• Asian-Australasian Journal of Animal Sciences
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• v.29 no.10
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• pp.1371-1382
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• 2016

MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying variation in this measure of feed efficiency in bovines.

• Journal of the Korea Convergence Society
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• v.8 no.12
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• pp.55-62
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• 2017

The Named Entity Recognition system is a system that recognizes words or phrases with object names such as personal name (PS), place name (LC), and group name (OG) in the document as corresponding object names. Traditional approaches to named entity recognition include statistical-based models that learn models based on hand-crafted features. Recently, it has been proposed to construct the qualities expressing the sentence using models such as deep-learning based Recurrent Neural Networks (RNN) and long-short term memory (LSTM) to solve the problem of sequence labeling. In this research, to improve the performance of the Korean named entity recognition system, we used a hand-crafted feature, part-of-speech tagging information, and pre-built lexicon information to augment features for representing sentence. Experimental results show that the proposed method improves the performance of Korean named entity recognition system. The results of this study are presented through github for future collaborative research with researchers studying Korean Natural Language Processing (NLP) and named entity recognition system.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.3
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• pp.251-255
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• 2004

The epidemics of rice blast which occurred in south parts of Korea during the period from 1999 to 2001 and damaged several high quality rice cultivars developed using "Milyang 95" and/or "Milyang 96" as a parent. Genetic diversity of 23 rice cultivars including "Milyang 95" and it's relatives was assessed using 54 simple sequence repeats (SSR) markers reported to be linked to major blast resistance genes. Fifty-four SSR markers representing fifty-seven loci in the rice genome detected polymorphism among the 23 cultivars and revealed a total of 170 alleles with an average of 3.0 alleles per primer, The number of amplified bands ranged from 1 to 7. Several SSR markers including RM249, RM206 and OSR20 were informative for assessing the genetic diversity of relatively closed japonica rice cultivars. The 23 cultivars were classified into four groups by cluster analysis based on Nei's genetic distances, and the cultivars developed from same parents showed a tendency to cluster together that is consistant with genealogical information. High quality rice cultivars, Daesanbyeo, Donganbyeo, and Milyang 95 belonged to the same cluster, At the loci, RM254 and OSR32, all of the cultivars derived from the crosses using "Milyang 95" shared same alleles, suggesting that these japonica cultivars might carry alleles that are identical by descent. Evaluation of 23 rice cultivars against blast needs to be confirmed regarding the relationship between genotype and blast resistance.p between genotype and blast resistance.

• Journal of KIISE:Software and Applications
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• v.35 no.12
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• pp.780-788
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• 2008

Modeling hand poses and tracking its movement are one of the challenging problems in computer vision. There are two typical approaches for the reconstruction of hand poses in 3D, depending on the number of cameras from which images are captured. One is to capture images from multiple cameras or a stereo camera. The other is to capture images from a single camera. The former approach is relatively limited, because of the environmental constraints for setting up multiple cameras. In this paper we propose a method of reconstructing 3D hand poses from a 2D input image sequence captured from a single camera by means of Belief Propagation in a graphical model and recognizing a finger clicking motion using a hidden Markov model. We define a graphical model with hidden nodes representing joints of a hand, and observable nodes with the features extracted from a 2D input image sequence. To track hand poses in 3D, we use a Belief Propagation algorithm, which provides a robust and unified framework for inference in a graphical model. From the estimated 3D hand pose we extract the information for each finger's motion, which is then fed into a hidden Markov model. To recognize natural finger actions, we consider the movements of all the fingers to recognize a single finger's action. We applied the proposed method to a virtual keypad system and the result showed a high recognition rate of 94.66% with 300 test data.

• Korean Journal of Plant Taxonomy
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• v.43 no.4
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• pp.267-273
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• 2013

This study employed inter-simple-sequence repeat (ISSR) to assess genetic variation among 189 individuals representing 10 populations (nine in Korea and one in Japan) of Millettia japonica, which has recently been lifted from the endangered species of Korea. The calculated Shannon's information index value (I = 0.2689) of the species was appreciable and was higher than other endangered leguminous woody taxa. Gochang (I = 0.2968), Namhae (I = 0.2951), and Mt. Toham (I = 0.2823) populations showed relatively high genetic diversity, whereas the Kyushu (in Japan) population (I = 0.2487) exhibited the lowest. The results of an analysis of molecular variance indicated that 86.49% of the diversity was attributed to within populations, and 13.51% to differences among populations, suggesting that M. japonica populations do not have significant geographic differentiation and that the gene flow between populations exists to some extent (Nm = 1.8446). Continuous habitat monitoring should be conducted to conserve genetic diversity of M. japonica, particularly for those populations with relatively high genetic diversity. Selection of many individuals from the populations in Gochang, Namhae, and Mt. Toham is thought to be an appropriate strategy for ex situ conservation of M. japonica in Korea.

