• Genomics & Informatics
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• v.19 no.3
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• Animal Bioscience
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• v.35 no.4
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• pp.511-516
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• 2022

Objective: A genomic region associated with a particular phenotype is called quantitative trait loci (QTL). To detect the optimal F₂ population size associated with QTLs in native chicken, we performed a simulation study on F₂ population derived from crosses between two different breeds. Methods: A total of 15 males and 150 females were randomly selected from the last generation of each F₁ population which was composed of different breed to create two different F₂ populations. The progenies produced from these selected individuals were simulated for six more generations. Their marker genotypes were simulated with a density of 50K at three different heritability levels for the traits such as 0.1, 0.3, and 0.5. Our study compared 100, 500, 1,000 reference population (RP) groups to each other with three different heritability levels. And a total of 35 QTLs were used, and their locations were randomly created. Results: With a RP size of 100, no QTL was detected to satisfy Bonferroni value at three different heritability levels. In a RP size of 500, two QTLs were detected when the heritability was 0.5. With a RP size of 1,000, 0.1 heritability was detected only one QTL, and 0.5 heritability detected five QTLs. To sum up, RP size and heritability play a key role in detecting QTLs in a QTL study. The larger RP size and greater heritability value, the higher the probability of detection of QTLs. Conclusion: Our study suggests that the use of a large RP and heritability can improve QTL detection in an F₂ chicken population.

• Animal Bioscience
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• v.37 no.1
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• pp.50-60
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• 2024

Objective: Testicular fat deposition has been reported to affect animal reproduction. However, the underlying mechanism remains poorly understood. The present study explored whether sperm meiosis and testosterone synthesis contribute to mouse testicular fat deposition-induced reproductive performance. Methods: High fat diet (HFD)-induced obesity CD1 mice (DIO) were used as a testicular fat deposition model. The serum hormone test was performed by agent kit. The quality of sperm was assessed using a Sperm Class Analyzer. Testicular tissue morphology was analyzed by histochemical methods. The expression of spermatocyte marker molecules was monitored by an immuno-fluorescence microscope during meiosis. Analysis of the synthesis of testosterone was performed by real-time polymerase chain reaction and reagent kit. Results: It was found that there was a significant increase in body weight among DIO mice, however, the food intake showed no difference compared to control mice fed a normal diet (CTR). The number of offspring in DIO mice decreased, but there was no significant difference from the CTR group. The levels of follicle-stimulating hormone were lower in DIO mice and their luteinizing hormone levels were similar. The results showed a remarkable decrease in sperm density and motility among DIO mice. We also found that fat accumulation affected the meiosis process, mainly reflected in the cross-exchange of homologous chromosomes. In addition, overweight increased fat deposition in the testis and reduced the expression of testosterone synthesis-related enzymes, thereby affecting the synthesis and secretion of testosterone by testicular Leydig cells. Conclusion: Fat accumulation in the testes causes testicular cell dysfunction, which affects testosterone hormone synthesis and ultimately affects sperm formation.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.4
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• pp.448-457
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• 2015

Developing rice lines with various amylose contents is necessary to diverse usages of rice in terms of raw materials for processed food production, and thereby to promote rice consumption in Korea. A rice mutant line, 'Namil(SA)-dull1' was established through sodium azide mutagenesis on 'Namil', a non-glutinous Korean Japonica rice cultivar. Namil(SA)-dull1' had dull endosperm characteristics and the evaluated amylose content was 12.2%. A total of 94 F2 progenies from a cross between 'Namil(SA)-dull1' and 'Milyang23', a non-glutinous Tongil-type rice cultivar, was used for genetic studies on the endosperm amylose content. Association analyses, between marker genotypes of 53 SSR anchor markers and evaluated amylose contents of each 94 F2:3 seeds, initially localized rice chromosome 6 as the harboring place for the modified allele(s) directing low amylose content of 'Namil(SA)-dull1'. By increasing SSR marker density on the putative chromosomal region followed by association analyses, the target region was narrowed down 0.94 Mbp segment, expanding from 28.95 Mbp to 29.89 Mbp, on rice chromosome 6 pseudomolecule. Among the SSR loci, RM7555 explained 84.2% of total variation of amylose contents in the $F_2$ population. Further physical mapping on the target region directing low amylose content of 'Namil(SA)-dull1' would increase the breeding efficiency in developing promising rice cultivars with various endosperm characteristics.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.33-48
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• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.

