Nature
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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 -
New BioFactory Technique Developed using sRNAs
Professor Sang Yup Lee
- published on the online edition of Nature Biotechnology. “Expected as a new strategy for the bio industry that may replace the chemical industry.”-
KAIST Chemical & Biomolecular engineering department’s Professor Sang Yup Lee and his team has developed a new technology that utilizes the synthetic small regulatory RNAs (sRNAs) to implement the BioFactory in a larger scale with more effectiveness.
* BioFactory: Microbial-based production system which creates the desired compound in mass by manipulating the genes of the cell.
In order to solve the problems of modern society, such as environmental pollution caused by the exhaustion of fossil fuels and usage of petrochemical products, an eco-friendly and sustainable bio industry is on the rise. BioFactory development technology has especially attracted the attention world-wide, with its ability to produce bio-energy, pharmaceuticals, eco-friendly materials and more.
For the development of an excellent BioFactory, selection for the gene that produces the desired compounds must be accompanied by finding the microorganism with high production efficiency; however, the previous research method had a complicated and time-consuming problem of having to manipulate the genes of the microorganism one by one.
Professor Sang Yup Lee’s research team, including Dr. Dokyun Na and Dr. Seung Min Yoo, has produced the synthetic sRNAs and utilized it to overcome the technical limitations mentioned above.
In particular, unlike the existing method, this technology using synthetic sRNAs exhibits no strain specificity which can dramatically shorten the experiment that used to take months to just a few days.
The research team applied the synthetic small regulatory RNA technology to the production of the tyrosine*, which is used as the precursor of the medicinal compound, and cadaverine**, widely utilized in a variety of petrochemical products, and has succeeded developing BioFactory with the world’s highest yield rate (21.9g /L, 12.6g / L each).
*tyrosine: amino acid known to control stress and improve concentration
**cadaverine: base material used in many petrochemical products, such as polyurethane
Professor Sang Yup Lee highlighted the significance of this research: “it is expected the synthetic small regulatory RNA technology will stimulate the BioFactory development and also serve as a catalyst which can make the chemical industry, currently represented by its petroleum energy, transform into bio industry.”
The study was carried out with the support of Global Frontier Project (Intelligent Bio-Systems Design and Synthesis Research Unit (Chief Seon Chang Kim)) and the findings have been published on January 20th in the online edition of the worldwide journal Nature Biotechnology.
2013.02.21 View 9899
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The control of light at the nano-level
Professor Min Bumki
Professor Min Bumki’s research team from the Department of Mechanical Engineering at KAIST have successfully gained control of the transmittance of light in optical devices using graphene* and artificial 2-dimensional metamaterials**.
* Graphene : a thin membrane composed of pure carbon, with atoms arranged in a regular hexagonal pattern
** Metamaterials : artificial materials engineered to have properties that may not be found in nature
The research results were published in the recent online edition (September 30th) of Nature Materials, a sister journal of the world renowned Nature journal, under the title ‘Terahertz waves with gate-controlled active graphene metamaterials’
Since the discovery of graphene in 2004 by Professors Novoselov and Geim from the University of Manchester (2010 Nobel Prize winners in Physics), it has been dubbed “the dream material” because of its outstanding physical properties.
Graphene has been especially praised for its ability to absorb approximately 2.3% of near infrared and visible rays due to its characteristic electron structure. This property allows graphene to be used as a transparent electrode, which is a vital electrical component used in touch screens and solar batteries. However, graphene’s optical transmittance was largely ignored by researchers due to its limited control using electrical methods and its small optical modulation in data transfer.
Professor Min’s team combined 0.34 nanometer-thick graphene with metamaterials to allow a more effective control of light transmittance and greater optical modulation. This graphene metamaterial can be integrated in to a thin and flexible macromolecule substrate which allows the control of transmittance using electric signals.
This research experimentally showed that graphene metamaterials can not only effective control optical transmittance, but can also be used in graphene optical memory devices using electrical hysteresis.
