomyocytes.”
The β-adrenergic receptor signal transduction pathway can promote cell survival (mediated by β2 receptors), but also can result in cell death by inducing toxin (mediated by β1 receptors) that leads to various heart diseases including heart failure. Past attempts to identify the fundamental principle in the fate determining process of cardiomyocyte based on β-adrenergic receptor signalling concluded without much success.
The β-adrenergic receptor is a type of protein on the cell membrane of cardiomyocyte (heart muscle cell) that when stimulated by neurohormones such as epinephrine or norepinephrine would transduce signals making the cardiomyocyte contract faster and stronger.
The research team used large-scale computer simulation analysis and systems biology to identify ERK* and ICER** signal transduction pathways mediated by a feed-forward circuit as a key molecular switch that decides between cell survival and death.
Weak β-adrenergic receptor stimulations activate ERK signal transduction pathway, increasing Bcl-2*** protein expression to promote cardiomyocyte survival. On the other hand, strong β-adrenergic receptor stimulations activate ICER signal transduction pathway, reducing Bcl-2 protein expression to promote cardiomyocyte death.
Researchers used a systems biology approach to identify the mechanism of B-blocker****, a common drug prescribed for heart failure. When cardiomyocyte is treated with β1 inhibitor, strong stimulation on β-adrenergic receptor increases Bcl-2 expression, improving the chance of cardiomyocyte survival, a cell protection effect.
Professor Kwang-Hyun Cho said, “This research used systems biology, an integrated, convergence research of IT (information technology) and BT (biotechnology), to successfully identify the mechanism in deciding the fate of cardiomyocytes based on the β-adrenergic receptor signal transduction pathway for the first time. I am hopeful that this research will enable the control of cardiomyocyte survival and death to treat various heart diseases including heart failure.”
Professor Cho’s team was the first to pioneer a new field of systems biology, especially concerning the complex signal transduction network involved in diseases. Their research is focused on modelling, analyzing simulations, and experimentally proving signal pathways. Professor Cho has published 140 articles in international journals including Cell, Science, and Nature.
* ERK (Extracellular signal-regulated kinases): Signal transduction molecule involved in cell survival
** ICER (Inducible cAMP early repressor): Signal transduction molecule involved in cell death
*** Bcl-2 (B-cell lymphoma 2): Key signal transduction molecule involved in promotion of cell survival
**** β-blocker: Drug that acts as β-adrenergic receptor inhibitor known to slow the progression of heart failure, hence used most commonly in medicine.
Picture: A schematic diagram for the β-AR signalling network
2015.01.05 View 12266 -
The KAIST Graduate School of Future Strategy Publishes a Book on the Future Strategy for the Development of Korea
As science and technology play an integral role in shaping the future of a nation, a group of scientists at KAIST recently published a book entitled “The National Future Strategy 2015.” The book is available in Korean only.
In the book, the writers propose strategic thinking and plans for Korea to become one of the leading nations on the global stage in the next 30 years. It also suggests a strategic vision for the development of Korea by 2045, the centenary of Korea’s independence from Japan, and recommends specific approaches to address some of the important issues facing Korea: social conflict from the unequal distribution of wealth, low birthrates, an aging population, climate change, the reunification of the Korean peninsula, sustainability, and protection of democracy.
In addition to writings contributed by KAIST professors, the book contains the results of public hearings on major social issues, as well as insights offered by one hundred experts including politicians, government officials, and business representatives.
2014.12.27 View 5910 -
Professor Mikyoung Lim Receives the MediaV Young Researcher Award
Professor Mikyoung Lim of the Department of Mathematical Sciences at KAIST received the MediaV Young Researchers Award at the International Conference on Inverse Problems and Related Topics that took place at the National Taiwan University, Taiwan, on December 15-19, 2014.
The Conference established the MediaV Young Researcher Award in 2010 to recognize distinguished scholars who are age 40 or younger and have made important contributions to the field of inverse problems. This year, two recipients were chosen for the award.
Professor Lim has focused her research on the incremental reading of incomprehensible materials’ imaging and the effect of invisibility cloaking.
The other awardee was Kui Ren, a professor at the University of Texas at Austin.
2014.12.27 View 9812 -
How Science Understands the Beauty of Fine Arts from the Medieval Era to the 19th Century
A research team, consisting of Professor Hawoong Jeong of the Department of Physics at KAIST and Assistant Professor Seung-Woo Son of the Department of Applied Physics at Hanyang University, conducted a research project to understand visual representations through the eyes of science, i.e., quantitative analyses. Researchers took a sample of reproductions of European paintings from the 11th to the early 19th centuries and analyzed them based on three elements: the usage of color, the variety of painted colors, and the brightness of the images.
