Department+of+Chemical+and+Biomolecular+Engineering
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KAIST Develops Ultrathin Polymer Insulators Key to Low-Power Soft Electronics
Using an initiated chemical vapor deposition technique, the research team created an ultrathin polymeric insulating layer essential in realizing transistors with flexibility and low power consumption. This advance is expected to accelerate the commercialization of wearable and soft electronics.
A group of researchers at the Korea Advanced Institute of Science and Technology (KAIST) developed a high-performance ultrathin polymeric insulator for field-effect transistors (FETs). The researchers used vaporized monomers to form polymeric films grown conformally on various surfaces including plastics to produce a versatile insulator that meets a wide range of requirements for next-generation electronic devices. Their research results were published online in Nature Materials on March 9th, 2015.
FETs are an essential component for any modern electronic device used in our daily life from cell phones and computers, to flat-panel displays. Along with three electrodes (gate, source, and drain), FETs consist of an insulating layer and a semiconductor channel layer. The insulator in FETs plays an important role in controlling the conductance of the semiconductor channel and thus current flow within the translators. For reliable and low-power operation of FETs, electrically robust, ultrathin insulators are essential. Conventionally, such insulators are made of inorganic materials (e.g., oxides and nitrides) built on a hard surface such as silicon or glass due to their excellent insulating performance and reliability.
However, these insulators were difficult to implement into soft electronics due to their rigidity and high process temperature. In recent years, many researchers have studied polymers as promising insulating materials that are compatible with soft unconventional substrates and emerging semiconductor materials. The traditional technique employed in developing a polymer insulator, however, had the limitations of low surface coverage at ultra-low thickness, hindering FETs adopting polymeric insulators from operating at low voltage.
A KAIST research team led by Professor Sung Gap Im of the Chemical and Biomolecular Engineering Department and Professor Seunghyup Yoo and Professor Byung Jin Cho of the Electrical Engineering Department developed an insulating layer of organic polymers, “pV3D3,” that can be greatly scaled down, without losing its ideal insulating properties, to a thickness of less than 10 nanometers (nm) using the all-dry vapor-phase technique called the “initiated chemical vapor deposition (iCVD).”
The iCVD process allows gaseous monomers and initiators to react with each other in a low vacuum condition, and as a result, conformal polymeric films with excellent insulating properties are deposited on a substrate. Unlike the traditional technique, the surface-growing character of iCVD can overcome the problems associated with surface tension and produce highly uniform and pure ultrathin polymeric films over a large area with virtually no surface or substrate limitations. Furthermore, most iCVD polymers are created at room temperature, which lessens the strain exerted upon and damage done to the substrates.
With the pV3D3 insulator, the research team built low-power, high-performance FETs based on various semiconductor materials such as organics, graphene, and oxides, demonstrating the pV3D3 insulator’s wide range of material compatibility. They also manufactured a stick-on, removable electronic component using conventional packaging tape as a substrate. In collaboration with Professor Yong-Young Noh from Dongguk University in Korea, the team successfully developed a transistor array on a large-scale flexible substrate with the pV3D3 insulator.
Professor Im said, “The down-scalability and wide range of compatibility observed with iCVD-grown pV3D3 are unprecedented for polymeric insulators. Our iCVD pV3D3 polymeric films showed an insulating performance comparable to that of inorganic insulating layers, even when their thickness were scaled down to sub-10 nm. We expect our development will greatly benefit flexible or soft electronics, which will play a key role in the success of emerging electronic devices such as wearable computers.”
The title of the research paper is “Synthesis of ultrathin polymer insulating layers by initiated chemical vapor deposition for low-power soft electronics” (Digital Object Identifier (DOI) number is 10.1038/nmat4237).
Picture 1: A schematic image to show how the initiated chemical vapor deposition (iCVD) technique produces pV3D3 polymeric films: (i) introduction of vaporized monomers and initiators, (ii) activation of initiators to thermally dissociate into radicals, (iii) adsorption of monomers and initiator radicals onto a substrate, and (iv) transformation of free-radical polymerization into pV3D3 thin films.
Picture 2: This is a transistor array fabricated on a large scale, highly flexible substrate with pV3D3 polymeric films.
Picture 3: This photograph shows an electronic component fabricated on a conventional packaging tape, which is attachable or detachable, with pV3D3 polymeric films embedded.
2015.03.10 View 12433 -
System Approach Using Metabolite Structural Similarity Toward TOM Suggested
A Korean research team at KAIST suggests that a system approach using metabolite structural similarity helps to elucidate the mechanisms of action of traditional oriental medicine.
Traditional oriental medicine (TOM) has been practiced in Asian countries for centuries, and is gaining increasing popularity around the world. Despite its efficacy in various symptoms, TOM has been practiced without precise knowledge of its mechanisms of action. Use of TOM largely comes from empirical knowledge practiced over a long period of time. The fact that some of the compounds found in TOM have led to successful modern drugs such as artemisinin for malaria and taxol (Paclitaxel) for cancer has spurred modernization of TOM.
