• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.316-327
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• 2007

In this study, a Korean native cattle strain (Hanwoo) evidencing high performance in terms of both meat quality and quantity was employed in the generation of 150,000 BAC clones with an average insert size of 140 kb, and corresponding to about a 6X coverage of bovine chromosomal DNA. The BAC clones were pooled in a mini-scale via three rounds of a pooling protocol, and the efficiency of this pooling protocol was evaluated by testing the accuracy of accessibility to the positive clones, via a PCR-based screening method. Two sets of primers designed from each of two known genes were tested, and each yielded 2 or 3 positive clones for each gene, thereby indicating that the BAC library pooling system was appropriate with regard to the accession of the target BAC clones. Analyses of $3.3{\times}10^6$ base pairs obtained from the 7,090 BAC end sequence (BES) showed that 34.88% of the DNA sequence harbored the repetition sequence. Analysis of the 7,090 BES to the $1^{st}$ and $2^{nd}$ generation radiation hybrid map of the cattle genome, using the COMPASS program designed for the construction of a cattle-human comparative mapping, resulted in the localization of a total of 1,374 clones proximal to 339 $1^{st}$ generation markers, and 1,721 clones proximal to 664 $2^{nd}$ generation markers. Collectively, the BAC library and pooling system of the BAC clones from the Korean cattle, coupled with the chromosome-localized BAC clones, will provide us with novel tools for the excavation of desired clones for genome mapping and sequencing, and will also furnish us with additional information regarding breed differences in cattle.

• Journal of Korean Medical Science
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• v.33 no.52
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• pp.337.1-337.14
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• 2018

Background: Mitochondrial heteroplasmy, the co-existence of different mitochondrial polymorphisms within an individual, has various forensic and clinical implications. But there is still no guideline on the application of massively parallel sequencing (MPS) in heteroplasmy detection. We present here some critical issues that should be considered in heteroplasmy studies using MPS. Methods: Among five samples with known innate heteroplasmies, two pairs of mixture were generated for artificial heteroplasmies with target minor allele frequencies (MAFs) ranging from 50% to 1%. Each sample was amplified by two-amplicon method and sequenced by Ion Torrent system. The outcomes of two different analysis tools, Torrent Suite Variant Caller (TVC) and mtDNA-Server (mDS), were compared. Results: All the innate heteroplasmies were detected correctly by both analysis tools. Average MAFs of artificial heteroplasmies correlated well to the target values. The detection rates were almost 90% for high-level heteroplasmies, but decreased for low-level heteroplasmies. TVC generally showed lower detection rates than mDS, which seems to be due to their own computation algorithms which drop out some reference-dominant heteroplasmies. Meanwhile, mDS reported several unintended low-level heteroplasmies which were suggested as nuclear mitochondrial DNA sequences. The average coverage depth of each sample placed on the same chip showed considerable variation. The increase of coverage depth had no effect on the detection rates. Conclusion: In addition to the general accuracy of the MPS application on detecting heteroplasmy, our study indicates that the understanding of the nature of mitochondrial DNA and analysis algorithm would be crucial for appropriate interpretation of MPS results.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.31 no.4
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• pp.587-604
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• 2021

Because the library cannot be run independently and used by many applications, it is important to detect vulnerabilities in the library. Fuzzing, which is a dynamic analysis, is used to discover vulnerabilities for the library. Although this fuzzing technique shows excellent results in terms of code coverage and unique crash counts, it is difficult to apply its effects to library fuzzing. In particular, a fuzzing executable and a seed corpus are needed that execute the library code by calling a specific function sequence and passing the input of the fuzzer to reproduce the various states of the library. Generating the fuzzing environment such as fuzzing executable and a seed corpus is challenging because it requires both understanding about the library and fuzzing knowledge. We propose a novel method to improve the ease of library fuzzing and enhance code coverage and crash detection performance by using a test framework. The systems's performance in this paper was applied to nine open-source libraries and was verified through comparison with previous studies.

• Korean Journal of Microbiology
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• v.51 no.3
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• pp.194-198
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• 2015

Enterococcus faecalis is a Gram-positive and facultative anaerobic bacterium that causes many hospital-acquired infections. Novel E. faecalis specific bacteriophage (phage) ECP3 that had been isolated from thirty-four environmental samples and characterized phenotypically and genotypically. ECP3 phage belongs to the family Myoviridae with contractile tail and lysed E. faecalis specifically but other bacteria including Enterococcus faecium. The genome was double-stranded linear DNA and its size was 145,518 bp comprising of 220 open reading frames. The GC content was 35.9%. The genome sequence showed 97% identity in 90% coverage region with Myoviridae phage PhiEF24C. ECP3 is the first E. faecalis-specific Myoviridae phage isolated in Korea which can be a promising antimicrobial agent against E. faecalis infections.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.24 no.7B
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• pp.1322-1330
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• 1999

