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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Journal of Life Science
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Korean Society of Life Science
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Volume & Issues
Volume 25, Issue 12 - Dec 2015
Volume 25, Issue 11 - Nov 2015
Volume 25, Issue 10 - Oct 2015
Volume 25, Issue 9 - Sep 2015
Volume 25, Issue 8 - Aug 2015
Volume 25, Issue 7 - Jul 2015
Volume 25, Issue 6 - Jun 2015
Volume 25, Issue 5 - May 2015
Volume 25, Issue 4 - Apr 2015
Volume 25, Issue 3 - Mar 2015
Volume 25, Issue 2 - Feb 2015
Volume 25, Issue 1 - Jan 2015
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DNA Polymorphism and Assessments of Genetic Relationships in genus Zoysia Based on Simple Sequence Repeat Markers
Huh, Man Kyu ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 257~262
DOI : 10.5352/JLS.2015.25.3.257
The genetic variability of four species of the genus Zoysia collected from South Korea was analyzed using an inter-simple sequence repeat (ISSR) marker system. Polymerase chain reactions (PCR) with eight ISSR primers generated 86 amplicons, 76 (87.1%) of which were polymorphisms. The polymorphism information content (PIC) value of the ISSR marker system was 0.848. The percentage of polymorphic loci (P
) ranged from 41.2% to 44.7%. Nei’s gene diversity (H) ranged from 0.149 to 0.186, with an average overall value of 0.170. The mean of Shannon’s information index (I) value was 0.250. Total genetic diversity values (H
) varied between 0.356 (ISSR-1) and 0.418 (ISSR-16), for an average overall polymorphic loci of 0.345. Interlocus variation in within-species genetic diversity (H
) was low (0.170). On a per-locus basis, the proportion of total genetic variation due to differences among species (G
) was 0.601. This indicated that about 60.1% of the total variation was among species. Thus, about 39.9 of genetic variation was within species. The estimate of gene flow, based on G
, was very low among species of the genus Zoysia (N
= 0.332). The phylogenic tree showed three distinct groups: Z. macrostachya and Z. tenuifolia clades and other species were formed the separated clusters. In conclusion, the ISSR assay was useful for detecting genetic variation in the genus Zoysia, and its discriminatory power was comparable to that of other genotyping tools.
Role of Coelomocytes in Stress Response and Fertility in Caenorhabditis elegans
Park, Jin-Kook ; Hwang, Jin-Kyu ; Song, Keon-Hyoung ; Park, Sang-Kyu ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 263~268
DOI : 10.5352/JLS.2015.25.3.263
Coelomocytes are specialized cells that continually and nonspecifically scavenge fluid from the body cavity through endocytosis in Caenorhabditis elegans. Our previous study revealed that coelmocytes were specifically required for dietary-restriction-induced longevity in C. elegans. In the present study, we examined the effect of coelomocyte ablation on the response to environmental stressors and reproduction in C. elegans. Coelomocytes were ablated using diphtheria toxin specifically expressed in coelomocytes. After exposing worms to 20 J/cm
/min of ultraviolet irradiation in vivo, the survival of the worms was monitored daily. To examine their response to heat stress, their survival after 10 h of 35℃ heat shock was measured. Oxidative stress was induced using paraquat, and the susceptibility to oxidative stress was compared between wild-type control and coelomocyte-ablated worms. The total number of progeny produced was counted, and the time-course distribution of the progeny was determined. The worms with ablated coelomocytes showed reduced resistance to ultraviolet irradiation, but the ablation of coelomocytes had no effect on their response to heat or oxidative stress. The number of progeny produced during the gravid period was significantly decreased in the coelomocyte-ablated worms. These findings suggest that coelomocytes specifically modulate the response to ultraviolet irradiation and are required for normal reproduction in C. elegans. The findings could contribute to understanding of the mechanisms underlying dietary-restriction-induced longevity.