A research team led by Sang-Yup Lee at KAIST has focused on structural similarities between compounds in TOM and human metabolites to help explain TOM’s mechanisms of action. This systems approach using structural similarities assumes that compounds which are structurally similar to metabolites could affect relevant metabolic pathways and reactions by biosynthesizing structurally similar metabolites.
Structural similarity analysis has helped to identify mechanisms of action of TOM. This is described in a recent study entitled “A systems approach to traditional oriental medicine,” published online in Nature Biotechnology on March 6, 2015. In this study, the research team conducted structural comparisons of all the structurally known compounds in TOM and human metabolites on a large-scale. As a control, structures of all available approved drugs were also compared against human metabolites. This structural analysis provides two important results. First, the identification of metabolites structurally similar to TOM compounds helped to narrow down the candidate target pathways and reactions for the effects from TOM compounds. Second, it suggested that a greater fraction of all the structurally known TOM compounds appeared to be more similar to human metabolites than the approved drugs. This second finding indicates that TOM has a great potential to interact with diverse metabolic pathways with strong efficacy. This finding, in fact, shows that TOM compounds might be advantageous for the multitargeting required to cure complex diseases. “Once we have narrowed down candidate target pathways and reactions using this structural similarity approach, additional in silico tools will be necessary to characterize the mechanisms of action of many TOM compounds at a molecular level,” said Hyun Uk Kim, a research professor at KAIST.
TOM’s multicomponent, multitarget approach wherein multiple components show synergistic effects to treat symptoms is highly distinctive. The researchers investigated previously observed effects recorded since 2000 of a set of TOM compounds with known mechanisms of action. TOM compounds’ synergistic combinations largely consist of a major compound providing the intended efficacy to the target site and supporting compounds which maximize the efficacy of the major compound. In fact, such combination designs appear to mirror the Kun-Shin-Choa-Sa design principle of TOM.
That principle, Kun-Shin-Choa-Sa (君臣佐使 or Jun-Chen-Zuo-Shi in Chinese) literally means “king-minister-assistant-ambassador.” In ancient East Asian medicine, treating human diseases and taking good care of the human body are analogous to the politics of governing a nation. Just as good governance requires that a king be supported by ministers, assistants and/or ambassadors, treating diseases or good care of the body required the combined use of herbal medicines designed based on the concept of Kun-Shin-Choa-Sa. Here, the Kun (king or the major component) indicates the major medicine (or herb) conveying the major drug efficacy, and is supported by three different types of medicines: the Shin (minister or the complementary component) for enhancing and/or complementing the efficacy of the Kun, Choa (assistant or the neutralizing component) for reducing any side effects caused by the Kun and reducing the minor symptoms accompanying major symptom, and Sa (ambassador or the delivery/retaining component) which facilitated the delivery of the Kun to the target site, and retaining the Kun for prolonged availability in the cells.
The synergistic combinations of TOM compounds reported in the literature showed four different types of synergisms: complementary action (similar to Kun-Shin), neutralizing action (similar to Kun-Choa), facilitating action or pharmacokinetic potentiation (both similar to Kun-Choa or Kun-Sa). Additional structural analyses for these compounds with synergism show that they appeared to affect metabolism of amino acids, co-factors and vitamins as major targets.
Professor Sang Yup Lee remarks, “This study lays a foundation for the integration of traditional oriental medicine with modern drug discovery and development. The systems approach taken in this analysis will be used to elucidate mechanisms of action of unknown TOM compounds which will then be subjected to rigorous validation through clinical and in silico experiments.”
Sources: Kim, H.U. et al. “A systems approach to traditional oriental medicine.” Nature Biotechnology. 33: 264-268 (2015).
This work was supported by the Bio-Synergy Research Project (2012M3A9C4048759) of the Ministry of Science, ICT and Future Planning through the National Research Foundation. This work was also supported by the Novo Nordisk Foundation.
The picture below presents the structural similarity analysis of comparing compounds in traditional oriental medicine and those in all available approved drugs against the structures of human metabolites.
2015.03.09 View 9443 -
An Artist and Scientist, the Dean of Northwestern University speaks at KAIST
How does an abstract artist look at the world of science? Can art enhance scientific inquiry?
The Department of Chemical and Biomolecular Engineering (CBE), KAIST, invited Professor Julio Mario Ottino to speak at its fourth Annual KAIST CBE Global Distinguished Lectureship from the 15th to 16th October. Professor Ottino is the Dean of the Robert R. McCormick School of Engineering and Applied Science at Northwestern University.
Professor Ottino is a famous artist as well as a scientist. He pursues his disciplines in engineering and art as ways by which an artistic value and scientific truth can coexist. By merging these disciplines, he is praised for adopting balanced engineering education that emphasizes analytical skills and creativity at Northwestern University.