• Analytical Science and Technology
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• v.18 no.4
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• pp.362-367
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• 2005

The human mitochondrial genome (mtDNA) has been an important tool in the field of forensic investigations. Within the entire mtDNA molecule, the non-coding control region which is approximately 1,100 bp including hypervariable region I and II (HV1 and HV2) is widely studied because it is highly polymorphic and useful for human identification purposes. In this study, 360 unrelated Koreans were analyzed in HV1. The number of polymorphic sites and genetic lineage were 124 and 210, respectively. The most prevalent substitution was C-T and 75.8% of DNA showed C-T substitution at 16223. There were 20 kinds of polymorphism between 16180 and 16193 including insertion and deletion. The most frequent haplotype was [16223T, 16362C] representing 5%. Approximately 25.9% of DNA showed the same haplotype in at least two samples. The gene diversity was calculated to 0.996 and the probability of two unrelated perosons having the same haplotype was determined to 0.7%.

• Journal of Life Science
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• v.22 no.11
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• pp.1545-1551
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• 2012

Authors report the glycoside hydrolase (GH) family 16 ${\beta}$-agarase from the strain of Agarivorans sp. JA-1, which authors previously stated as recombinant expression and characterization of GH-50 and GH-118 ${\beta}$-agarase. It comprised an open reading frame of 1,362 base pairs, which encodes a protein of 49,830 daltons consisting of 453 amino acid residues. Valuation of the total sequence showed that the enzyme has 98% nucleotide and 99% amino acid sequence similarities to those of GH-16 ${\beta}$-agarase from Pseudoalteromonas sp. CY24. The gene corresponding to a mature protein of 429 amino acids was recombinantly expressed in Escherichia coli, and the enzyme was purified to homogeneity by affinity chromatography. It showed maximal activity at $40^{\circ}C$ and pH 5.0, representing 67.6 units/mg. Thin layer chromatography revealed that mainly neoagarohexaose and neoagarotetraose were produced from agarose. The enzyme would be valuable for the industrial production of functional neoagarooligosaccharides.

• Korean Journal of Plant Taxonomy
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• v.33 no.4
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• pp.373-386
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• 2003

Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA were determined for 14 individuals representing eight taxa from Scopolia s. str. and related genera, Anisodus and Atropanthe. We found that the ITS sequences of Korean endemic species, S. parviflora, are significantly different from its allied species, S. japonica. This is contradictory to traditional taxonomic treatments in which those species are regarded as conspecific. S. parviflora exhibited closer relationship to S. carniolica, which is disjunctly distributed in Europe. In spite of substantially high sequence divergence between S. japonica and S. parvlflora/S. carniolica clade, morphological resemblance is evident among the species. Morphological stasis concept (retardation of morphological differentiation or evolution of similar characters among the disjuncts in a similar ecological habitat) was referred to understand this rather unusual evolutionary feature. S. lutescens, another Korean endemic species, shared almost identical ITS sequences with S. parviflora. Lack of diagnostic character distinguishing the taxa suggests that they are conspecific. Anisodus carniolicoides, which was originally described in Scopolia, was grouped with A. luridus and A. tanguticus. The monophyletic Anisodus formed a sister group relationship with a monotypic genus Atropanthe.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.283-294
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• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1065-1071
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• 2013

The swine leukocyte antigen class II molecules are possibly associated with the induction of protective immunity. The study described here was to investigate the relationship between polymorphisms in exon 2 of the swine DQA gene and piglet diarrhea. This study was carried out on 425 suckling piglets from three purebred pig strains (Large White, Landrace and Duroc). The genetic diversity of exon 2 in swine DQA was detected by PCR-SSCP and sequencing analysis, eight unique SSCP patterns (AB, BB, BC, CC, CD, BD, BE and DD) representing five specific allele (A to E) sequences were detected. Sequence analysis revealed 21 nucleotide variable sites and resulting in 12 amino acid substitutions in the populations. A moderate level polymorphism and significant deviations from Hardy-Weinberg equilibrium of the genotypes distribution were observed in the populations (p<0.01). The association analysis indicated that there was a statistically significant difference in the score of piglet diarrhea between different genotypes, individuals with genotype CC showed a lower diarrhea score than genotypes AB ($0.98{\pm}0.09$), BB ($0.85{\pm}0.77$) and BC ($1.25{\pm}0.23$) (p<0.05), and significantly low than genotype BE ($1.19{\pm}0.19$) (p<0.01), CC genotype may be a most resistance genotype for piglet diarrhea.