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A quantitative shotgun proteomic study of rice grain development
Wondo Lee,Jaebok Cho,Hijin Kim,Joohyun Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Although a great deal of rice proteomic research has been conducted, there are relatively few studies specifically addressing the rice grain proteome. The existing rice grain proteomic research has focused on the identification of deferentially expressed proteins. Here, we performed comparative shotgun proteomic analysis of rice grain development to construct an in-depth proteome reference map, to reveal the expression patterns of the identified proteins, and to detect proteins that are expressed deferentially during grain development. A Korean rice variety, Ilpumbyeo was used. Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from mature grains. The protein expression patterns were revealed by a quantitative shotgun proteoemic analysis. By merging all of the identified proteins in this study, we identified 4,172 non-redundant. A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain.
Hijin Kim,Jaebok Cho,Wondo Lee,Joohyun Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
As the drought is getting worse, Lot of studies related to drought stress in plant have been conducted. Recently whole genome sequencing of Brassica rapa ssp which is important vegetable crop to East Asians has been completed to enable Omic research. It is known that the drought damages occur in the early stage of plant development. Here, we performed shotgun proteomics analysis of B. rapa to observe the morphological characters, monitor the expression patterns of the identified proteins during drought stress, and detect the proteins related to drought stress. The three week old B. rapa grown in density of single plant in a single pot were used. Drought stress were treated as that a single plant in soil was removed from the pot and the plant with soil was exposed to air and light without watering. Leaves were immediately harvested before drought treatment, 24hr after drought treatment, and 48hr after drought treatment. The protein expression patterns were monitored by a quantitative shotgun proteomics analysis. Extracted proteins were separated in 1D-SDS-PAGE then the gel sliced into seven pieces. Chopped gels were ingel-digested. Peptides were assigned to mass spectrometry (Q-Exactive). The ms/ms spectra were analyzed through Proteome Discoverer. By combining all of the identified proteins in the seven sliced gel samples, total B. rapa proteome reference map was completed. Protein expression patterns were investigated by comparing the quantity of protein. With shotgun proteomic approach, we evaluated the changes in the quantity and finally discovered the candidate proteins related with drought stress.
SSR 마커를 활용한 한국의 26개 지역에서 수집된 더덕의 집단구조 분석
Jaebok Lee,Jinsu Gil,Yurry Um,Ho Bang Kim,Seong Cheol Kim,Sungcheol Koo,Yi Lee 한국약용작물학회 2017 한국약용작물학술대회 발표집 Vol.2017 No.05
Background : Codonopsis lanceolata is a perennial plant of Campanulaceae with characteristic flavor and aroma and this plant has saponin, flavonoid, and inulin, which are reported to have physiological activity and antioxidant activity. In contrast, breeding or study of C. lanceolata varieties had not been done for a long time. Genetic polymorphism and phylogenetic relationship analysis of the plants by region of the crops can help the collection of genetic backgroud data for variety development. Methods and Results : In this study, we collected 26 C. lanceolata lines (95 individual plants) from 26 regions in Korea. We genotyped the collected lines using SSR markers developed in the previous study and analyzed the population structure based on the results. Population structures were analyzed using model-based STRUCTURE software (version 2.3.4) using the following parameters: Number of clusters (K) set = 1 to 12; Number of Iterations = 5; Length of Burning Period = 100,000; Number of MCMC (Markov Chain Monte Carlo) Reps after Burnin = 100,000. As a result, Of the 26 collections, were genetically grouped into 6 or 7 groups. Conclusion : The 26 C. lanceolata collections (95 individual plants) were genetically grouped but not grouped by collected regions. These results suggest that C. lanceolata has diverse genetic backgrounds and this data could be used as a basis for genetic polymorphism analysis of Codonopsis species.