The lecture took place over two days. The topic of the first day was “Creativity” and the next day, “Formalism in Science.”
On the first day, Professor Ottino spoke about “Creativity in Science, Art, and Technology -- How art is separated from science.” He argues that as creativity is essential in art, science, and technology, artistic creativity can help develop scientific and technological creativity.
The next lecture featured “Mixing of Fluids and Solids: Parallels, Divergences, and Lessons.”
He emphasized that the birth of mixing of fluids and researches on granular matter and segregation offered valuable insights and lessons. Although these two topics have developed in different ways, he laid down some examples on how scientific theories have progressed under formalism.
2014.10.16 View 7757 -
KAIST Researchers Fabricate Defect-free Graphene for Lithium-ion Batteries
Although graphene has been hailed as promising materials for lithium-ion batteries, making it for large-scale production has remained a challenging task for researchers. So far, high-quality graphene has been produced at the expense of large volume. It is possible to fabricate bulk quantities of graphene, but they will likely contain many defects.
Recently, a KAIST research team, headed by Professors Jung-Ki Park and Hee-Tak Kim from the Department of Chemical and Biomolecular Engineering, developed a fabrication method to produce a large amount of defect-free graphene (df-G) while preserving the structural integrity of the graphene.
This research result was published online in the July 11, 2014 issue of Nano Letters, entitled "Defect-free, Size-tunable Graphene for High-performance Lithium Ion Battery."
Phys.org, a science, research and technology news website, published an article on this research. To read article, please visit the link below:
Phys.org, August 22, 2014
“Scientists fabricate defect-free graphene, set record reversible capacity for Co3O4 node in Li-ion batteries”
http://phys.org/news/2014-08-scientists-fabricate-defect-free-graphene-reversible.html
2014.09.07 View 9381 -
Clear Display Technology Under Sunlight Developed
The late Professor Seung-Man Yang
The last paper of the late Professor Seung-Man Yang, who was a past master of colloids and fluid mechanics
Practical patterning technology of the next generation optical materials, photonic crystals
The mineral opal does not possess any pigments, but it appears colorful to our eyes. This is because only a particular wavelength is reflected due to the regular nano-structure of its surface. The material that causes selective reflection of the light is called photonic crystals.
The deceased Professor Seung-Man Yang and his research team from KAIST’s Chemical and Biomolecular Engineering Department ha ve developed micro-pattern technology using photolithographic process. This can accelerate the commercialization of photonic crystals, which is hailed as the next generation optics material.
The research results were published in the April 16th edition of Advanced Materials, known as the most prestigious world-renowned journal in the field of materials science.
The newly developed photonic crystal micro-pattern could be used as a core material for the next generation reflective display that is clearly visible even under sunlight. Since it does not require a separate light source, a single charge is enough to last for several days.
Until now, many scientists have endeavored to make photonic crystals artificially, however, most were produced in a lump and therefore lacked efficiency. Also, the low mechanical stability of the formed structure prevented from commercialization.
In order to solve these problems, the research team has copied the nano-structure of opals.
Glass beads were arranged in the same nano-structure as the opal on top of the photoresist material undergoing photocuring by ultraviolet light. The glass beads were installed in the photoresist materials, and UV light was selectively exposed on micro regions. The remaining region was developed by photolithographic process to successfully produce photonic crystals in micro-patterns.
The co-author of the research, KAIST Chemical and Biomolecular Engineering Department’s Professor Sin-Hyeon Kim, said, “Combining the semiconductor process technology with photonic crystal pattern technology can secure the practical applications for photonic crystals.”He also predicted “This technology can be used as the key optical material that configures the next generation reflective color display device with very low power consumption.”
The late Professor Seung-Man Yang was a world-renowned expert in the field of colloids and fluid mechanics. Professor Yang published over 193 papers in international journals and continued his research until his passing in last September.
He received Du Pont Science and Technology Award in 2007, KAIST Person of the Year 2008, Gyeong-Am Academy Award in 2009, as well as the President’s Award of the Republic of Korea in March 2014. The researchers devoted the achievement of this year’s research to Professor Yang in his honor.
Research was conducted by KAIST Photonic-fluidic Integrated Devices Research Team, as a part of the Creative Research Program funded by the Ministry of Science, ICT and Future Planning, Republic of Korea.
Figure 1. Opal [left] and the nano glass bead arrangement structure within the opal [right]
Figure 2. Process chart of the photonic crystal micro-pattern formation based on photolithography
Figure 3. Opal structure [left] and inverted structure of the opal [right]
Figure 4. Photonic crystal micro-pattern in solid colors
Figure 5. Photonic crystal micro-pattern that reflects two different crystals (Red, Green) [left] and pixelated pattern of photonic crystal in three primary colors (Red, Green, Blue) [right] that is applicable to reflective displays
2014.05.14 View 11315 -
Spillover Phenomenon Identified Using Model Catalyst System
Researchers at KAIST have identified spillover phenomenon, which has remained controversial since its discovery in the early 1960s.