For the large-scale quantitative analysis, the research team utilized digital images of the paintings obtained from the Web Gallery of Art, a virtual museum and searchable database of European fine arts that includes over 29,000 pieces, ranging from the years 1000 to 1850. The Web Gallery classifies paintings into ten art historical periods such as Medieval, Renaissance, Mannerist, Baroque, Rococo, Romantic, and Realist.
For each period, researchers investigated the frequency of certain colors which appear in paintings and examined the variety of painted colors, paying particular attention to paintings created by two iconoclastic artists from different eras: Pieter Bruegel the Elder and Jackson Pollock. In their works, the researchers discovered that specific pigments were preferred in each period, the result of reflecting historical facts into fine arts. For example, certain rare colors were used in the medieval age for political and religious reasons, and artists in that era employed a technique to layer one color over another dry color in order to express mixed colors, resulting in thickly textured brushstrokes because they considered mixing colors impure. Moreover, oil colors and color mixing techniques were not fully developed until the Renaissance age.
According to the research team, fewer numbers of colors were used before the 20th century, and the introduction of new expressionist tools, like the use of pastels and fingers directly on canvas, and painting techniques, such as “chiaroscuro” and “sfumato,” made much more colorful and natural expressions possible after the Renaissance period. The team said that the color arrangement of Jackson Pollock’s drip paintings differed substantially from other paintings, showing randomness, especially in the spatial arrangement of colors.
Researchers also examined one of the artistic effects applied to paintings, contrast, an important element to express shape and space in two dimensional fine arts. Among various types of contrasts, they said, brightness contrast is the most important in art history due to the cultural background of Europe which usually adopts the contrast of light and darkness as a metaphorical expression. Taking the color information of pixels and their spatial arrangement, the researchers studied the prevalence of brightness contrast in European paintings over ten artistic periods by developing a correlation function to measure the contrast. These mathematical measurements quantitatively describe the birth of new painting techniques including chiaroscuro and sfumato and their increasing use. For instance, in the medieval age, the contour of objects or images in paintings was vague, but it became much clearer later in the Romantic period.
Professor Jeong said, “The complexity of the material world has been a long-lasting topic of interest in natural science, but research in the structural complexity of art and humanities has only begun since the development of the Internet, with the availability of big data in these fields. Our research is a meaningful attempt to understand the underling intricacy of art and humanities based on a scientific approach, expressed quantitatively.”
The research results were published online on December 11, 2014 in Scientific Reports, entitled “Large-Scale Quantitative Analysis of Painting Arts.” The paper was also selected as one of the weekly research highlights by Nature and is noted on its online journal’s website.
YouTube link on “the brightness contrast”: http://youtu.be/SFo0h1EU2aw
Figure 1: Constructing brightness surfaces and measuring roughness exponents
Figure 2: Visual representations of Mona Lisa painted by Leonardo da Vinci, which was reproduced in accordance with the art historical periods
Figure 3: The screenshot of Nature online webpage
2014.12.23 View 8230 -
IamCompany and KAIST's Midam Scholarship Contribute Scholarship to High School Students
IamCompany, a venture company established by a KAIST student which provides mobile users with educational applications, and Midam Scholarship, a volunteer group consisting of KAIST students that helps junior and high school students study math and science, selected a total of 118 students and presented them with scholarships.
Among the students, Ki-Bum Kim of Kyung-Hee High School in Seoul received USD 1,300, the largest sum.
In-Mo Chung, the President of IamCompany, who once worked as a member of Midam Scholarship, said, “I joined this scholarship program to support the Midam Scholarhsip which offers educational services to less privileged students. I hope many young students will benefit from this and receive an equal opportunity for better education.”
2014.12.15 View 6292 -
KAIST wins second place in unmanned boat competition
KAIST took second place in an international competition to promote technologies of the autonomous underwater vehicle (AUV).
Professor Jin-hwan Kim’s research team from KAIST’s Ocean Systems Engineering Department won the second place in Maritime RobotX Challenge which took place for the first time from October 20 - 26 in Marina Bay, Singapore.
Along with automobiles and drones, the necessity for unmanned boats has grown. To encourage and examine the development of these technologies, the U.S. Office of Naval Research decided to organize an unmanned boat competition which took place for the first time this year.
After three teams were selected from a domestic competition in each countries, a total of fifteen teams from five countries from the Pacific Rim including Korea, the United States, Australia, Japan, and Singapore competed. Teams from such universities as MIT, Tokyo University, Tokyo Institute of Technology, National University of Singapore, Nanyang Technological University, and Queensland University of Technology participated. In addition to KAIST, Seoul National University and Ulsan University participated.
Using a 4.5 meters long and 2.5 meters wide unmanned boat provided by the organizer, each team had to implement an integrated system that combined a propulsion system, hardware, and autonomous software. Each team’s vessel had to perform tasks without manual control, employing autonomous driving through recognition of the course, searching underwater for acoustic sources, automatically approaching piers, remote observation of buoy, and avoidance and detection of obstacles.
