• Journal of Embryo Transfer
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• v.28 no.4
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• pp.355-360
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• 2013

Precise, rapid and simple methods for species identification in animals are among the most important techniques in the livestock industry and research fields including meat classification. In this study, polymerase chain reaction (PCR) based molecular identification using inter species polymorphisms were examined by PCR-restriction fragment length polymorphism (RFLP) analysis for mitochondrial DNA (mtDNA) cytochrome b (CYTB) gene sequences among four mammalian livestock animals (cattle, horse, goat and pig). The results from PCR-RFLP analysis using the AluI restriction enzyme were also provided for the species-specific band patterns among CYTB gene sequences in these four species. The AluI-digestion for CYTB genes provided interesting migration patterns differentially displayed according to each species. Cattle and horse had one AluI-recognition site at different nucleotide positions and their AluI-digested fragments showed different band patterns on the gels. Pig had two AluI-recognition sites within the amplified CYTB sequences and produced three bands on the gels. Goat had no AluI-recognition site and was located at the same position as the uncut PCR product. The results showed the species-specific band patterns on a single gel among the four livestock animal species by AluI-RFLP. In addition, the results from blind tests for the meat samples collected from providers without any records showed the identical information on the species recorded by observing their phenotypes before slaughter. The application of this PCR-RFLP method can be useful and provide rapid, simple, and clear information regarding species identification for various tissue samples originating from tested livestock species.

• Genomics & Informatics
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• v.17 no.2
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• pp.17.1-17.3
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• 2019

Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific papers. However, few thorough studies on text mining and application development, for plant molecular biology data, have been performed, especially for rice, resulting in a lack of datasets available to solve named-entity recognition tasks for this species. Since there are rare benchmarks available for rice, we faced various difficulties in exploiting advanced machine learning methods for accurate analysis of the rice literature. To evaluate several approaches to automatically extract information from gene/protein entities, we built a new dataset for rice as a benchmark. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and is downloaded from PubMed. During the 5th Biomedical Linked Annotation Hackathon, a portion of the dataset was uploaded to PubAnnotation for sharing. Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of different approaches to the task.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.6 no.11
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• pp.2784-2799
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• 2012

Biological data have been increased exponentially in recent years, and analyzing these data using data mining tools has become one of the major issues in the bioinformatics research community. This paper focuses on the protein construction process in higher organisms where the deoxyribonucleic acid, or DNA, sequence is filtered. In the process, "unmeaningful" DNA sub-sequences (called introns) are removed, and their meaningful counterparts (called exons) are retained. Accurate recognition of the boundaries between these two classes of sub-sequences, however, is known to be a difficult problem. Conventional approaches for recognizing these boundaries have sought for solely enhancing machine learning techniques, while inherent nature of the data themselves has been overlooked. In this paper we present an approach which makes use of the data attributes inherent to species in order to increase the accuracy of the boundary recognition. For experimentation, we have taken the data sets for four different species from the University of California Santa Cruz (UCSC) data repository, divided the data sets based on the species types, then trained a preprocessed version of the data sets on neural network(NN)-based and support vector machine(SVM)-based classifiers. As a result, we have observed that each species has its own specific features related to the splice sites, and that it implies there are related distances among species. To conclude, dividing the training data set based on species would increase the accuracy of predicting splicing junction and propose new insight to the biological research.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2018.05a
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• pp.464-465
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• 2018

Bass and Bluegill, which are representative ecosystem disturbance species, are reported to be the most important factor in the reduction of domestic native fish populations in Korea. Therefore, it is necessary to develop system and field application technology for the extermination of these foreign species. Recently, the CNN(Convolutional Neural Network), one of the deep learning systems for the recognition, classification, and learning, has shown excellent performance. However, CNN data used for object recognition and classification were mainly applied to recognition and classification of other objects with distinct characteristics. This study proposes a system that applies CNN to the classification of fish species with similar characteristics.

• Mycobiology
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• v.49 no.5
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• pp.521-526
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• 2021

Three isolates belonging to the ascomycetous genus Zygotorulaspora were obtained from the fruits of Cornus officinalis and Smilax china, and flowers of Dendranthema zawadskii var. latilobum in Gongju-si, Korea. Phylogenetic Analyses of the LSU D1/D2 domain and ITS region sequences supported the recognition of two new species: Zygotorulaspora cornina sp. nov. (type strain NIBRFGC000500475 = KACC93346P^PP) and Zygotorulaspora smilacis sp. nov. (type strain NIBRFGC000500476 = KACC93347P^PP). The two novel species revealed no growth on D-Galactose, unlike the other six species in the genus Zygotorulaspora. They are distinguished from each other by their phylogenetic differences and phenotypic characteristics such as assimilation of xylitol, 5-keto-D-gluconate, and ethanol. All species in the genus Zygotorulaspora including the two novel species have phenotypic traits of genus Zygotorulaspora: asci are persistent, sucrose and raffinose are assimilated, and m-inositol is not required for growth, and they are mainly associated with plants.