KAIST Department of Chemical and Biomolecular Engineering’s Professor Min-Gi Choi and his team has explained the "spillover phenomenon," using their own model catalyst system where platinum is selectively located within the amorphous aluminosilicate.
The research results were published on the 25th February online edition of Nature Communications.
Spillover refers to a phenomenon that occurs when hydrogen atoms that have been activated on the surface of metals, such as platinum, move to the surface of the catalyst. It was predicted that this phenomenon can be used to design a catalyst with high activity and stability, and thus has been actively studied over the last 50 years.
However, many cases of the known catalysts involved competing reactions on the exposed metal surface, which made it impossible to directly identify the presence and formation mechanism of spillover.
The catalysts developed by the researchers at KAIST used platinum nanoparticles covered with aluminosilicate. This only allowed the hydrogen molecules to pass through and has effectively blocked the competing reactions, enabling the research team to study the spillover phenomenon.
Through various catalyst structure and reactivity analysis, as well as computer modeling, the team has discovered that Brönsted acid sites present on the aluminosilicate plays a crucial role in spillover phenomenon.
In addition, the spillover-based hydrogenation catalyst proposed by the research team showed very high hydrogenation and dehydrogenation activity. The ability of the catalyst to significantly inhibit unwanted hydrogenolysis reaction during the petrochemical processes also suggested a large industrial potential.
Professor Min-Gi Choi said, “This particular catalyst, which can trigger the reaction only by spillover phenomenon, can be properly designed to exceed the capacity of the conventional metal catalysts. The future goal is to make a catalyst with much higher activity and selectivity.”
The research was conducted through funds subsidized by SK Innovation and Ministry of Science, ICT and Future Planning.
The senior research fellow of SK Innovation Seung-Hun Oh said, “SK Innovation will continue to develop a new commercial catalyst based on the technology from this research.”
Juh-Wan Lim and Hye-Yeong Shin led the research as joint first authors under supervision of Professor Min-Gi Choi and computer modeling works were conducted by KAIST EEWS (environment, energy, water, and sustainability) graduate school’s Professor Hyeong-Jun Kim.
2014.03.03 View 9321 -
Metabolically engineered E. coli producing phenol
Many chemicals we use in everyday life are derived from fossil resources. Due to the increasing concerns on the use of fossil resources, there has been much interest in producing chemicals from renewable resources through biotechnology.
Phenol is an important commodity chemical, and is a starting material for the production of numerous industrial chemicals and polymers, including bisphenol A and phenolic resins, and others. At present, the production of phenol entirely depends on the chemical synthesis from benzene, and its annual production exceeds 8 million tons worldwide. Microbial production of phenol seems to be a non-viable process considering the high toxicity of phenol to the cell.
In the paper published online in Biotechnology Journal, a Korean research team led by Distinguished Professor Sang Yup Lee at the Department of Chemical and Biomolecular Engineering from the Korea Advanced Institute of Science and Technology (KAIST) reported the successful development of an engineered Escherichia coli (E. coli) strain which can produce phenol from glucose. E. coli has been a workhorse for biological production of various value-added compounds such as succinic acid and 1,4-butanediol in industrial scale. However, due to its low tolerance to phenol, E. coli was not considered a viable host strain for the biological production of phenol.
Professor Lee"s team, a leading research group in metabolic engineering, noted the genetic and physiological differences of various E. coli strains and investigated 18 different E. coli strains with respect to phenol tolerance and engineered all of the 18 strains simultaneously. If the traditional genetic engineering methods were used, this work would have taken years to do. To overcome this challenge, the research team used synthetic small RNA (sRNA) technology they recently developed (Nature Biotechnology, vol 31, pp 170-174, 2013). The sRNA technology allowed the team to screen 18 E. coli strains with respect to the phenol tolerance, and the activities of the metabolic pathway and enzyme involved in the production of phenol. The research team also metabolically engineered the E. coli strains to increase carbon flux toward phenol and finally generated an engineered E. coli strain which can produce phenol from glucose.
Furthermore, the team developed a biphasic extractive fermentation process to minimize the toxicity of phenol to E. coli cells. Glycerol tributyrate was found to have low toxicity to E. coli and allowed efficient extraction of phenol from the culture broth. Through the biphasic fed-batch fermentation using glycerol tributyrate as an in situ extractant, the final engineered E. coli strain produced phenol to the highest titer and productivity reported (3.8 g/L and 0.18 g/L/h, respectively). The strategy used for the strain development and the fermentation process will serve as a framework for metabolic engineering of microorganisms for the production of toxic chemicals from renewable resources.
This work was supported by the Intelligent Synthetic Biology Center through the Global Frontier Project (2011-0031963) of the Ministry of Science, ICT & Future Planning through the National Research Foundation of Korea.
