• Journal of Plant Biotechnology
• /
• v.33 no.3
• /
• pp.153-160
• /
• 2006

Brassica rape is an important species used as a vegetable, oil, and fodder worldwide. It is related phylogenically to Arabidopsis thaliana, which has already been fully sequenced as a model plant. The 'Multinational Brassica Genome Project (MBGP)'was launched by the international Brassica community with the aim of sequencing the whole genome of B. rapa in 2003 on account of its value and the fact that it has the smallest genome among the diploid Brassica. The genome study was carried out not only to know the structure of genome but also to understand the function and the evolution of the genes comprehensively. There are two mapping populations, over 1,000 molecular markers and a genetic map, 2 BAC libraries, physical map, a 22 cDHA libraries as suitable genomic materials for examining the genome of B. rapa ssp. pekinensis Chinese cabbage. As the first step for whole genome analysis, 220,000 BAC-end sequences of the KBrH and KBrB BAC library are achieved by cooperation of six countries. The results of BAC-end sequence analysis will provide a clue in understanding the structure of the genome of Brassica rapa by analyzing the gene sequence, annotation and abundant repetitive DHA. The second stage involves sequencing of the genetically mapped seed BACs and identifying the overlapping BACs for complete genome sequencing. Currently, the second stage is comprises of process genetic anchoring using communal populations and maps to identify more than 1,000 seed BACs based on a BAC-to-BAC strategy. For the initial sequencing, 629 seed BACs corresponding to the minimum tiling path onto Arabidopsis genome were selected and fully sequenced. These BACs are now anchoring to the genetic map using the development of SSR markers. This information will be useful for identifying near BAC clones with the seed BAC on a genome map. From the BAC sequences, it is revealed that the Brassica rapa genome has extensive triplication of the DNA segment coupled with variable gene losses and rearrangements within the segments. This article introduces the current status and prospective of Korea Brassica Genome Project and the bioinformatics tools possessed in each national team. In the near future, data of the genome will contribute to improving Brassicas for their economic use as well as in understanding the evolutional process.

• Journal of the Korean Society of Radiology
• /
• v.81 no.2
• /
• pp.365-378
• /
• 2020

Purpose This study was performed to determine whether the T1 relaxation time of gadoxetic acid-enhanced liver MR imaging is useful for detecting and staging liver fibrosis in patients with chronic liver disease. Materials and Methods One hundred and three patients with suspected focal liver lesion underwent MR imaging and Fibroscan. Fibroscan was chosen as the reference standard for classifying liver fibrosis. T1 relaxation times were acquired before (preT1), 20 minutes after (postT1) contrast administration, and reduction rate of T1 relaxation time (rrT1) on transverse 3D VIBE (volumetric interpolated breath-hold examination) sequence using 3T MR imaging. The optimal cut-off values for the fibrosis staging were determined with ROC analysis. Results PreT1 and postT1 increased and rrT1 decreased constantly with increasing severity of liver fibrosis according to the METAVIR score (F0-F4). There were statistically significant differences between F2 and F3 in preT1 (F2, 836.0 ± 74.7 ms; F3, 888.6 ± 77.5 ms, p < 0.05) and between F3 and F4 in postT1 (F3, 309.0 ± 80.2 ms; F4, 406.6 ± 147.7 ms, p < 0.05) and rrT1 (F3, 65.4 ± 7.7%; F4, 57.3 ± 11.4%, p < 0.05). ROC analysis revealed that combination test (preT1 + postT1) was the best test for predicting liver fibrosis. Conclusion PreT1 and postT1 increased constantly with increasing severity of liver fibrosis. T1 mapping in gadoxetic acid-enhanced liver MR imaging could be a helpful complementary sequence to determine the liver fibrosis stage.

• Journal of KIISE:Computing Practices and Letters
• /
• v.13 no.7
• /
• pp.508-519
• /
• 2007

Flash memory based storage has been used in various mobile systems and now is to be used in Laptop computers in the name of Solid State Disk. The Flash memory has not only merits in terms of weight, shock resistance, and power consumption but also limitations like erase-before-write property. To overcome these limitations, Flash memory based storage requires special address mapping software called FTL(Flash-memory Translation Layer), which often performs merge operation for block recycling. In order to reduce block recycling cost in NAND Flash memory based storage, we introduce another block recycling scheme which we call migration. As a result, the FTL can select either merge or migration depending on their costs for each block recycling. Experimental results with Postmark benchmark and embedded system workload show that this cost-based selection of migration/merge operation improves the performance of Flash memory based storage. Also, we present a solution of macroscopic optimal migration/merge sequence that minimizes a block recycling cost for each migration/merge combination period. Experimental results show that the performance of Flash memory based storage can be more improved by the macroscopic optimization than the simple cost-based selection.