Peptides-derived from Scales of Branchiostegus japonicus Inhibit Ultraviolet B-induced Oxidative Damage and Photo-aging in Skin Cells
Oh, Min Chang ; Kim, Ki Cheon ; Ko, Chang-ik ; Ahn, Yong Seok ; Hyun, Jin Won ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 269~275
DOI : 10.5352/JLS.2015.25.3.269
Collagen peptides, which are found at high concentrations in the human body, are present in animal bones and the skin of marine organisms, namely, fish scales. Collagen is the most abundant structural protein of various connective tissues in animals. Furthermore, it is widely used in biomedical material, pharmaceutical, cosmetic, food, and leather industries. Peptides extracted from scales of various fish protect against ultraviolet B (UVB)-induced skin damage and photo-aging. However, the protective effects of collagen peptides derived from the scales of Branchiostegus japonicus against UVB exposure are unclear. This study investigated the effects of peptides larger than 1 kDa (high-molecular weight peptides [HMP]) and smaller than 1 kDa (low-molecular weight peptides [LMP]), derived from extracts of B. japonicus scales, against UVB-induced skin damage and photo-aging. These peptides scavenged 1,1-diphenyl-2-picrylhydrazyl radicals in a dose-dependent manner. In UVB-exposed HaCaT human keratinocytes, LMP inhibited 8-isoprostane generation, a marker of cellular lipid peroxidation. The peptides also suppressed the UVB-induced increase in tyrosinase activity and melanin content in B16F10 mouse melanoma cells. In addition, the LMP and HMP treatment suppressed UVB-induced elastase and matrix metalloproteinase-1 activities in the HaCaT cells. These results indicate that peptides derived from B. japonicus scales have antioxidant, antiphoto-aging, and skin-whitening effects.
Effects of Garlic Shoot Extract on Lipid Metabolism in Hyperlipidemic Rats Fed a High-fat Diet
Hwang, Cho-Rong ; Kang, Jae-Ran ; Kang, Min-Jung ; Sim, Hye-Jun ; Shin, Jung-Hye ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 276~284
DOI : 10.5352/JLS.2015.25.3.276
This study was designed to investigate the effect of garlic shoot extract administration on serum and liver tissue lipid levels in hyperlipidemic rats. The rats were fed a 45% high-fat diet to induce hyperlipidemia. They were then administered garlic shoot extract (50%) and ethanol extract (75%) at 200 mg/kg B.W./day (GSA-1, GSB-1) and 400 mg/kg B.W./day (GSA-2, GSB-2) for 5 weeks. The total lipid and triglyceride contents in serum were lowest in the GSB-2 group, and the total cholesterol content was significantly lower in the GSA-2 and GSB-2 groups than in the control group. The high density lipoprotein (HDL)-cholesterol content of the GSB-2 group was similar to that of the normal group. The low density lipoprotein (LDL) and very low density lipoprotein (VLDL)-cholesterol contents were significantly lower in the GSB-1 and GSB-2 group than in the control group. atherogenic index (AI) and cardiac risk factor (CRF) were lowest in the GSB-2 group (0.58 and 1.57, respectively). Aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (ALP) activities were significantly higher in the control group than in the normal group, and the levels of AST, ALT, and ALP were significantly lower in the GSA-2 and GSB-2 groups than in the control group. The total lipid content in liver tissue was significantly lower in all the experimental groups compared to that of the control group, but it was not significantly different among the experimental groups. The total cholesterol and triglyceride content in liver tissue was lowest in the GSB-2 group. Antioxidant activity in serum and liver tissue was highest in the GSB-2 group (40.16% and 47.41%, respectively).The thiobarbituric acid reactive substance (TBARS) content in serum and liver tissue was lowest in the GSB-2 group, with the significant difference. Our results suggest that garlic shoot extracts may improve lipid metabolism in serum and liver tissue and potentially reduce hyperlipidemia.
Ethanol Extracts of Citrus Peel Inhibits Adipogenesis through AMPK Signaling Pathway in 3T3-L1 Preadipocytes
Jo, Hyun Kyun ; Han, Min Ho ; Hong, Su Hyun ; Choi, Yung Hyun ; Park, Cheol ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 285~292
DOI : 10.5352/JLS.2015.25.3.285
Citrus peel (CP) is used as a traditional herb with diverse beneficial pharmacological activities, such as anti-inflammatory, anti-oxidant, and anti-allergic effects. However, the anti-obesity effects of citrus peel are poorly defined. The aim of this study was to evaluate ethanol extracts of citrus peel (EECP) for its adipocyte differentiation and adipogenesis in 3T3-L1 preadipocytes. The aim of this study was to evaluate an EECP for its adipocyte differentiation and adipogenesis in 3T3-L1 preadipocytes. Treatment with EECP significantly suppressed the terminal differentiation of 3T3-L1 preadipocytes in a dose-dependent manner, as confirmed by a decrease in lipid droplet number and lipid content and an accumulation of cellular triglyceride. EECP exhibited potential adipogenesis inhibition and downregulated the expression of pro-adipogenic transcription factors, such as sterol regulatory elementbinding protein-1c (SREBP-1c), peroxisome proliferator-activated receptor-γ (PPARγ), CCAAT/enhancerbinding proteins α (C/EBPα) and C/EBPβ, and adipocyte expressed genes, such as adipocyte fatty acid binding protein (aP2) and Leptin. In addition, EECP treatment effectively activated the AMP-activated protein kinase (AMPK) signaling pathway; however, compound C, a specific inhibitor of AMPK, significantly reduced the EECP-induced inhibition of adipogenesis. Taken together, these results indicate EECP showed strong anti-obesity effects through the AMPK signaling pathway, and further studies will be needed to identify the active compounds that confer the anti-obesity activity of EECP.