Process of Phenol Production
2013.11.05 View 9244 -
KAIST announced a novel technology to produce gasoline by a metabolically engineered microorganism
A major scientific breakthrough in the development of renewable energy sources and other important chemicals; The research team succeeded in producing 580 mg of gasoline per liter of cultured broth by converting in vivo generated fatty acids
For many decades, we have been relying on fossil resources to produce liquid fuels such as gasoline, diesel, and many industrial and consumer chemicals for daily use. However, increasing strains on natural resources as well as environmental issues including global warming have triggered a strong interest in developing sustainable ways to obtain fuels and chemicals.
Gasoline, the petroleum-derived product that is most widely used as a fuel for transportation, is a mixture of hydrocarbons, additives, and blending agents. The hydrocarbons, called alkanes, consist only of carbon and hydrogen atoms. Gasoline has a combination of straight-chain and branched-chain alkanes (hydrocarbons) consisted of 4-12 carbon atoms linked by direct carbon-carbon bonds.
Previously, through metabolic engineering of Escherichia coli (E. coli), there have been a few research results on the production of long-chain alkanes, which consist of 13-17 carbon atoms, suitable for replacing diesel. However, there has been no report on the microbial production of short-chain alkanes, a possible substitute for gasoline.
In the paper (entitled "Microbial Production of Short-chain Alkanes") published online in Nature on September 29, a Korean research team led by Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST) reported, for the first time, the development of a novel strategy for microbial gasoline production through metabolic engineering of E. coli.
The research team engineered the fatty acid metabolism to provide the fatty acid derivatives that are shorter than normal intracellular fatty acid metabolites, and introduced a novel synthetic pathway for the biosynthesis of short-chain alkanes. This allowed the development of platform E. coli strain capable of producing gasoline for the first time. Furthermore, this platform strain, if desired, can be modified to produce other products such as short-chain fatty esters and short-chain fatty alcohols.
In this paper, the Korean researchers described detailed strategies for 1) screening of enzymes associated with the production of fatty acids, 2) engineering of enzymes and fatty acid biosynthetic pathways to concentrate carbon flux towards the short-chain fatty acid production, and 3) converting short-chain fatty acids to their corresponding alkanes (gasoline) by introducing a novel synthetic pathway and optimization of culture conditions. Furthermore, the research team showed the possibility of producing fatty esters and alcohols by introducing responsible enzymes into the same platform strain.
Professor Sang Yup Lee said, "It is only the beginning of the work towards sustainable production of gasoline. The titer is rather low due to the low metabolic flux towards the formation of short-chain fatty acids and their derivatives. We are currently working on increasing the titer, yield and productivity of bio-gasoline. Nonetheless, we are pleased to report, for the first time, the production of gasoline through the metabolic engineering of E. coli, which we hope will serve as a basis for the metabolic engineering of microorganisms to produce fuels and chemicals from renewable resources."
This research was supported by the Advanced Biomass Research and Development Center of Korea (ABC-2010-0029799) through the Global Frontier Research Program of the Ministry of Science, ICT and Future Planning (MSIP) through the National Research Foundation (NRF), Republic of Korea. Systems metabolic engineering work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012-C1AAA001-2012M1A2A2026556) by MSIP through NRF.
Short-Chain Alkanes Generated from Renewable Biomass
This diagram shows the metabolic engineering of Escherichia coli for the production of short-chain alkanes (gasoline) from renewable biomass.
Nature Cover Page (September 29th, 2013)
2013.11.04 View 10911 -
A powerful strategy for developing microbial cell factories by employing synthetic small RNAs
The current systems for the production of chemicals, fuels and materials heavily rely on the use of fossil resources. Due to the increasing concerns on climate change and other environmental problems, however, there has been much interest in developing biorefineries for the production of such chemicals, fuels and materials from renewable resources. For the biorefineries to be competitive with the traditional fossil resource-based refineries, development of high performance microorganisms is the most important as it will affect the overall economics of the process most significantly. Metabolic engineering, which can be defined as purposeful modification of cellular metabolic and regulatory networks with an aim to improve the production of a desired product, has been successfully employed to improve the performance of the cell. However, it is not trivial to engineer the cellular metabolism and regulatory circuits in the cell due to their high complexity.
In metabolic engineering, it is important to find the genes that need to be amplified and attenuated in order to increase the product formation rate while minimizing the production of undesirable byproducts. Gene knock-out experiments are often performed to delete those metabolic fluxes that will consequently result in the increase of the desired product formation. However, gene knock-out experiments require much effort and time to perform, and are difficult to do for a large number of genes. Furthermore, the gene knock-out experiments performed in one strain cannot be transferred to another organism and thus the whole experimental process has to be repeated. This is a big problem in developing a high performance microbial cell factory because it is required to find the best platform strain among many different strains. Therefore, researchers have been eager to develop a strategy that allows rapid identification of multiple genes to be attenuated in multiple strains at the same time.