The major source of errors in high-speed networks such as Broadband ISDN(B-ISDN) is buffer overflow during congested conditions. These congestion errors are the dominant sources of errors in high-speed networks and result in cell losses. Conventional communication protocols use error detection and retransmission to deal with lost packets and transmission errors. As an alternative, we have presented a method to recover consecutive cell losses using forward error correction(FEC) in ATM(Asynchronous Transfer Mode) networks to reduce the problem. The method finds the lost cells by observing new cell sequence number($SN^{\ast}$). We have used the LI field together with SN and ST fields to consider the $SN^{\ast}$ which provides more correcting coverage than SN in ATM standards. The $SN^{\ast}$ based on the additive way such as the addition of LI capacity to original SN capacity is numbered a repeatedly 0-to-80 cycle. Another extension can be based on the multiplicative way such that LI capacity is multiplied by SN capacity. The multiplicative $SN^{\ast}$ is numbered in a repeatedly 0-to-1025 cycle.

• Investigative Magnetic Resonance Imaging
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• v.12 no.1
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• pp.27-32
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• 2008

Purpose : We developed a 3D CSI (chemical shift imaging) sequence that uses the PRESS (point resolved spectroscopy) excitation scheme and spiral-based readout gradients. Materials and Methods : We implemented constant-density spirals ($32{\times}32$ matrix, $24{\times}24\;cm$ FOV) which use analytic equations to enable real-time prescription on the scanner. In-vivo data from the brain were collected and reconstructed using the gridding algorithm. Results : Data illustrate that with our imaging sequence, the benefits of the PRESS technique, which include elimination of lipid artifacts, remain intact while flexible scan time versus resolution tradeoffs can be achieved using the constant-density spirals. Volumetric high resolution 3D CSI covering 5760 cm3 could be obtained in 12.5 minutes. Conclusion : Spiral-based readout gradients offer a flexible tradeoff between scan time versus resolution. By combining this feature with PRESS based excitation, efficient methods of volumetric spectroscopic imaging can be accomplished by obtaining whole brain coverage while eliminating lipid contamination.

• Molecules and Cells
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• v.26 no.3
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• pp.250-257
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• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.33 no.5C
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• pp.351-360
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• 2008

In cellular mobile radio systems with frequency reuse, the interference signals degrade the channel estimation and signal detection performance due to the low signal-to-interference ratio near coverage boundaries. When the preamble pilot sequences from different cells are orthogonal or located in disjointed positions, they can be used for multi-cell channel estimation and interference cancellation. In time-varying channels caused by Doppler spread, data pilot symbols are needed for channel estimations. However, data pilot symbols are usually located in identical positions for the overhead reduction, which degrades the channel estimation performance. In this paper, we demonstrate a significant amount of performance improvement is achieved by multiplying different pseudonoise(PN) sequences to the data pilot symbols from adjacent interference cells. In particular, for detection scheme using maximal ratio combining(MRC) and inter-cell spatial demultiplexing(ISD), quantitative performance gain of spectral efficiency for different values of Doppler frequency and interference power is presented.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.11
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• pp.1532-1539
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• 2014

Although growth rate is one of the main economic traits of concern in pig production, there is limited knowledge on its epigenetic regulation, such as DNA methylation. In this study, we conducted methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) to compare genome-wide DNA methylation profile of small intestine and liver tissue between fast- and slow-growing weaning piglets. The genome-wide methylation pattern between the two different growing groups showed similar proportion of CpG (regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence) coverage, genomic regions, and gene regions. Differentially methylated regions and genes were also identified for downstream analysis. In canonical pathway analysis using differentially methylated genes, pathways (triacylglycerol pathway, some cell cycle related pathways, and insulin receptor signaling pathway) expected to be related to growth rate were enriched in the two organ tissues. Differentially methylated genes were also organized in gene networks related to the cellular development, growth, and carbohydrate metabolism. Even though further study is required, the result of this study may contribute to the understanding of epigenetic regulation in pig growth.

• Bulletin of the Korean Chemical Society
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• v.27 no.3
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• pp.389-394
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• 2006

Fragmentation efficiencies of various ‘activated-ion’ electron capture dissociation (AI-ECD) methods are compared for a model system of bovine ubiquitin 7+ cations. In AI-ECD studies, sufficient internal energy was given to protein cations prior to ECD application using IR laser radiation, collisions, blackbody radiation, or in-beam collisions, in turn. The added energy was utilized in increasing the population of the precursor ions with less intra-molecular noncovalent bonds or enhancing thermal fluctuations of the protein cations. Removal of noncovalent bonds resulted in extended structures, which are ECD friendly. Under their best conditions, a variety of activation methods showed a similar effectiveness in ECD fragmentation. In terms of the number of fragmented inter-residue bonds, IR laser/blackbody infrared radiation and ‘in-beam’ activation were almost equally efficient with ~70% sequence coverage, while collisions were less productive. In particular, ‘in-beam’ activation showed an excellent effectiveness in characterizing a pre-fractionated single kind of protein species. However, its inherent procedure did not allow for isolation of the protein cations of interest.