Professor Min said that “this research allows the effective control of light at the nanometer level” and that “this research will help in the development of microscopic optical modulators or memory disks”.
figure 1. The working drawing of graphene metamaterials
figure 2. Conceptual diagram (Left) and microscopic photo (right) of graphene metamaterials
2012.11.23 View 9891 -
The hereditary factor of autism revealed
Korean researchers have successfully investigated the causes and hereditary factors for autistic behavior and proposed a new treatment method with fewer side effects.
This research was jointly supported by the Ministry of Education, Science and Technology and the National Research Foundation as part of the Leading Researcher and Science Research Center Program
The research findings were publishing in the June edition of Nature magazine and will also be introduced in the July edition of Nature Reviews Drug Discovery, under the title ‘Autistic-like social behavior in Shank2-mutant mice improved by restoring NMDA receptor function’.
The research team found that lack of Shank2 genes in mice, which are responsible for the production of synapse proteins, caused autistic-like behavior. The results strongly suggested that the Shank2 gene was linked to autistic behavior and that Shank2 deficiency induced autistic behaviors.
Autism is a neural development disorder characterized by impaired social interaction, repetitive behavior, mental retardation, anxiety and hyperactivity. Around 100 million people worldwide display symptoms of autistic behavior. Recent studies conducted by the University of Washington revealed that 1 out of 3 young adults who display autistic behavior do not fit into the workplace or get accepted to college, a much higher rate than any other disorder. However, an effective cure has not yet been developed and current treatments are limited to reducing repetitive behavior.
The research team confirmed autistic-like social behavior in mice without the Shank2 genes and that the mice had decreased levels of neurotransmission in the NMDA receptor. The mice also showed damaged synaptic plasticity* in the hippocampus**.
* Plasticity: ability of the connectionbetween two neurons to change in strength in response to transmission of information
**Hippocampus: part of the brain responsible for short-term and long-term memory as well as spatial navigation.
The research team also found out that, to restore the function of the NMDA receptor, the passive stimulation of certain receptors, such as the mGLuR5, yielded better treatment results than the direct stimulation of the NMDA. This greatly reduces the side effects associated with the direct stimulation of receptors, resulting in a more effective treatment method.
This research successfully investigated the function of the Shank2 gene in the nerve tissue and showed how the reduced function of the NMDA receptor, due to the lack of the gene, resulted in autistic behavior. It also provided new possibilities for the treatment of autistic behavior and impaired social interaction
2012.06.24 View 10786
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Biomimetic reflective display technology developed
Professor Shin Jung Hoon
The bright colors of a rainbow or a peacock are produced by the reflection and interference of light in transparent periodic structures, producing what is called a structural color. These colors are very bright and change according to the viewing angle. On the other hand, the wings of a morpho-butterfly also have structural colors but are predominantly blue over a wide range of angles. This is because the unique structure of the morpho-butterfly’s wings contains both order and chaos.
Professor Shin Jung Hoon’s team from the Department of Physics and the Graduate School of Nanoscience and Technology at KAIST produced a display that mimics the structure of the morpho-butterfly’s wings using glass beads.
This research successfully produced a reflective display (one that reflects external light to project images), which could be used to make very bright displays with low energy consumption. This technology can also be used to make anti-counterfeit bills, as well as coating materials for mobile phones and wallets.
The structure of the morpho-butterfly’s wings seems to be in periodic order at the 1-micrometer level, but contains disorder at the 100-nanometer level. So far, no one had succeeded in reproducing a structure with both order and disorder at the nanometer level.
Professor Shin’s team randomly aligned differently sized glass beads of a few hundred nanometers to create chaos and placed a thin periodic film on top of it using the semiconductor deposition method, thereby creating the morpho-butterfly-like structure over a large area.
This new development produced better color and brightness than the morpho-butterfly wing and even exhibited less color change according to angle. The team sealed the film in thin plastic, which helped to maintain the superior properties whilst making it more firm and paper-like.
Professor Shin emphasized that the results were an exemplary success in the field of biomimetics and that structural colors could have other applications in sensors and fashion, for example.
The results were first introduced on May 3rd in Nature as one of the Research Highlights and will be published in the online version of the material science magazine, Advanced Materials.