A Korean research team led by Distinguished Professor Sang Yup Lee at the Department of Chemical and Biomolecular Engineering from the Korea Advanced Institute of Science and Technology (KAIST) reported the development of a strategy for efficiently developing microbial cell factories by employing synthetic small RNAs (sRNAs). They first reported the development of such system in Nature Biotechnology last February. This strategy of employing synthetic sRNAs in metabolic engineering has been receiving great interest worldwide as it allows easy, rapid, high-throughput, tunable, and un-doable knock-down of multiple genes in multiple strains at the same time. The research team published a paper online on August 8 as a cover page (September issue) in Nature Protocols, describing the detailed strategy and protocol to employ synthetic sRNAs for metabolic engineering.
In this paper, researchers described the detailed step-by-step protocol for synthetic sRNA-based gene expression control, including the sRNA design principles. Tailor-made synthetic sRNAs can be easily manipulated by using conventional gene cloning method. The use of synthetic sRNAs for gene expression regulation provides several advantages such as portability, conditionality, and tunability in high-throughput experiments. Plasmid-based synthetic sRNA expression system does not leave any scar on the chromosome, and can be easily transferred to many other host strains to be examined. Thus, the construction of libraries and examination of different host strains are much easier than the conventional hard-coded gene manipulation systems. Also, the expression of genes can be conditionally repressed by controlling the production of synthetic sRNAs. Synthetic sRNAs possessing different repression efficiencies make it possible to finely tune the gene expression levels as well. Furthermore, synthetic sRNAs allow knock-down of the expression of essential genes, which was not possible by conventional gene knock-out experiments.
Synthetic sRNAs can be utilized for diverse experiments where gene expression regulation is needed. One of promising applications is high-throughput screening of the target genes to be manipulated and multiple strains simultaneously to enhance the production of chemicals and materials of interest. Such simultaneous optimization of gene targets and strains has been one of the big challenges in metabolic engineering. Another application is to fine tune the expression of the screened genes for flux optimization, which would enhance chemical production further by balancing the flux between biomass formation and target chemical production. Synthetic sRNAs can also be applied to finely regulating genetic interactions in a circuit or network, which is essential in synthetic biology. Once a sRNA scaffold-harboring plasmid is constructed, tailor-made, synthetic sRNAs can be made within 3-4 days, followed by the desired application experiments.
Dr. Eytan Zlotorynski, an editor at Nature Protocols, said "This paper describes the detailed protocol for the design and applications of synthetic sRNA. The method, which has many advantages, is likely to become common practice, and prove useful for metabolic engineering and synthetic biology studies."
This paper published in Nature Protocols will be useful for all researchers in academia and industry who are interested in the use of synthetic sRNAs for fundamental and applied biological and biotechnological studies.
This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012-C1AAA001-2012M1A2A2026556) and the Intelligent Synthetic Biology Center through the Global Frontier Project (2011-0031963) of the Ministry of Science, ICT and Future Planning through the National Research Foundation of Korea.
2013.10.31 View 8791 -
Top Ten Ways Biotechnology Could Improve Our Everyday Life
The Global Agenda Council on Biotechnology, one of the global networks under the World Economic Forum, which is composed of the world’s leading experts in the field of biotechnology, announced on February 25, 2013 that the council has indentified “ten most important biotechnologies” that could help meet rapidly growing demand for energy, food, nutrition, and health. These new technologies, the council said, also have the potential to increase productivity and create new jobs.
“The technologies selected by the members of the Global Agenda Council on Biotechnology represent almost all types of biotechnology.Utilization of waste, personalized medicine,and ocean agricultureare examples of the challenges where biotechnology can offer solutions,”said Sang Yup Lee, Chair of the Global Agenda Council on Biotechnology and Distinguished Professor in the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST). He also added that “the members of the council concluded that regulatory certainty, public perception, and investment are the key enablers for the growth of biotechnology.”
These ideas will be further explored during “Biotechnology Week” at the World Economic Forum’s Blog (http://wef.ch/blog) from Monday, 25 February, 2013. The full list follows below:
Bio-based sustainable production of chemicals, energy, fuels and materials
Through the last century, human activity has depleted approximately half of the world’s reserves of fossil hydrocarbons. These reserves, which took over 600 million years to accumulate, are non-renewable and their extraction, refining and use contribute significantly to human emissions of greenhouse gases and the warming of our planet. In order to sustain human development going forward, a carbon-neutral alternative must be implemented. The key promising technology is biological synthesis; that is, bio-based production of chemicals, fuels and materials from plants that can be re-grown.
Engineering sustainable food production
The continuing increase in our numbers and affluence are posing growing challenges to the ability of humanity to produce adequate food (as well as feed, and now fuel). Although controversial, modern genetic modification of crops has supported growth in agricultural productivity. In 2011, 16.7 million farmers grew biotechnology-developed crops on almost 400 million acres in 29 countries, 19 of which were developing countries. Properly managed, such crops have the potential to lower both pesticide use and tilling which erodes soil.
