• Journal of Life Science
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• v.19 no.10
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• pp.1463-1467
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• 2009

Telomeres, comprised of tandem repeats of TTAGGG sequences, are special nucleoprotein structures that protect and stabilize chromosome ends. These structures form the crux of the telomere concept of aging, senescence and genomic instability. The classic terminal restriction fragment (TRF) analysis to quantify the amount of telomeric DNA is disadvantageous in species containing ultra long telomeres like in mice (100Kb). In this study, we used a more sensitive quantitative fluorescence in situ hybridization (Q FISH) technique to quantify telomeric DNA, and used it as a biological aging marker in mice. 12 litters each of Senescence-Resistant (SAMR1) and -Prone (SAMP1) known as senescence accelerated mouse strains were purchased from Central Lab, Animal Inc. We quantified the amount of telomeric DNA using telomere specific DNA probes on the two strains of male mice at 8 weeks, 18 weeks and 26 weeks of age. The amount of telomeric DNA correlated with aging and age associated changes in body and organ weight between SAMR1 and SAMP1 strains of mice. These data suggest the usefulness of the amount of telomeric DNA as a biological aging marker in human aging studies.

• Animal Bioscience
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• v.35 no.10
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• pp.1489-1498
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• 2022

Objective: The objective of this study was to identify polymorphism in olfactomedin like 3 (OLFML3) gene, and association analysis with meat quality, carcass characteristics, retail meat cut, and fatty acid composition in sheep, and expression quantification of OLFML3 gene in phenotypically divergent sheep. Methods: A total of 328 rams at the age of 10 to 12 months with an average body weight of 26.13 kg were used. A novel polymorphism was identified using high-throughput sequencing in sheep and genotyping of OLFML3 polymorphism was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Among 328 rams, 100 rams representing various sheep genotypes were used for association study and proc general linear model was used to analyse association between genotypes and phenotypic traits. Quantitative real-time polymerase chain reaction (qRT-PCR) was used for the expression analysis of OLFML3 mRNA in phenotypically divergent sheep population. Results: The findings revealed a novel polymorphism in the OLFML3 gene (g.90317673 C>T). The OLFML3 gene revealed three genotypes: CC, CT, and TT. The single nucleotide polymorphism (SNP) was found to be significantly (p<0.05) associated with meat quality traits such as tenderness and cooking loss; carcass characteristics such as carcass length; retail meat cut such as pelvic fat in leg, intramuscular fat in loin and tenderloin, muscle in flank and shank; fatty acids composition such as tridecanoic acid (C13:0), palmitoleic acid (C16:1), heptadecanoic acid (C17:0), ginkgolic acid (C17:1), linolenic acid (C18:3n3), arachidic acid (C20:0), eicosenoic acid (C20:1), arachidonic acid (C20:4n6), heneicosylic acid (C21:0), and nervonic acid (C24:1). The TT genotype was associated with higher level of meat quality, carcass characteristics, retail meat cut, and some fatty acids composition. However, the mRNA expression analysis was not different among genotypes. Conclusion: The OLFML3 gene could be a potential putative candidate for selecting higher quality sheep meat, carcass characteristics, retail meat cuts, and fatty acid composition in sheep.

• Analytical Science and Technology
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• v.31 no.5
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• pp.208-218
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• 2018

Autophagy is a cellular process whereby cytosolic materials or organelles are taken up in a double-membrane vesicle structure known as an autophagosome and transported into a lysosome for degradation. Although autophagy has been studied at the genetic, cellular, or biochemical level, systematic ultrastructural quantitative analysis of autophagosomes during the autophagy process by using transmission electron microscopy (TEM) has not yet been reported. In this study, we performed ultrastructural analysis of autophagosomes in wild-type (WT) mouse embryonic fibroblasts (MEFs) and autophagy essential gene (atg5) knockout (KO) MEFs. First, we performed ultrastructural analysis of autophagosomes in WT MEFs compared to atg5 KO MEFs in basal autophagy or starvation-induced autophagy. Although we observed phagopore, early, late autophagosomes, or autolysosomes in WT MEFs, atg5 KO MEFs had immature autophagosomes that showed incomplete closure. Upon starvation, late autophagosomes accumulated in WT MEFs while the number of immature autophagosomes significantly increased in atg5 KO MEF indicating that atg5 plays an important role in the maturation of autophagosomes. Next, we examined autophagosomes in the cell model expressing polyQ-expanded N-terminal fragment of huntingtin. Our TEM analysis indicates that the number of late autophagosomes was significantly increased in the cells expressing the mutant huntingtin, indicating that improving the fusion of autophagosome with lysosome may be effective to enhance autophagy for the treatment of Huntington's disease. Taken together, the results of our study indicate that ultrastructural and quantitative analysis of autophagosomes using TEM can be applied to various human cellular disease models, and that they will provide an important insight for cellular pathogenesis of human diseases associated with autophagy.

