• Animal Systematics, Evolution and Diversity
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• v.13 no.1
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• pp.29-36
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• 1997

한국산 기름종개속 어류중 Cobitis taenia complex의 집단간 유전적 차이에 따른 종 분화 여부를 밝히고자 6개 집단을 대상으로 mitochondrial DNA(mtDNA)의 RFLP분석을 실 시하였다. C. taenia complex mtDNA를 10개의 6-base cutting 제한효소로 처리한 다음 그 절편 양상을 비교, 분석한 결과 6개 집단 공히 mtDNA 의 전체 genome 크기는 약 17.0$\pm$ 0.5Kbp였으며 공동절편수(F)에서 C. t. taenia 2개집단과 C. t. stria와 C. t. lutheri 4개 집단 간의 F값은 평균 0.263으로 차이가 있었으나, C. t. striata 와 C. t. lutheri 사이는 F=0.569로 가깝게 나타났다. 염기치환율 (p)에 있어 C. t. taenia는 C. t. striata 및 C. t. lutheri와 평균 p=0.082로 뚜렷한 종간차이를 보였으나, C. t. striata와 C. t. lutheri 집단들은 p=0.033으로 매우 가까운 유사성을 나타내었다. MtDNA 분석결과 C. taenia complex 중 C. t. taenia는 완전히 종분화가 이루어진 별종으로, C. t. striata와 C. t. lutherisms 아직 종수준의 분화가 이루어지지 않은 아종으로 분류함이 타당하다고 사료된다.

• BMB Reports
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• v.51 no.10
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• pp.500-507
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• 2018

Cell reprogramming has been considered a powerful technique in the regenerative medicine field. In addition to diverse its strengths, cell reprogramming technology also has several drawbacks generated during the process of reprogramming. Telomere shortening caused by the cell reprogramming process impedes the efficiency of cell reprogramming. Transcription factors used for reprogramming alter genomic contents and result in genetic mutations. Additionally, defective mitochondria functioning such as excessive mitochondrial fission leads to the limitation of pluripotency and ultimately reduces the efficiency of reprogramming. These problems including genomic instability and impaired mitochondrial dynamics should be resolved to apply cell reprograming in clinical research and to address efficiency and safety concerns. Sirtuin (NAD+-dependent histone deacetylase) has been known to control the chromatin state of the telomere and influence mitochondria function in cells. Recently, several studies reported that Sirtuins could control for genomic instability in cell reprogramming. Here, we review recent findings regarding the role of Sirtuins in cell reprogramming. And we propose that the manipulation of Sirtuins may improve defects that result from the steps of cell reprogramming.

• Genomics & Informatics
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• v.21 no.1
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• pp.10.1-10.6
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• 2023

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

• Journal of Ginseng Research
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• v.47 no.2
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• pp.302-310
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• 2023

Background: The most common type of dementia, Alzheimer's disease (AD), is marked by the formation of extracellular amyloid beta (Aβ) plaques. The impairments of axons and synapses appear in the process of Aβ plaques formation, and this damage could cause neurodegeneration. We previously reported that non-saponin fraction with rich polysaccharide (NFP) from Korean Red Ginseng (KRG) showed neuroprotective effects in AD. However, precise molecular mechanism of the therapeutic effects of NFP from KRG in AD still remains elusive. Methods: To investigate the therapeutic mechanisms of NFP from KRG on AD, we conducted proteomic analysis for frontal cortex from vehicle-treated wild-type, vehicle-treated 5XFAD mice, and NFP-treated 5XFAD mice by using nano-LC-ESI-MS/MS. Metabolic network analysis was additionally performed as the effects of NFP appeared to be associated with metabolism according to the proteome analysis. Results: Starting from 5,470 proteins, 2,636 proteins were selected for hierarchical clustering analysis, and finally 111 proteins were further selected for protein-protein interaction network analysis. A series of these analyses revealed that proteins associated with synapse and mitochondria might be linked to the therapeutic mechanism of NFP. Subsequent metabolic network analysis via genome-scale metabolic models that represent the three mouse groups showed that there were significant changes in metabolic fluxes of mitochondrial carnitine shuttle pathway and mitochondrial beta-oxidation of polyunsaturated fatty acids. Conclusion: Our results suggested that the therapeutic effects of NFP on AD were associated with synaptic- and mitochondrial-related pathways, and they provided targets for further rigorous studies on precise understanding of the molecular mechanism of NFP.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.921-926
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• 2012

In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

• BMB Reports
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• v.52 no.12
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• pp.689-694
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• 2019