Sea-water based bio-processes
Over 70% of the earth surface is covered by seawater, and it is the most abundant water source available on the planet. But we are yet to discover the full potential of it. For example with halliophic bacteria capable of growing in the seawater can be engineered to grow faster and produce useful products including chemicals, fuels and polymeric materials. Ocean agriculture is also a promising technology. It is based on the photosynthetic biomass from the oceans, like macroalgae and microalgae.
Non-resource draining zero waste bio-processing
The sustainable goal of zero waste may become a reality with biotechnology. Waste streams can be processed at bio-refineries and turned into valuable chemicals and fuels, thereby closing the loop of production with no net waste. Advances in biotechnology are now allowing lower cost, less draining inputs to be used, including methane, and waste heat. These advances are simplifying waste streams with the potential to reduce toxicity as well as support their use in other processes, moving society progressively closer to the sustainable goal of zero waste.
Using carbon dioxide as a raw material
Biotechnology is poised to contribute solutions to mitigate the growing threat of rising CO2 levels. Recent advances are rapidly increasing our understanding of how living organisms consume and use CO2. By harnessing the power of these natural biological systems, scientists are engineering a new wave of approaches to convert waste CO2 and C1 molecules into energy, fuels, chemicals, and new materials.
Regenerative medicine
Regenerative medicine has become increasingly important due to both increased longevity and treatment of injury. Tissue engineering based on various bio-materials has been developed to speed up the regenerative medicine. Recently, stem cells, especially the induced pluripotent stem cells (iPS), have provided another great opportunity for regenerative medicine. Combination of tissue engineering and stem cell (including iPS) technologies will allow replacements of damaged or old human organs with functional ones in the near future.
Rapid and precise development and manufacturing of medicine and vaccines
A global pandemic remains one of the most real and serious threats to humanity. Biotechnology has the potential to rapidly identify biological threats, develop and manufacture potential cures. Leading edge biotechnology is now offering the potential to rapidly produce therapeutics and vaccines against virtually any target. These technologies, including messenger therapeutics, targeted immunotherapies, conjugated nanoparticles, and structure-based engineering, have already produced candidates with substantial potential to improve human health globally.
Accurate, fast, cheap, and personalized diagnostics and prognostics
Identification of better targets and combining nanotechnology and information technology it will be possible to develop rapid, accurate, personalized and inexpensive diagnostics and prognostics systems.
Bio-tech improvements to soil and water
Arable land and fresh water are two of the most important, yet limited, resources on earth. Abuse and mis-appropriation have threatened these resources, as the demand on them has increased. Advances in biotechnology have already yielded technologies that can restore the vitality and viability of these resources. A new generation of technologies: bio-remediation, bio-regeneration and bio-augmentation are being developed, offering the potential to not only further restore these resources, but also augment their potential.
Advanced healthcare through genome sequencing
It took more than 13 years and $1.5 billion to sequence the first human genome and today we can sequence a complete human genome in a single day for less than $1,000. When we analyze the roughly 3 billion base pairs in such a sequence we find that we differ from each other in several million of these base pairs. In the vast majority of cases these difference do not cause any issues but in rare cases they cause disease, or susceptibility to disease. Medical research and practice will increasingly be driven by our understanding of such genetic variations together with their phenotypic consequences.
2013.03.19 View 10968
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An efficient strategy for developing microbial cell factories by employing synthetic small regulatory RNAs
A new metabolic engineering tool that allows fine control of gene expression level by employing synthetic small regulatory RNAs was developed to efficiently construct microbial cell factories producing desired chemicals and materials
Biotechnologists have been working hard to address the climate change and limited fossil resource issues through the development of sustainable processes for the production of chemicals, fuels and materials from renewable non-food biomass. One promising sustainable technology is the use of microbial cell factories for the efficient production of desired chemicals and materials. When microorganisms are isolated from nature, the performance in producing our desired product is rather poor. That is why metabolic engineering is performed to improve the metabolic and cellular characteristics to achieve enhanced production of desired product at high yield and productivity. Since the performance of microbial cell factory is very important in lowering the overall production cost of the bioprocess, many different strategies and tools have been developed for the metabolic engineering of microorganisms.
One of the big challenges in metabolic engineering is to find the best platform organism and to find those genes to be engineered so as to maximize the production efficiency of the desired chemical. Even Escherichia coli, the most widely utilized simple microorganism, has thousands of genes, the expression of which is highly regulated and interconnected to finely control cellular and metabolic activities. Thus, the complexity of cellular genetic interactions is beyond our intuition and thus it is very difficult to find effective target genes to engineer. Together with gene amplification strategy, gene knockout strategy has been an essential tool in metabolic engineering to redirect the pathway fluxes toward our desired product formation. However, experiment to engineer many genes can be rather difficult due to the time and effort required; for example, gene deletion experiment can take a few weeks depending on the microorganisms. Furthermore, as certain genes are essential or play important roles for the survival of a microorganism, gene knockout experiments cannot be performed. Even worse, there are many different microbial strains one can employ. There are more than 50 different E. coli strains that metabolic engineer can consider to use. Since gene knockout experiment is hard-coded (that is, one should repeat the gene knockout experiments for each strain), the result cannot be easily transferred from one strain to another.