• International Journal of Oral Biology
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• v.32 no.3
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• pp.85-91
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• 2007

Dlx3 is a homeodomain protein and is known to playa role in development and differentiation of many tissues. Deletion of four base pairs in DLX3 (NT3198) is causally related to tricho-dento-osseous (TDO) syndrome (OMIM # 190320), a genetic disorder manifested by taurodontism, hair abnormalities, and increased bone density in the cranium. Although the observed defects of TDO syndrome involves bone, little is known about the role of Dlx3 in bone remodeling process. In this study, we examined the effect of wild type DLX3 (wtDlx3) expression on osteoclast differentiation and compared it with that of 4-BP DEL DLX3 (TDO mtDlx3). To examine whether Dlx3 is expressed during RANKL-induced osteoclast differentiation, RAW264.7 cells were cultured in the presence of receptor activator of nuclear factor-B ligand (RANKL). Dlx3 protein level increased slightly after RANKL treatment for 1 day and peaked when the fusion of prefusion osteoclasts actively progressed. When wtDlx3 and TDO mtDlx3 were overexpressed in RAW264.7 cells, they enhanced RANKL-induced osteoclastogenesis and the expression of osteoclast differentiation marker genes such as calcitonin receptor, vitronectin receptor and cathepsin K. Since osteoclast differentiation is critically regulated by the balance between RANKL and osteoprotegerin (OPG), we examined the effect of Dlx3 overexpression on expression of RANKL and OPG in C2C12 cells in the presence of bone morphogenetic protein 2. Overexpression of wtDlx3 enhanced RANKL mRNA expression while slightly suppressed OPG expression. However, TDO mtDlx3 did not exert significant effects. This result suggests that inability of TDO mtDlx3 to regulate expression of RANKL and OPG may contribute to increased bone density in TDO syndrome patients. Taken together, it is suggested that Dlx3 playa role as a positive regulator of osteoclast differentiation via up-regulation of osteoclast differentiation-associated genes in osteoclasts, as well as via increasing the ratio of RANKL to OPG in osteoblastic cells.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2277-2281
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• 2015

Objectives: To explore the expression of astrocyte elevated gene-1 (AEG-1) in cervical cancer and analyze its correlation with microvascular density (MVD), nuclear factor kappaB (NF-kB p65) and vascular endothelial growth factor (VEGF). Materials and Methods: Immunohistochemical MaxVision method was adopted to detect the expression level of AEG-1, NF-kB p65 and VEGF in 45 samples of invading cervical cancer and 12 samples of cervicitis from The First Affiliated Hospital of Wenzhou Medical University. Tumor microvascular endothelial marker CD34 combined with Weidner was used to determine the MVD in cervical cancer tissue. The positive expression and staining conditions of AEG-1, NF-kB p65 and VEGF in cervical cancer tissues were observed under a light microscope. Correlations between expression of AEG-1 protein and those of NF-Kb p65 and VEGF, as well as MVD, were analyzed using Pearson correlation. Results: The expression levels of AEG-1 were $0.186{\pm}0.043$ in cervical cancer and $0.051{\pm}0.002$ in chronic cervicitis (p<0.01). Moreover, expression of AEG-1 was related to vascular invasion and lymphatic metastasis of cervical cancer (p<0.01), but not with age of the patients, differentiation degree, tumour size, pathological type and parametrial infiltration (p>0.05). Pearson correlation analysis showed that the expression of AEG-1 was linked with NF-kB p65 (r=0.501, p=0.000), VEGF (r=0.718, p=0.000) as well as MVD in cervical cancer tissue (r=0.815, p=0.000). Conclusions: AEG-1 is highly expressed in cervical cancer and promotes angiogenesis, which might be related to the fact that AEG-1 activating the signal pathway of NF-kB could up-regulate the level of VEGF expression.