• Environmental Analysis Health and Toxicology
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• v.15 no.4
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• pp.131-137
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• 2000

The release of hazardous waste materials into the environment poses serious risks in humans and ecosystems. The risk assessment of environmental pollutants including hazardous chemicals requires a comprehensive measurement of hazard and exposure of the chemicals that can be achieved by toxicity evaluation using a biological system such as biomarkers. In this report we have tried to develop a biomarker used to elucidate a molecular basis of, and to monitor abnormal behaviors caused by diazinon in Japanese medaka (Oryzias latipes) as a model organism. First, an attempt was made to clone tyrosine hydroxylase gene from Japanese medaka that would be a candidate for a biomarker for neuronal modulations and behaviors. For monitoring experiments at behavioral and molecular biological levels, the fish were treated under different sublethal conditions of diazinon and their behavioral responses were observed . In this study we have successfully cloned a partial TH gene from the medaka fish through PCR screening of an ovary cDNA library. DNA sequencing analysis revealed that the amplified fragment was 327 bp encoding 109 amino acids. Comparing the DNA sequence of medaka TH with other species, TH gene revealed the DNA sequence was completely identical to that of rat TH. In the RT-PCR, 330 Up of mRNA was consistently amplified in all the treated samples including control There were no significant differences in the TH expression level regardless of treating concentrations (1∼5,000 ppb) and time (0∼48 hr) The reason appeared to be that RT-PCR was not performed using through a quantitative analysis normalized against an actin gene expression. Organ or tissue - specific detection of TH activity and mRNA as biomarkers will be a useful monitoring tool for neurobehavioral changes in fish influenced by toxic chemicals. Furthermore, quantitative analysis of locomotive patterns and its correlation with the neurochemical and molecular data would be highly useful in measuring toxicity and hazard ofvarious environmental pollutants.

• Journal of Food Hygiene and Safety
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• v.25 no.4
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• pp.388-394
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• 2010

Metabolomics aims at the comprehensive, qualitative and quantitative analysis of wide arrays of endogenous metabolites in biological samples. It has shown particular promise in the area of toxicology and drug development, functional genomics, system biology and clinical diagnosis. In this study, analytical technique of MS instrument with high resolution mass measurement, such as time-of-flight (TOF) was validated for the purpose of investigation of amino acids, sugars and fatty acids. Rat urine and serum samples were extracted by selected each solvent (50% acetonitrile, 100% acetonitrile, acetone, methanol, water, ether) extraction method. We determined the optimized liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) system and selected appropriated columns, mobile phases, fragment energy and collision energy, which could search 17 metabolites. The spectral data collected from LC/TOFMS were tested by ANOVA. Obtained with the use of LC/TOFMS technique, our results indicated that (1) MS and MS/MS parameters were optimized and most abundant product ion of each metabolite were selected to be monitorized; (2) with design of experiment analysis, methanol yielded the optimal extraction efficiency. Therefore, the results of this study are expected to be useful in the endogenous metabolite fields according to validated SOP for endogenous amino acids, sugars and fatty acids.

• Journal of the Korean Chemical Society
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• v.48 no.5
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• pp.483-490
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• 2004

We have developed a novel polymerase chain reaction (PCR)-microchip gel electrophoresis (MGE) method based on the sieving gel mixture of commercially available poly(vinylpyrrolidone) (PVP) and hydroxy ethyl cellulose (HEC) for the rapid detection and diagnosis of the orf virus (ORFV) from Korean indigenous goat. After amplification of 594-bp DNA fragment from the B2L gene of ORF virus, the amplicon was analyzed by the MGE separation. The glass microfluidic chip (64 mm total length (36 mm effective length)${\times}$90 ${\mu}$m width${\times}$20 ${\mu}$m depth) allowed the fast detection and diagnosis of ORFV in the mixture of 1.0% PVP ($M_r$ 360,000) and 1.0% HEC ($M_r$250,000) as a sieving matrix with better resolution and reproducibility of DNA fragments. Under the electric field of 277.8 V/cm, the 594-bp DNA was analyzed within 4 min. Compared to traditional slab gel electrophoresis, the PCR-MGE method was twenty times faster and an effective clinical method for the quantitative analysis of ORFV.