Ethanol Extract of Schisandra chinensis (Turcz.) Baill. Reduces AICAR-induced Muscle Atrophy in C2C12 Myotubes
Kang, Young-Soon ; Park, Cheol ; Han, Min-Ho ; Hong, Su-Hyun ; Hwang, Hye-Jin ; Kim, Byung Woo ; Kim, Cheol Min ; Choi, Yung Hyun ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 293~298
DOI : 10.5352/JLS.2015.25.3.293
Muscle atrophy, known as a sarcopenia, is defined as a loss of muscle mass resulting from a reduction in the muscle fiber area or density due to a decrease in muscle protein synthesis and an increase in protein breakdown. Schisandrae fructus (SF) extract of the fruits of Schisandra chinensis (Turcz) Baillon has been used as a tonic in traditional medicine for thousands of years. Although a great deal of work has been carried out on the therapeutic potential of SF, its pharmacological mechanisms of action in muscle diseases actions remain unclear. In the present study, we investigated the inhibitory effects of SF ethanol extracts on the production of muscle atrophy factors in C2C12 myotubes stimulated with 5-aminoimidazole-4-carboxamide-ribonucleotide (AICAR), an AMP-activated kinase (AMPK) activator, and sought to determine the underlying mechanisms of action. AICAR upregulated atrophy-related ubiquitin ligase muscle RING finger-1 (MuRF-1) and stimulated the levels of the forkhead box O3a (FoxO3a) transcription factor in the C2C12 myotubes. SF supplementation effectively and concentration- dependently counteracted AICAR-induced muscle cell atrophy and reversed the increased expression of MuRF-1 and FoxO3a. Our study demonstrates that SF can reverse the muscle cell atrophy caused by AICAR through regulation of the AMPK and FoxO3a signaling pathways, followed by inhibition of MuRF-1.
Antiobesity Activity of Chrysanthemum zawadskii Methanol Extract
Park, Jung Ae ; Jin, Kyong-Suk ; Kwon, Hyun Ju ; Kim, Byung Woo ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 299~306
DOI : 10.5352/JLS.2015.25.3.299
Chrysanthemum zawadskii, a herbaceous perennial plant belonging to the Compositae, grows wild in Asian countries, including Japan, China, and Korea. The biological, antioxidative, anti-inflammatory, and antibacterial activities of C. zawadskii have been reported, its antiobesity activity has not been elucidated. In the present study, the effect of C. zawadskii methanol extract (CZME) on pancreatic lipase enzyme activity, adipocyte differentiation, and adipogenesis was investigated using an in vitro assay and a cell model system. CZME effectively suppressed lipase enzyme activity in a dose-dependent manner. CZME also inhibited insulin, dexamethasone, 3-isobutyl-1-methylxanthine (MDI)-induced adipocyte differentiation, lipid accumulation, and the level of triglyceride in 3T3-L1 preadipocytes in a dose-dependent manner, without cytotoxicity. The antiobesity effect of CZME might be modulated by gene and protein expression of cytidine-cytidine-adenosine-adenosine-thymidine (CCAAT)/enhancer binding proteins (C/EBP) α, C/EBPβ, and the peroxisome proliferator-activated receptor γ (PPAR γ). CZME also triggered lipolysis in a dose-dependent manner in MDI-induced 3T3-L1 preadipocytes. Taken together, these results provide important new insights into the antiobesity activities of C. zawadskii, showing that they involve pancreatic lipase inhibition, as well as antiadipogenic and lipolysis effects. CZME might be a promising source in the field of nutraceuticals. However, the active compounds that confer the antiobesity activities of CZME need to be identified.