• Journal of KIISE:Software and Applications
• /
• v.36 no.2
• /
• pp.169-177
• /
• 2009

In this paper, we propose a new shot boundary detection method which is optimized for news video story parsing. This new news shot boundary detection method was designed to satisfy all the following requirements: 1) minimizing the incorrect data in data set for anchor shot detection by improving the recall ratio 2) detecting abrupt cuts and gradual transitions with one single algorithm so as to divide news video into shots with one scan of data set; 3) classifying shots into static or dynamic, therefore, reducing the search space for the subsequent stage of anchor shot detection. The proposed method, based on singular value decomposition with incremental clustering and mercer kernel, has additional desirable features. Applying singular value decomposition, the noise or trivial variations in the video sequence are removed. Therefore, the separability is improved. Mercer kernel improves the possibility of detection of shots which is not separable in input space by mapping data to high dimensional feature space. The experimental results illustrated the superiority of the proposed method with respect to recall criteria and search space reduction for anchor shot detection.

• Korean Journal of Plant Taxonomy
• /
• v.42 no.4
• /
• pp.247-252
• /
• 2012

Seed morphology in the subtribe Agrimoniinae (Rosaceae) was examined using scanning electron microscopy to identify distinct characters and evaluate their evolution in a phylogenetic framework for five genera in the subtribe: Agrimonia L., Aremonia Neck. ex Nestl., Hagenia J.F. Gmel., Leucosidea Eckl. & Zeyh., and Spenceria Trimen. All genera have one or two mature achenes in a fruiting hypanthium. In the seed coats, the cell shape, size, wall features, and sculpturing vary across genera. Of most significance is the presence of papillae structures in both Agrimonia and Aremonia. Through the mapping of papillae features onto phylogenetic trees, either one or two changes in seed coats are hypothesized. The phylogenetic tree inferred from four nuclear and six chloroplast regions of sequence data suggests that at least two steps of papillae sculpturing on seed coats are required. On the other hand, in the phylogenetic tree of a low-copy nuclear gene, one independent evolutionary step is postulated to explain the current character states. In the latter hypothesis, the seed coat sculpturing also supports a monophyletic relationship for cosmopolitan Agrimonia and European endemic Aremonia. The seed coat sculpturing provides valuable information for inferring phylogenetic relationships at the generic level in the subtribe Agrimoniinae.

• Journal of The Korean Astronomical Society
• /
• v.47 no.6
• /
• pp.235-253
• /
• 2014

Intensity interferometry, based on the Hanbury Brown-Twiss effect, is a simple and inexpensive method for optical interferometry at microarcsecond angular resolutions; its use in astronomy was abandoned in the 1970s because of low sensitivity. Motivated by recent technical developments, we argue that the sensitivity of large modern intensity interferometers can be improved by factors up to approximately 25 000, corresponding to 11 photometric magnitudes, compared to the pioneering Narrabri Stellar Interferometer. This is made possible by (i) using avalanche photodiodes (APD) as light detectors, (ii) distributing the light received from the source over multiple independent spectral channels, and (iii) use of arrays composed of multiple large light collectors. Our approach permits the construction of large (with baselines ranging from few kilometers to intercontinental distances) optical interferometers at the cost of (very) long-baseline radio interferometers. Realistic intensity interferometer designs are able to achieve limiting R-band magnitudes as good as $m_R{\approx}14$, sufficient for spatially resolved observations of main-sequence O-type stars in the Magellanic Clouds. Multi-channel intensity interferometers can address a wide variety of science cases: (i) linear radii, effective temperatures, and luminosities of stars, via direct measurements of stellar angular sizes; (ii) mass-radius relationships of compact stellar remnants, via direct measurements of the angular sizes of white dwarfs; (iii) stellar rotation, via observations of rotation flattening and surface gravity darkening; (iv) stellar convection and the interaction of stellar photospheres and magnetic fields, via observations of dark and bright starspots; (v) the structure and evolution of multiple stars, via mapping of the companion stars and of accretion flows in interacting binaries; (vi) direct measurements of interstellar distances, derived from angular diameters of stars or via the interferometric Baade-Wesselink method; (vii) the physics of gas accretion onto supermassive black holes, via resolved observations of the central engines of luminous active galactic nuclei; and (viii) calibration of amplitude interferometers by providing a sample of calibrator stars.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.140-140
• /
• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.11
• /
• pp.1544-1550
• /
• 2008