This research was jointly conducted by Professor Shin Jung Hoon (Department of Physics / Graduate School of Nanoscience and Technology at KAIST), Professor Park NamKyoo (Department of Electrical and Computer Engineering at Seoul National University), and Samsung Advanced Institute of Technology. The funding was provided by the National Research Foundation of Korea and the Ministry of Education, Science and Technology as part of the World Class University (WCU) project.
Figure 2. The biomimetic film can express many different colors
Figure 3. The biomimetic diplay and a morpho-butterfly
2012.05.07 View 13373 -
Closer to the Dream: Graphene
A technique that allows easy and larger observation area of graphene’s crystal face was developed by Korean Research Team.
The research team, led by Professor Jeong Hui Tae (KAIST), consists of Doctorate candidate Kim Dae Woo, Dr. Kim Yoon Ho (primary author), Doctorate candidate Jeong Hyun Soo. The research is supported by WCU (World Class Research University) Development Plan, Mid-Aged Researcher Support Business and was published in the online edition of Nature Nanotechnology.
(Dissertation: Direct visualization of large0area graphene domains and boundaries by optical birefringency)
Professor Jeong’s team used the optical property of the liquid display used in LCD to visualize the size and shape of the single crystals along a flat surface. The visualization of the single crystal allowed the measurement of a near theoretical value of electrical conductivity of graphene.
Graphene has great electrical conductivity, transparent, mechanically stable, flexible, and is therefore regarded as the next generation electrical material. However the polycrystalinity of graphene meant that the actual electrical, mechanical properties were lower than the theoretical values. The reason was thought to be because of the size of the crystal faces and boundary structures.
Therefore, in order to create graphene that has good properties, observing the domain and boundary of graphene crystal faces is essential.
The new technique developed by the research team is another step towards commercializing transparent electrodes, flexible display, and electric materials like solar cells.
2012.01.31 View 9553
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Genetic Cause of ADHD (Attention Deficit Hyperactivity Disorder) Found
The cooperative research team consisting research teams under Professor Kim Eun Joon and Professor Kang Chang Won of the department of Biological Sciences discovered that ADHD arises from the deficiency of GIT1 protein in the brain’s neural synapses.
ADHD (Attention Deficit Hyperactivity Disorder) is found in around 5% of children around the world and is a disorder where the child becomes unable to concentrate, show over the top responses, and display impulsive behavior.
The research team found that the difference between children with ADHD and those without it is one base in the GIT1 gene. The difference of a single base causes the underproduction of this protein, and those children with low levels of the protein had a higher probability to develop ADHD.
In addition, further evidence was provided when the research team conducted mice experiments. Those mice with low levels of GIT1 exhibited impulsive and exaggerated reactions like humans with ADHD, had learning disabilities, and produced abnormal brain waves. And upon injecting these mice with cure for ADHD, the symptoms of ADHD disappeared.
The impulsive behavior of ADHD children disappears as the child enters adulthood and a similar pattern was found in mice. A mice with low levels of GIT1 showed impulsive behaviors when 2 months old, but these behaviors disappeared as it got older to around 7 months old (equivalent to 20~30 years old for humans).
Professor Kim Eun Joon commented that there has to be equilibrium between mechanisms that excite the neurons and mechanisms that calm the neurons, but the lack of GIT1 leads to the decrease in the mechanisms that calm the neurons which causes the impulsive behavior of ADHD patients.
In addition, Professor Kang Chang Won commented that the results of the experiment has been receiving rave reviews and is being seen as the new method in the production of the cure for ADHD.
The result of the experiment was published in the online edition of Nature Medicine magazine.
2011.04.30 View 9955
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The Irish Times: Gene link identified in ADHD, April 18, 2011
The Irish Times wrote an article on the recent research breakthrough made by a KAIST research team to identify a gene that triggers the syndrome of Attention Deficit Hyperactivity Disorder (ADHD) among children. Given the heightened attention to the syndrome across the world, the research result has received a great deal of attention not only from the academia but also from the media and public.
For the article, please visit http://www.irishtimes.com/newspaper/ireland/2011/0418/1224294910305.html. The research paper was appeared online April 17, 2011 in Nature Medicine, which will be printed in its May 2011 issue. For the paper, please click the link of http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.2330.html.