• Journal of Life Science
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• v.29 no.6
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• pp.631-636
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• 2019

A new nitric oxide-induced (NOI) gene was isolated by screening ESTs from a cDNA library of dehydration-treated fibrous roots of sweetpotato (Ipomoea batatas). The 720 bp cDNA fragment, IbNOI, was sequenced, from which a 77 amino acid residue protein was deduced. A search of the protein BLAST database identified significant similarity to other plant NOI protein sequences. Quantitative RT-PCR analysis revealed diverse expression patterns of IbNOI in various tissues of the intact sweetpotato plant, and in leaves exposed to different stresses. The IbNOI gene was highly expressed in storage roots and suspension-cultured cells. In leaf tissues, IbNOI showed strong expression during sodium nitroprusside (SNP)-induced NO accumulation and chemical stress treatments. Expression of IbNOI was also induced under various abiotic stress conditions, such as dehydration, salt, and bacterial pathogen infection. These results suggest that IbNOI is involved in plant responses to diverse abiotic stresses and pathogen infection through a NO-related pathway.

• Korean Journal of Environmental Biology
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• v.40 no.3
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• pp.307-315
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• 2022

In terms of habitat conservation, it is essential to develop a habitat assessment system that can evaluate not only the suitability of the current habitat, but also the health and stability of the habitat. This study aimed to develop a methodology of habitat quality assessment for endangered species by analyzing various existing habitat assessment methods. The habitat quality assessment consisted of selecting targeted species, planning of assessment, selecting targeted sites, assessing performance, calculating grade, and expert verification. Target sites were selected separately from core and potential habitats using a species distribution model or habitat suitability index. Habitat assessment factors were classified into ecological characteristic, landscape characteristic, and species-habitat characteristic. Ecological characteristic consisted of thirteen factors related to health of tree, vegetation, and soil. Landscape characteristic consisted of five factors related to fragment and connectivity of habitat. Species-habitat characteristic consisted of factors for evaluating habitat suitability depending on target species. Since meanings are different depending on characteristics, habitat quality assessment of this study could be used by classifying results for each characteristic according to various assessment purposes, such as designation of alternative habitats, assessment of restoration project, and protected area valuation for endangered species. Forest habitat quality assessment is expected to play an important role in conservation acts of endangered species in the future through continuous supplementation of this system in regard to quantitative assessment criteria and weighting for each factor with an influence.

• Journal of Life Science
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• v.27 no.11
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• pp.1331-1339
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• 2017

DNA barcoding is the identification of a species based on the DNA sequence of a fragment of the cytochrome C oxidase subunit I (COI) gene in the mitochondrial genome. It is widely applied to assist with the sustainable development of fishery-product resources and the protection of fish biodiversity. This study attempted to verify horse-head fish (Branchiostegus japonicus) and fake horse-head fish (Branchiostegus albus) species, which are commonly consumed in Korea. For the validation of the two species, a real-time PCR method was developed based on the species' mitochondrial DNA genome. Inter-species variations in mitochondrial DNA were observed in a bioinformatics analysis of the mitochondrial genomic DNA sequences of the two species. Some highly conserved regions and a few other regions were identified in the mitochondrial COI of the species. In order to test whether variations in the sequences were definitive, primers that targeted the varied regions of COI were designed and applied to amplify the DNA using the real-time PCR system. Threshold-cycle (Ct) range results confirmed that the Ct ranges of the real-time PCR were identical to the expected species of origin. Efficiency, specificity and cross-reactivity assays showed statistically significant differences between the average Ct of B. japonicus DNA ($21.85{\pm}3.599$) and the average Ct of B. albus DNA ($33.49{\pm}1.183$) for confirming B. japonicus. The assays also showed statistically significant differences between the average Ct of B. albus DNA ($22.49{\pm}0.908$) and the average Ct of B. japonicus DNA ($33.93{\pm}0.479$) for confirming B. albus. The methodology was validated by using ten commercial samples. The genomic DNA-based molecular technique that used the real-time PCR was a reliable method for the taxonomic classification of animal tissues.