Ethical and safety issues have rendered mesenchymal stem cells (MSCs) popular candidates in regenerative medicine, but their therapeutic capacity is lower than that of induced pluripotent stem cells (iPSCs). This study compared original, dental tissue-derived MSCs with re-differentiated MSCs from iPSCs (iPS-MSCs). CD marker expression in iPS-MSCs was similar to original MSCs. iPS-MSCs expressed higher in pluripotent genes, but lower levels in mesodermal genes than MSCs. In addition, iPS-MSCs did not form teratomas. All iPSCs carried mtDNA mutations; some shared with original MSCs and others not previously detected therein. Shared mutations were synonymous, while novel mutations were non-synonymous or located on RNA-encoding genes. iPS-MSCs also harbored mtDNA mutations transmitted from iPSCs. Selected iPS-MSCs displayed lower mitochondrial respiration than original MSCs. In conclusion, screening for mtDNA mutations in iPSC lines for iPS-MSCs can identify mutation-free cell lines for therapeutic applications.

• Animal Bioscience
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• v.34 no.6
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• pp.941-948
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• 2021

Objective: In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan. Methods: Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences. Results: This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1. Conclusion: The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.

• International Journal of Industrial Entomology and Biomaterials
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• v.45 no.1
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• pp.29-34
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• 2022

Silkworms have recently attracted attention as healthy functional foods. Different varieties of silkworms have functional differences; thus, there is an emerging need for variety identification. In this study, we sequenced complete mitochondrial genomes (mitogenomes) of ten government-recommended silkworm varieties (BaekHwang, BaekOk, DaeBaek, DaeBak, DaeHwang, GoldenSilk, HanSaeng, JooHwang, KumKang, and KumOk). Comparison of these sequences allowed us to select the single nucleotide polymorphisms (SNPs) in 34 sites that are specific to six silkworm varieties: 13 in DaeBak, 8 in GoldenSilk, 9 in KumKang, 2 in BaekHwang, 1 in BaekOk, and 1 in DaeHwang. Among these each one SNP per variety was amplified by preparing variety-specific primers and then using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR). As a result, it was possible to identify these six varieties among the ten silkworm varieties, evidencing that SNPs developed from mitogenomes are useful marker for the discrimination of genetically closer silkworm varieties.

• Animal Systematics, Evolution and Diversity
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• v.36 no.2
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• pp.182-184
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• 2020

Isaacsicalanus paucisetus Fleminger, 1983, a monotypic species of the family Spinocalanidae Vervoort, 1951, was first reported from a hydrothermal vent field in the East Pacific Rise off the mouth of the Gulf of California. The mitochondrial cytochrome oxidase I(mtCOI) DNA barcodes are considered a useful tool to assist traditional taxonomy and species discrimination in calanoid copepods. However, the mtCOI DNA barcodes of I. paucisetus have not been reported due to the species rarity and the difficulty of sampling. In this study, we firstly determined the mtCOI DNA barcodes of the I. paucisetus newly collected from a hydrothermal vent in the North Fiji Basin of the southwestern Pacific. All mtCOI DNA barcodes of I. paucisetus were identical and intraspecies variations of spinocalanid species were 0.0-3.0%. Interspecies and intergeneric variations were 13.4-25.2% and 16.7-24.1%, respectively. The DNA barcodes of I. paucisetus obtained in the present study would be helpful for understanding taxonomic relationships of widespread spinocalanid species.

• Journal of Aquaculture
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• v.17 no.1
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• pp.1-7
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• 2004

A rainbow trout uncoupling protein 3 (UCP3) cDNA clone, encoding a 310 amino acid protein, was cloned and sequenced from a liver cDNA library. Two different splice variants designated UCP3-vl and UCP3-v2, were identified through liver cDNA library screening using rainbow trout UCP3 cDNA clone as a probe. UCP3-vl has 3 insertions in the UCP3 cDNA: the first insertion (133 bp), the second (141 bp), and the third (370 bp) were located 126 bp, 334 bp and 532 bp downstream from the start codon, respectively. UCP3-v2 contained a single insertion, identical in sequence and location to the second insertion of UCP3-vl. UCP3, a mitochondrial protein, functions to modulate the efficiency of oxidative phosphorylation. UCP3 has been detected from heart, testis, spinal cord, eye, retina, colon, muscle, brown adipose tissue and white adipose tissue in mammalian animals. Human and rodent UCP3s are highly expressed in skeletal muscle and brown adipose tissue, while they show weak expression of UCP3 in heart and white adipose tissue. In contrast to mammalian studies, RT-PCR and Southern blot analysis of the rainbow trout demonstrated that UCP3 is strongly expressed in liver and heart. UCP3, UCP3-vl, and UCP3-v2 all contain an Ava III short interspersed element (SINE), located in the 3'untraslated region (UTR). PCR using primers from the Ava III SINE and the UCP3 3'UTR region indicates that the UCP3 cDNA is structurally conserved among salmonids and that these primers may be useful for salmonid species genotyping.