2011.04.18 View 9101
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Professor Min Beom Ki develops metamaterial with high index of refraction
Korean research team was able to theoretically prove that a metamaterial with high index of refraction does exist and produced it experimentally.
Professor Min Beom Ki, Dr. Choi Moo Han, and Doctorate candidate Lee Seung Hoon was joined by Dr. Kang Kwang Yong’s team from ETRI, KAIST’s Professor Less Yong Hee’s team, and Seoul National University’s Professor Park Nam Kyu’s team. The research was funded by the Basic Research Support Program initiated by the Ministry of Education, Science, and Technology and Korea Research Federation.
The result of the research was published in ‘Nature’ magazine and is one of the few researches carried out by teams composed entirely of Koreans.
Metamaterials are materials that have physical properties beyond those materials’ properties that are found in nature. It is formed not with atoms, but with synthetic atoms which have smaller structures than wavelengths.
The optical and electromagnetic waves’ properties of metamaterials can be altered significantly which has caught the attention of scientists worldwide.
Professor Min Beom Ki’s team independently designed and created a dielectric metamaterial with high polarization and low diamagnetism with an index of refraction of 38.6, highest synthesized index value.
It is expected that the result of the experiment will help develop high resolution imaging system and ultra small, hyper sensitive optical devices.
2011.02.23 View 15456
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New Bio-Clock gene and its function found
The Ministry of Education, Science and Technology announced that a Korean research team has found a new gene responsible for maintaining the bio-clock (twenty-four) and its mechanism.
Twnety-four was led by Professor Choi Joon Ho and Dr. Lee Jong Bin of KAIST (department of Biology) and was a joint operation with Professor Ravi Allada and Dr.Lim Jeong Hoon of Northwestern University (department of neurobiology) and the result was published in ‘Nature’ magazine.
The research team experimented with transformed small fruit flies for 4 years and found that there was an undiscovered gene that deals with the bio rhythm in the brain which they named ‘twenty-four’.
The understanding with genes prior to twenty-four was that these genes regulate biorhythm in the transcription phase (DNA to mRNA). Twenty-four operates in the step after transcription when the ribosome creates proteins. Especially twenty-four has a great effect on the ‘period protein’ which acts as a sub-atomic clock that regulates the rhythm and life of each cell.
The experiment was innovational in that it was able to scientifically prove the function of the protein produced by the gene.
The result is expected to help solve the problems associated with sleep disorders, jetlags, eating rhythms, bio rhythms, etc.
The name twenty-four was the fact that a day, a cycle, is 24 hours long and the gene’s serial numbers CG4857 adds up to twenty four.
2011.02.23 View 10898
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Waking Up Is Hard to Do: Scientists have discovered a new mechanism in the core gears of the circadian clock.
The US News & World Report released an article (Feb. 18, 2011) on KAIST’s research collaboration with Northwestern University in the US to identify a gene that regulates the rhythm of a fruit fly’s circadian clock, which may be applied to explain human’s sleep-wake cycle. The research result was published February 17 in the journal Nature.
For the link of the US News & World Report article, please go to the following link:
http://www.usnews.com/science/articles/2011/02/18/waking-up-is-hard-to-do_print.html
2011.02.21 View 9492
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"Supersolidity flows back," Nature, September 2, 2010
Supersolidity, discovered for the first time in 2004 by two physicists—one of them is Professor Eun-Seong Kim from the Department of Physics, KAIST—was discussed once again in the September 2, 2010 issue of Nature, an internationally well-known science journal.
The article mentioned “supersolidity” as one of the rare examples of quantum effects on a macroscopic scale, together with “superconductivity” and “superfluidity.” The phenomenon of supersolidity was evidenced by Professor Kim and his colleague through an experiment of placing helium-4 in a torsional oscillator under a low temperature.
The phenomenon, however, has been in debate among scientists in the physics community since the discovery, and Professor Kim has recently released his research results to further support his claim. For the full article, please click the link below:
http://www.nature.com/news/2010/100902/full/news.2010.443.html.
2010.09.08 View 9180