• Journal of the Korean Society of Food Science and Nutrition
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• v.42 no.2
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• pp.195-202
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• 2013

This study was carried out to identify the relationship of biochemical bone turnover markers, bone mineral density (BMD), and general characteristics in Korean women. One hundred eighty healthy women, 20 to 50 years of age, living in Gwangju and Chonnam participated. Serum bone-specific alkaline phosphatase (BAP) and osteocalcin (OC) were used as bone formation markers and N-telopeptide of type 1 collagen (NTx) was used as a bone resorption maker to evaluate the state of bone turnover. T-scores were measured to evaluate BMD. We analyzed general characteristics, including age, menopause status, osteoporosis history, alcohol consumption, physical activity level, and degree of obesity (BMI, percent of fat). The BAP level significantly decreased in the group of twenty-year olds and increased in the non-alcohol consuming group, the group with a family history of osteoporosis, the menopause group, and the obese group (p<0.05). The OC level was lower in the group of twenty-year olds and increased in the non-alcohol intake group and the menopause group (p<0.05). BMD significantly decreased in the obese group (p<0.05). In conclusion, BAP and OC were affected by age, alcohol consumption, osteoporosis history, menopause status, and obesity. BMD was affected by obesity degree. These results suggest that the management of alcohol consumption and obesity are important for maintaining bone status during aging in Korean women.

• Childhood Kidney Diseases
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• v.1 no.1
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• pp.13-16
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• 1997

Steroid induced bone loss is a serious problem in frequently relapsing nephrotic syndrome especially in growing children. In order to evaluate whether $1-(OH)D_3$ (IL Sung Pharma.Co.) is effective in preventing steroid induced bone loss, we gave $0.5{\mu}g$ of $1-(OH)D_3$ for one year to forty patients with frequently relapsing nephrotic syndrome, receiving longterm prednisolone therapy (mean duration $50.12{\pm}29.40$ months). We checked the following markers before and after $1-(OH)D_3$ therapy. i.e. bone mineral density(BMD) using dual energy X-ray absorptiometry(DEXA) at the 2nd to 4th lumbar spine, serum calcium, phosphorus, parathyroid hormone(PTH), osteocalcin and urine pyridinoline(U-PYD). BMD($g/cm^2$) was increased even steroid therapy from $0.71{\pm}0.0\;to\;0.73{\pm}0.0$ (p<0.05). Lumbar spine BMD is a sensitive marker for evaluating steroid induced bone loss in children receiving longterm corticosteroid therapy and that $1-(OH)D_3$ appears to be effective in treating and preventing steroid induced bone loss.

• Journal of Korean Neurosurgical Society
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• v.29 no.4
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• pp.461-470
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• 2000

Objective : Many investigators have demonstrated the protective effects of hypothermia following traumatic brain injury(TBI) in both animals and humans. It has long been recognized that mild to moderate hypothermia improves neurologic outcomes as well as reduces histologic and biochemical sequelae after TBI. In this study, two immunohistochemical staining using terminal deoxynucleotidyl-transferase-mediated biotin dUTP nick end labeling(TUNEL), staining of apoptosis, and ${\beta}$-amyloid precursor protein(${\beta}$-APP), a marker of axonal injury, were done and the authors evaluated the protective effects of hypothermia on axonal and neuronal injury after TBI in rats. Material and Method : The animals were prepared for the delivery of impact-acceleration brain injury as described by Marmarou and colleagues. TBI is achieved by allowing of a weight drop of 450gm, 1 m height to fall onto a metallic disc fixed on the intact skull of the rats. Fourty Sprague-Dawley rats weighing 400 to 450g were subjected to experimental TBI induced by an impact-acceleration device. Twenty rats were subjected to hypothermia after injury, with their rectal temperatures maintained at $32^{\circ}C$ for 1 hour. After this 1-hour period of hypothermia, rewarming to normothermic levels was accomplished over 30-minute period. Following 12 hours, 24 hours, 1 week and 2 weeks later the animals were killed and semiserial sagittal sections of the brain were reacted for visualization of the apoptosis and ${\beta}$-APP. Results : The density of ${\beta}$-APP marked damaged axons within the corticospinal tract at the pontomedullary junction and apoptotic cells at the contused cerebral cortex were calculated for each animal. In comparison with the untreated controls, a significant reduction in ${\beta}$-APP marked damaged axonal density and apoptotic cells were found in all hypothermic animals(p<0.05). Conclusion : This study shows that the posttraumatic hypothermia result in substantial protection in TBI, at least in terms of the injured axons and neurons.