A paper published in Nature Biotechnology online today addresses this issue and suggests a new strategy for identifying gene targets to be knocked out or knocked down through the use of synthetic small RNA. A Korean research team led by Distinguished Professor Sang Yup Lee at the Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), a prestigeous science and engineering university in Korea reported that synthetic small RNA can be employed for finely controlling the expression levels of multiple genes at the translation level. Already well-known for their systems metabolic engineering strategies, Professor Lee’s team added one more strategy to efficiently develop microbial cell factories for the production of chemicals and materials.
Gene expression works like this: the hard-coded blueprint (DNA) is transcribed into messenger RNA (mRNA), and the coding information in mRNA is read to produce protein by ribosomes. Conventional genetic engineering approaches have often targeted modification of the blueprint itself (DNA) to alter organism’s physiological characteristics. Again, engineering the blueprint itself takes much time and effort, and in addition, the results obtained cannot be transferred to another organism without repeating the whole set of experiments. This is why Professor Lee and his colleagues aimed at controlling the gene expression level at the translation stage through the use of synthetic small RNA. They created novel RNAs that can regulate the translation of multiple messenger RNAs (mRNA), and consequently varying the expression levels of multiple genes at the same time. Briefly, synthetic regulatory RNAs interrupt gene expression process from DNA to protein by destroying the messenger RNAs to different yet controllable extents. The advantages of taking this strategy of employing synthetic small regulatory RNAs include simple, easy and high-throughput identification of gene knockout or knockdown targets, fine control of gene expression levels, transferability to many different host strains, and possibility of identifying those gene targets that are essential.
As proof-of-concept demonstration of the usefulness of this strategy, Professor Lee and his colleagues applied it to develop engineered E. coli strains capable of producing an aromatic amino acid tyrosine, which is used for stress symptom relief, food supplements, and precursor for many drugs. They examined a large number of genes in multiple E. coli strains, and developed a highly efficient tyrosine producer. Also, they were able to show that this strategy can be employed to an already metabolically engineered E. coli strain for further improvement by demonstrating the development of highly efficient producer of cadaverine, an important platform chemical for nylon in the chemical industry.
This new strategy, being simple yet very powerful for systems metabolic engineering, is thus expected to facilitate the efficient development of microbial cell factories capable of producing chemicals, fuels and materials from renewable biomass.
Source: Dokyun Na, Seung Min Yoo, Hannah Chung, Hyegwon Park, Jin Hwan Park, and Sang Yup Lee, “Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs”, Nature Biotechnology, doi:10.1038/nbt.2461 (2013)
2013.03.19 View 9306
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High Efficiency Bio-butanol production technology developed
KAIST and Korean Company cooperative research team has developed the technology that increases the productivity of bio-butanol to equal that of bio-ethanol and decreases the cost of production.
Professor Lee Sang Yeop (Department of Biological-Chemical Engineering) collaborated with GS Caltex and BioFuelChem Ltd. to develop a bio-butanol production process using the system metabolism engineering method that increased the productivity and decreased the production cost.
Bio-butanol is being widely regarded as the environmentally friendly next generation energy source that surpasses bio-ethanol.
The energy density of bio-butanol is 29.9MJ (mega Joule) per Liter, 48% larger than bio-ethanol (19.6MJ) and comparable to gasoline (32MJ). Bio-butanol is advantageous in that it can be processed from inedible biomass and is therefore unrelated to food crises.
Especially because bio-butanol shows similar characteristics especially in its octane rating, enthalpy of vaporization, and air-fuel ratio, it can be used in a gasoline engine.
However barriers such as difficulty in gene manipulation of producer bacterium and insufficient information prevented the mass production of bio-butanol.
Professor Lee’s team applied the system metabolism engineering method that he had invented to shift the focus to the production pathway of bio-butanol and made a new metabolism model.
In the new model the bio-butanol production pathway is divided into the hot channel and the cold channel.
The research team focused on improving the efficiency of the hot channel and succeeded in improving the product yield of 49% (compared to theoretical yield) to 87%.
The team furthered their research and developed a live bio-butanol collection and removal system with GS Caltex. The collaboration succeeded in producing 585g of butanol using 1.8kg of glucose at a rate of 1.3g per hour, boasting world’s highest concentration, productivity, and rate and improving productivity of fermentation by three fold and decreasing costs by 30%.
The result of the research was published in world renowned ‘mBio’ microbiology journal.
2012.12.21 View 8531