Jaebok Lee,Jun Zou,Jing Wan,Sughun Chang IEEE 2011 IEEE transactions on electromagnetic compatibility Vol.53 No.4
<P>The electromagnetic fields generated by a vertical electric dipole, expressed in the form of the Sommerfeld integral, are important in the study of lightning. In this paper, an algorithm, which can analytically approximate the Sommerfeld tail integral, is proposed. Due to the fact that the tail integral is expressed by a sum of several error functions, the tail integral of a vertical electric dipole can be evaluated without the truncation of the infinite upper limit. The comparison indicates that the results calculated by the proposed algorithm are accurate, and the computational time, compared to the one using direct numerical quadrature method, is much shorter.</P>
Lee, Sang Heun,Lee, Jaebok,Yoon, Young Joong,Park, Sangbok,Cheon, Changyul,Kim, Kihyun,Nam, Sangwook IEEE 2011 IEEE Transactions on Biomedical Engineering Vol.58 No.6
<P>This paper presents the design of a wideband spiral antenna for ingestible capsule endoscope systems and a comparison between the experimental results in a human phantom and a pig under general anesthesia. As wireless capsule endoscope systems transmit real-time internal biological image data at a high resolution to external receivers and because they operate in the human body, a small wideband antenna is required. To incorporate these properties, a thick-arm spiral structure is applied to the designed antenna. To make practical and efficient use of antennas inside the human body, which is composed of a high dielectric and lossy material, the resonance characteristics and radiation patterns were evaluated through a measurement setup using a liquid human phantom. The total height of the designed antenna is 5 mm and the diameter is 10 mm. The fractional bandwidth of the fabricated antenna is about 21% with a voltage standing-wave ratio of less than 2, and it has an isotropic radiation pattern. These characteristics are suitable for wideband capsule endoscope systems. Moreover, the received power level was measured using the proposed antenna, a circular polarized receiver antenna, and a pig under general anesthesia. Finally, endoscopic capsule images in the stomach and large intestine were captured using an on-off keying transceiver system.</P>
Jaebok Lee(이재복),Paulson Eberechukwu N,Sunwoo Kim(김선우) 한국통신학회 2022 한국통신학회 학술대회논문집 Vol.2022 No.2
This paper proposes a positioning algorithm that fuses inertial measurement unit (IMU) pedestrian dead reckoning (PDR) process and ultra-wideband (UWB) sensors using the alternating direction method of multipliers (ADMM) algorithm. The cooperative positioning algorithm uses the UWB measured distance between tags and an inertial sensor. The PDR coordinates are the measured every unit time as an initial value of the ADMM based. We have verified our approach and analyzed the performance of the positioning error in MATLAB.
Codonopsis laneolata 기반 EST-SSR 마커를 활용한 Codonopsis 속의 유전적 다양성 분석
Jaebok Lee,Jinsu Gil,Yurry Um,Ho Bang Kim,Seong Cheol Kim,Sungcheol Koo,Yi Lee 한국약용작물학회 2017 한국약용작물학술대회 발표집 Vol.2017 No.05
Background : Codonopsis lanceolata is a perennial plant of Campanulaceae and mainly distributed in East Asia such as Korea, China, and Japan. C. lanceolata has a unique taste and aroma, and it is rich in minerals such as phosphorus and calcium, and vitamin B1 and B2, so our ancestors used the plant as medicinal herb and edible vegetable. However, systematic cultivation and development of varieties have not been achieved compared to demand or high added value. The genetic diversity and relationship analysis of the plants help to increase the efficiency of breeding through genetic variation. Methods and Results : Ten species of Codonopsis plants were used as materials and DNA was extracted from each 4 individuals per species and quantified at a concentration of 10 ng /㎕. The extracted DNA was pooled by species and PCR was performed using the EST-SSR marker developed based on C. lanceolata in the previous study. PCR amplification was carried out using a denaturation at 94℃ for 30 sec, annealing at 58℃ for 30 sec and extension at 72℃ for 30 sec, repeated for 35 total cycles. The PCR products were separated in a 4% agarose gell at 100 V for 40 min. Conclusion : In this study, C. lanceolata collections was determined among several Codonopsis species using these molecular marker. It is expected that the data of this study can be used as reference for genetic polymorphism analysis and related gene studies of Codonopsis species.
Lee, Jaebok,Zhang, Boyuan,Zou, Jun,Ju, Mun-no IEEE 2017 IEEE transactions on electromagnetic compatibility Vol.59 No.1
<P>The evaluation of the earth return mutual impedance of arbitrary conductor arrangements with a horizontally multilayered nonmagnetic soil is of great significance when the electromagnetic compatibility is concerned. To evaluate the earth return impedance accurately and efficiently, a semianalytical approach is proposed in this paper. With the proposed approach, the expression of the earth return impedance, which includes a complex highly oscillatory integrand, is divided into two parts, i.e., the definite and the tail integral. The definite integral is evaluated by using the moment technique and the tail integral is evaluated by using the exponential integrals with an asymptotic integrand. The numerical examples show that the proposed algorithm can evaluate the earth return impedance with various parameters and arbitrary conductor arrangements accurately and efficiently and the required computational time of the proposed approach is almost independent of the geometric and electric parameters.</P>