Although KAIST outpaced MIT in the semifinal which selected six out of fifteen teams, it won the second place in the final. As well as winning second prize, KAIST also won best website prize and a special prize from the competition sponsor, Northrop Grumman Corporation, an American defense technology company, totaling 16,500 U.S. dollars of prize money.
The Vice President for Planning and Budget, Professor Seungbin Park said, “It was a great opportunity to showcase the advanced unmanned robot technology of Korea.” He added that “this raised KAIST’s reputation as a global research oriented university.”
Professor Kim commented, “Along with automobiles and drones, the necessity for the development of unmanned ocean vehicles such as unmanned boats and submarines are recognized these days.” He added that “the use of unmanned boats will make the process of channel investigation, ocean exploration, surveillance over water territories safer and more effective.”
Professor Kim’s team was sponsored by the U.S. Office of Naval Research, Samsung Heavy Industries, Sonar Tech, Daeyang Electric, and Red-one Technology.
KAIST Team's Unmanned Boat
The Competition's Missions
2014.12.12 View 10328 -
KAIST Establishes a Center for Human Rights and Ethics
KAIST hosted an opening ceremony on November 27, 2014 for its Center for Human Rights and Ethics (CHRE) located in the Education Support Building on campus.
President Steve Kang and other senior administrators participated in the ceremony, pledging to eliminate violence, corruption, and prejudice on the campus.
The CHRE was created to provide members of the KAIST community with one-stop service to report and process human rights violation cases and issues related to corruption and illegalities such as verbal abuse, physical assault, sexual harassment, and bribes. The center will also launch campaigns to promote and strengthen awareness of human rights and ethics within the university.
The Director of CHRE, Professor Young-hee Kim of the Department of Humanities and Social Sciences at KAIST said, “The center will serve an important role in the improvement of human rights and in the reestablishment of moral standards in KAIST. I hope KAIST members make the most of the center wherever they face injustice and unequal treatment during their study and work at the campus.”
2014.12.08 View 6639 -
Kimchi Making by Students and KAIPlus Members
Kimchi is a traditional Korean dish of fermented vegetables, with the most common ingredients of Napa cabbages and daikon radishes. Every winter, Koreans make bountiful amounts of kimchi for consumption in the winter months.
President Steve Kang and about 50 KAIST students and members of KAIPlus, a volunteer group consisted of spouses of KAIST Faculty, made kimchi on November 28, 2014 at the Sports Complex on campus. They prepared 500 Napa cabbages for kimchi which were donated to local people in need.
2014.12.08 View 5476 -
KAIST Partners with Science-focused Universities in Korea for Student Exchange Programs
KAIST and four science-focused universities in Korea (Pohang University of Science and Technology, Gwangju Institute of Science and Technology, Daegu Gyeongbuk Institute of Science and Technology, and Ulsan National Institute of Science and Technology) agreed to exchange programs during academic semesters including summer and winter terms by signing a memorandum of understanding (MOU) on November 28, 2014. The signing ceremony took place at the KAIST campus with the participation of academic affairs deans from all five universities.
Based on the agreement, KAIST students can take up to 12 credits of coursework at any of the said universities and have unimpeded access to the university facilities during their coursework.
Dean Hyun-Wook Park of Academic Affairs at KASIT said, “Through exchange programs, students can capitalize on each university’s advantages, and this eventually will lead to greater advancement in science and technology in the nation.”
2014.12.08 View 7572 -
KAIST Presents the Largest Number of Research Papers at the 2015 ISSCC
KAIST will present the largest number of research papers at the 2015 IEEE International Solid-State Circuits Conference (ISSCC), a leading global forum held every year to share professional knowledge and advancements in solid-state circuits and systems-on-a-chip. The Institute of Electrical and Electronics Engineers (IEEE) Solid-State Circuits Society sponsors the conference.
This year, the conference accepted 13 research papers from KAIST, ranking first among the participating organizations. Samsung Electronics Co., Ltd. took second (9 papers) place, and Intel Corporation and IMEC were in third place with 8 papers, respectively. A total of 610 papers were submitted, and reviewers selected only 206 papers for presentation at the next year's conference.
Since 2011, KAIST has been the number one institution among universities with the largest number of papers presented at the conference.
The Associate Chair of ISSCC Program Committee Chair, Professor Hoi-Jun Yoo of the Department of Electrical Engineering at KAIST, said, “Korea started the semiconductor industry in the 1970s, and since then, KAIST has been the center of research and development for the industry. With the establishment of IC (integrated circuit) Design Education Center in 1995, KAIST has contributed tremendously to the education and research of semiconductor production, nationally and globally. As shown from the record of presenting research results at the ISSCC, KAIST will continue to collaborate closely with the industry and lead the field.”
The 2015 IEEE ISSCC will take place on February 22-26, 2015 in San Francisco, CA, in the US.
2014.12.08 View 7857