Hepatoprotective and Anticancer Activities of Allomyrina dichotoma Larvae
Lee, Ji-Eun ; Jo, Da-Eun ; Lee, An-Jung ; Park, Hye-Kyung ; Youn, Kumju ; Yun, Eun-Young ; Hwang, Jae-Sam ; Jun, Mira ; Kang, Byoung Heon ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 307~316
DOI : 10.5352/JLS.2015.25.3.307
Beetle larvae have been used as a traditional medicine to treat various human liver diseases. To prove the liver protective function of Allomyrina dichotoma larvae (ADL), we induced liver damage by the intraperitoneal injection of a hepatotoxic reagent, diethylnitrosamine (DEN), to C3H/HeN male mice and orally administered freeze-dried ADL powder. ADL powder lessened DEN-induced hepatotoxicity considering the reduced signs of acute and chronic hepatotoxicities, such as the ALP level in the blood serum, TUNEL-positive hepatocytes, ductural reactions, steatotic hepatocytes, and collagen deposition of the Masson’s trichrome staining. In addition to hepatoprotection, the anti-cancer activity of ADL has been examined. The ADL powder was extracted with ethanol and then fractionated with hexane, ethyl acetate, and water by a solvent partition technique. The ethyl acetate fraction showed cytotoxicity to various cancer cells through induction of apoptosis and necrosis, as well as the perturbed metabolism of the cancer cell to trigger autophagy. Collectively, ADL contains bioactive substances that can protect hepatocytes from toxic chemicals and trigger cell death in cancer cells. Thus, further purification and analyses of ADL fractions could lead to the identification of novel bioactive compounds.
Protective Effects of Korean Red Ginseng against Alcohol-induced Hepatosteatosis
Kim, Sun Ju ; Ki, Sung Hwan ; Lee, Sangkyu ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 317~322
DOI : 10.5352/JLS.2015.25.3.317
Alcohol-induced fatty liver (steatosis) results from excessive generation of reducing equivalents by ethanol metabolism. Generally, chronic ethanol treatment causes hepatosteatosis by regulating sterol regulatory element-binding protein 1c (SREBP-1c), which increases the synthesis of hepatic lipids. The effect of ethanol on SREBP-1c is mediated through mammalian sirtuin-1 (SIRT-1), a NAD
-dependent protein deacetylase that regulates hepatic lipid metabolism. Ginseng is a widely used herbal medicine that is used in Asia for its anti-diabetes and anti-obesity effects. The pharmacological and therapeutic effects of ginseng are primarily produced by bioactive constituents known as ginsenosides. Here, we examined the regulatory effects of Korean red ginseng (KRG) extracts on SREBP-1c and SIRT-1 on lipid homeostasis in AML-12 mouse hepatocytes. AML-12 cells were treated with ethanol and/or KRG extracts (0 - 1,000 μg/ml). Lipid droplets were assayed using Oil red O staining, and western blotting was used to measure SIRT-1 and SREBP-1 expression. Treatment with KRG extracts restored SIRT-1 expression and reduced SREBP-1c expression in ethanol-treated cells. We also showed that KRG extract and ginsenosides Rb
and Rd significantly decreased SREBP-1 acetylation in ethanol-treated cells. These results show that treatment with KRG extract and its active ginsenoside constituents Rb
and Rd protected against alcohol-related hepatosteatosis via regulation of SIRT-1 and downstream acetylation of SREBP-1c, which altered hepatic lipid metabolism.
Analysis of Rhizosphere Soil Bacterial Communities on Seonginbong, Ulleungdo Island
Nam, Yoon-Jong ; Yoon, Hyeokjun ; Kim, Hyun ; Kim, Jong-Guk ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 323~328
DOI : 10.5352/JLS.2015.25.3.323
The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.
Optimization Mixture Ratio of Petasites japonicus, Luffa cylindrica and Houttuynia cordata to Develop a Functional Drink by Mixture Design
Jeong, Hae-Jin ; Lee, Kyoung-Pil ; Chung, Hun-Sik ; Kim, Dong-Seop ; Kim, Han-Soo ; Choi, Young-Whan ; Im, Dong-Soon ; Seong, Jong-Hwan ; Lee, Young-Guen ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 329~335
DOI : 10.5352/JLS.2015.25.3.329
This study was performed to determine the optimal ratio of Petasites japonicus, Luffa cylindrica, and Houttuynia cordata, all of which are supposed to have anti-respiratory disease effects, such as against rhinitis. The experiment incorporated a mixture design and included 12 experimental points with center replicates for three different independent variables (Petasites japonicus 30~70%; Luffa cylindrica 10~30%; and Houttuynia cordata 10~30%). Based on this design, the mixture was extracted in hot water at 121℃ for 45 min and anti-allergy and anti-microbial activities were observed. The response surface and trace plot described for the anti-allergy activity showed Petasites japonicas was a relatively important factor. The correlation coefficient (R
) value 82.10% for the inhibition effect of degranulation was analyzed by the regression equation. The analysis of variance showed the model fit was statistically significant (p<0.05). The optimal ratio of the mixture was Petasites japonicus 0.75%, Luffa cylindrica 0.11%, and Houttuynia cordata 0.14%. The anti-microbial activity for each extraction of the mixture was valid on gram-positive, such as Staphylococcus aureus (KCCM 40881) and Staphylococcus epidermidis (KCCM 35494), while it was less effective on gram-negative, such as Escherichia coli (KCCM 11234) and Pseudomonas aeruginosa (KCCM 11328).