• Genomics & Informatics
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• v.19 no.3
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• pp.27.1-27.4
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• 2021

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural language understanding. Biological named entity recognition (NER) and named entity normalisation (NEN) are two common tasks aiming at identifying and linking biologically important entities such as genes or gene products mentioned in the literature to biological databases. In this paper, we present an updated version of OryzaGP, a gene and protein dataset for rice species created to help natural language processing (NLP) tools in processing NER and NEN tasks. To create the dataset, we selected more than 15,000 abstracts associated with articles previously curated for rice genes. We developed four dictionaries of gene and protein names associated with database identifiers. We used these dictionaries to annotate the dataset. We also annotated the dataset using pretrained NLP models. Finally, we analysed the annotation results and discussed how to improve OryzaGP.

• The Korean Journal of Zoology
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• v.37 no.4
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• pp.573-579
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• 1994

본 연구는 1992년 3월에서 1993년 5월까지 충북 청원군 강내면 다락리 야산에 서식하는 노랑턱멧새(Emberizo elegans) 집단을 대상으로 이루어졌다. 종 인식을 위한 의미있는 song 특징을 알아보기 위해 같은 과(요)에 속하는 붉은뺨멧새(Emberizo fucata)와 쑥새(Emberiza rustsca)의 'stereotyped song'을 분석하였다 또한 세력권을 형성한 5개체를 대상으로 song에 기초한 playback 실험을 통하여 종 인식 능력을 알아보았다. 스피커에 가장 가까이 날라온 거리와 이 거리에서 머문 시간을 측정한 결과 붉은뺨멧새의 song에는 반응이 없었으나 쑥새의 song에는 의미있는 반응을 보였다. 따라서 노랑턱멧새와 두 종에 대한 song 특징의 분석을 토대로 종간 인식의 가능성에 대하여 논의하였다.

• Animal cells and systems
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• v.9 no.4
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• pp.211-213
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• 2005

In bird species that suffer brood parasitism, the question about which sex is responsible for egg rejection has important implications for determining the coevolutionary relationship between brood parasites and their hosts. In order to determine which sex rejects a parasitic egg in vinous-throated parrotbills (Paradoxornis webbianus) which have egg color dimorphism, we conducted model egg experiments and video-recorded the behavior of the focal pair. Both sexes showed rejection behavior to the parasitic eggs. It indicates that the vinous-throated parrotbill may have a high rejection rate and faster spread of any rejection alleles through out populations. However, further studies are still needed to confirm the egg recognition mechanism in this species, which will expand our knowledge of the evolutionary relationship between host and parasite.

• Korean Journal of Plant Taxonomy
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• v.46 no.2
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• pp.163-174
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• 2016

Gnetum (Gnetaceae, Gnetales) is a gymnosperm genus with ca. 35 species distributed in tropical forests around the world. Due to its dioecious habit and lack of diagnostic characters from vegetative tissue, the identification of Gnetum species is not easy without seeds or reproductive structures. To identify and verify their phylogenetic positions, we applied DNA barcoding to Cambodian Gnetum collections gathered between 2010 and 2015, with previously designed cp matK gene primers. We newly sequenced partial matK sequences from 72 Gnetum collections, 43 out of 72 from Cambodia, and analyzed 115 Gnetum accessions using the neighbor-joining method. The resulting neighbor-joining tree categorized Cambodian Gnetum samples into three clades of species: G. macrostachyum, G. montanum, and G. aff. gracilipes. The recognition of G. aff. gracilipes in Cambodia is reported here for the first time. Taxonomic information for the three recognized Cambodian Gnetum species is provided and the benefits of the taxonomic reevaluation assisted by DNA barcoding are emphasized in this work.

• ALGAE
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• v.31 no.3
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• pp.219-230
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• 2016

The Euglena deses group are common freshwater species composed of E. adhaerens, E. carterae, E. deses, E. mutabilis, and E. satelles. These species are characterized by elongated cylindrical worm-like cell bodies and numerous discoid chloroplasts with a naked pyrenoid. To understand the cryptic diversity, species delimitation and phylogenetic relationships among members of the group, we analyzed morphological data (light and scanning electron microscopy) and molecular data (nuclear small subunit [SSU] and large subunit [LSU] rDNAs and plastid SSU and LSU rDNAs). Bayesian and maximum likelihood analyses based on the combined four-gene dataset resulted in a tree consisting of two major clades within the group. The first clade was composed of two subclades: the E. mutabilis subclade, and the E. satelles, E. carterae, and E. adhaerens subclade. The E. mutabilis subclade was characterized by a lateral canal opening at the anterior end and a single pellicular stria, whereas the E. satelles, E. carterae, and E. adhaerens subclade was characterized by an apical canal opening at the anterior end of the cell and double pellicular striae. The second clade consisted of 20 strains of E. deses, characterizing by a subapical canal opening at the anterior end and double pellicular striae, but they showed cell size variation and high genetic diversity. Species boundaries were tested using a Bayesian multi-locus species delimitation method, resulting in the recognition of five cryptic species within E. deses clade.