The retinoids (vitamin A and its derivatives) play a critical role in vision, growth, reproduction, cell differentiation and embryonic development. Using the IMpRH panel, porcine cellular retinol binding protein genes 5 and 7 (RBP5 and RBP7) were assigned to porcine chromosomes 5 and 6, respectively. The complete coding sequences (CDS) of the RBP5 and RBP7 genes were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) method, and the deduced amino acid sequences of both genes were compared to human corresponding proteins. The mRNA distributions of the two genes in adult Wuzhishan pig tissues (lung, skeletal muscle, spleen, heart, stomach, large intestine, lymph node, small intestine, liver, brain, kidney and fat) were examined. A total of nine single nucleotide polymorphisms (SNPs) were identified in two genes. Three of these SNPs were analyzed using the polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) method in Laiwu, Wuzhishan, Guizhou, Bama, Tongcheng, Yorkshire and Landrace pig breeds. Association analysis of genotypes of these SNP loci with economic traits was done in our experimental populations. Significant associations of different genotypes of $RBP5-A/G^{63}$, $RBP5-A/G^{517}$ and $RPB5-T/C^{intron1-90}$ loci with traits including maximum carcass length (LM), minimum carcass length (LN), marbling score (MS), back fat thickness at shoulder (SBF), meat color score (MCS) and hematocrit (HCT) were detected. These SNPs may be useful as genetic markers in genetic improvement for porcine production.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.6
• /
• pp.976-986
• /
• 2018

Knowledge about the gut bacterial communities associated with insects is essential to understand their roles in the physiology of the host. In the present study, the gut bacterial communities of a laboratory-reared insecticide-susceptible (IS), and a field-collected insecticide-resistant (IR) population of a major rice pest, the brown planthopper Nilaparvata lugens, were evaluated. The deep-sequencing analysis of the V3 hypervariable region of the 16S rRNA gene was performed using Illumina and the sequence data were processed using QIIME. The toxicological bioassays showed that compared with the IS population, IR population exhibited 7.9-, 6.7-, 14.8-, and 18.7-fold resistance to acephate, imidacloprid, thiamethoxam, and buprofezin, respectively. The analysis of the alpha diversity indicated a higher bacterial diversity and richness associated with the IR population. The dominant phylum in the IS population was Proteobacteria (99.86%), whereas the IR population consisted of Firmicutes (46.06%), followed by Bacteroidetes (30.8%) and Proteobacteria (15.49%). Morganella, Weissella, and Enterococcus were among the genera shared between the two populations and might form the core bacteria associated with N. lugens. The taxonomic-to-phenotypic mapping revealed the presence of ammonia oxidizers, nitrogen fixers, sulfur oxidizers and reducers, xylan degraders, and aromatic hydrocarbon degraders in the metagenome of N. lugens. Interestingly, the IR population was found to be enriched with bacteria involved in detoxification functions. The results obtained in this study provide a basis for future studies elucidating the roles of the gut bacteria in the insecticide resistance-associated symbiotic relationship and on the design of novel strategies for the management of N. lugens.

• The Journal of Korea Institute of Information, Electronics, and Communication Technology
• /
• v.13 no.1
• /
• pp.35-41
• /
• 2020

Fast Fourier transform (FFT) processors have been widely used in various application such as communications, image, and biomedical signal processing. Especially, high-performance and low-power FFT processing is indispensable in OFDM-based communication systems. This paper presents a novel radix-26 FFT algorithm with low computational complexity and high hardware efficiency. Applying a 7-dimensional index mapping, the twiddle factor is decomposed and then radix-26 FFT algorithm is derived. The proposed algorithm has a simple twiddle factor sequence and a small number of complex multiplications, which can reduce the memory size for storing the twiddle factor. When the coefficient of twiddle factor is small, complex constant multipliers can be used efficiently instead of complex multipliers. Complex constant multipliers can be designed more efficiently using canonic signed digit (CSD) and common subexpression elimination (CSE) algorithm. An efficient complex constant multiplier design method for the twiddle factor multiplication used in the proposed radix-26 algorithm is proposed applying CSD and CSE algorithm. To evaluate performance of the previous and the proposed methods, 256-point single-path delay feedback (SDF) FFT is designed and synthesized into FPGA. The proposed algorithm uses about 10% less hardware than the previous algorithm.