Vitamin C Promoted Liver Regeneration Following Partial Hepatectomy-induced Hepatic Injury in Senescence Marker Protein-30-deficient Mice
Han, Seon Young ; Hwang, Meeyul ; Kim, Ah-Young ; Lee, Eun-Mi ; Lee, Eun-Joo ; Lee, Myeong-Mi ; Sung, Soo-Eun ; Kim, Sang-Hyeob ; Jeong, Kyu-Shik ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 336~344
DOI : 10.5352/JLS.2015.25.3.336
The capacity for liver regeneration involves a variety of nutritional factors. Vitamin C has multiple metabolic and antioxidant functions. In this study, we investigated the role of vitamin C in liver regeneration following hepatectomy in senescence marker protein (SMP)-30 knockout (KO) mice. Partial hepatectomy was performed by resecting the median and left lateral lobes of mice. Vitamin C accelerated liver recovery in SMP30 KO mice treated with vitamin C (KV). The livers of the KV mice exhibited lower levels of aspartate aminotransferase and lower injury than those of the KO mice. Increased type II transforming growth factor-β receptor (TGF-βRII)-mediated regeneration signaling was accompanied by HGF and cMet in the KV but not the KO mice. Consistent with this, the expression of cell cycle regulatory proteins, including cyclin D1 and proliferating cell nuclear antigen (PCNA), increased rapidly in the KV mice. Enhanced activation of ERK and GSK-3β proteins and a significantly increased number of binuclear hepatocytes were also detected in the livers of the KV mice. Moreover, the KV mice synthesized the highest levels of albumin. These data suggest that treating SMP30 knockout mice with vitamin C resulted in earlier recovery and liver regeneration by activation of the regeneration system.
Organic Solvent Stable Lipase from Pseudomonas sp. BCNU 171
Choi, Hye Jung ; Kwon, Gi-Seok ; Joo, Woo Hong ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 345~348
DOI : 10.5352/JLS.2015.25.3.345
An organic solvent stable lipase from solvent-tolerant Pseudomonas sp. BCNU 171 had an optimal pH of 8 and an optimal temperature of 37℃. This crude extracellular lipase from BCNU 171 exhibited increased stability in the presence of various types of solvents at high concentrations (25%, v/v). The lipase stability was found to be highest in the presence of xylene (137%), followed by toluene (131%), octane (130%), and butanol (104%). Overall, BCNU 171 lipase tended to be more stable than immobilized commercial lipase (Novozyme435) in the presence of organic solvents. Furthermore, BCNU 171 lipase maintained about 90% of its enzyme original activity in the presence of NH
, and Ca
ion and significantly increased its enzyme activity in the presence of various emulsifying agents. Thus, the organic solvent stable lipase from Pseudomonas sp. BCNU 171 could be usable as a potential whole cell biocatalyst and for synthetic applications of enzymes for industrial chemical processes in organic solvents without using immobilization.
Current Status of Cattle Genome Sequencing and Analysis using Next Generation Sequencing
Choi, Jung-Woo ; Chai, Han-Ha ; Yu, Dayeong ; Lee, Kyung-Tai ; Cho, Yong-Min ; Lim, Dajeong ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 349~356
DOI : 10.5352/JLS.2015.25.3.349
Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.
Next Generation Sequencing and Bioinformatics
Kim, Ki-Bong ;
Journal of Life Science, volume 25, issue 3, 2015, Pages 357~367
DOI : 10.5352/JLS.2015.25.3.357
With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome for less than $1,000 can be feasible in the near future. The rapid technological advances in NGS have brought about increasing demands for statistical methods and bioinformatics tools for the analysis and management of NGS data. Even in the early stages of the commercial availability of NGS platforms, a large number of applications or tools already existed for analyzing, interpreting, and visualizing NGS data. However, the availability of this plethora of NGS data presents a significant challenge for storage, analyses, and data management. Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection, and genome browsing. While the NGS technologies have allowed a massive increase in available raw sequence data, a number of new informatics challenges and difficulties must be addressed to improve the current state and fulfill the promise of genome research. This review aims to provide an overview of major NGS technologies and bioinformatics tools for NGS data analyses.