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Kim, Jeong-Soon,Ahn, Sang-Nag,Hong, Sung-Jun,Kwon, Jin-Hyeuk,Kim, Yeong-Ki,Jee, Hyeong-Jin,Shim, Chang-Ki The Korean Society of Crop Science 2011 한국작물학회지 Vol.56 No.4
The objective of this study was to determine the genetic diversities of major rice blast resistance genes among 84 accessions of aromatic rice germplasm. Eighty four accessions were characterized by a dominant 11 set of PCR-based SNP and CAPS marker, which showed the broad spectrum resistance and closest linkage to seven major rice blast resistance (R) genes, Pia, Pib, Pii, Pi5 (Pi3), Pita (Pita-2), and Pi9 (t). The allele specific PCR markers assay genotype of SCAR and STS markers was applied to estimate the presence or absence of PCR amplicons detected with a pair of PCR markers. One indica accession, Basmati (IT211194), showed the positive amplicons of five major rice blast resistance genes, Pia, Pi5 (Pi3), Pib, Pi-ta (Pi-ta2), and Pik-5 (Pish). Among 48 accessions of the PCR amplicons detected with yca72 marker, only five accessions were identified to Pia gene on chromosome 11. The Pib gene was estimated with the NSb marker and was detected in 65 of 84 accessions. This study showed that nine of 84 accessions contained the Pii gene and owned Pi5 (Pi3) in 42 of 84 accessions by JJ817 and JJ113-T markers, which is coclosest with Pii on chromosome 9. Only six accessions were detected two alleles of the Pita or Pita-2 genes. Three of accessions were identified as the Pi9 (t) gene locus.
Chromium Methionine Supplementation Decreases Obesity Indices in Rats
Sang Jip Ohh,Chang Hyeuk Kim,Jong Seo Shin,Kyung Il Sung,Hyun Sook Kim 한국식품영양과학회 2003 Preventive Nutrition and Food Science Vol.8 No.3
This study was conducted to determine the effects of chromium-methionine (CrMet) supplementation at various levels on obesity index, body fat, and serum glucose, insulin and leptin in rats. Forty male Sprague-Dawley rats were randomly assigned to one of four dietary groups and fed AIN-76 semi-purified basal diets supplemented with 0, 300, 600 or 1200 ppb Cr from CrMet. After 4 weeks on the respective diets, the rats were killed and serum glucose, insulin and leptin concentrations were determined. The CrMet supplementation did not affect weight gain, feed intake or feed efficiency ratio, fasting glucose, insulin or leptin levels among treatment groups. Although final body weight in all treatments were not significantly different, naso-anal length was longer in the 1200 ppb CrMet group than those of control or other groups (p<0.05). The lowest obesity index and body fat were observed in the 1200 ppb dietary group (p<0.05). The obesity index of the rats fed 1200 ppb supplemental CrMet was lower than in the other groups. These results suggest that CrMet supplementation results in a significant decrease in obesity index, possibly by decreasing the body fat that corresponded to increasing CrMet dosage.
Kim, Dae-Won,Kim, Ae-Ri,Kim, Ryong-Nam,Nam, Seong-Hyeuk,Kang, A-Ram,Chung, Wan-Tae,Choi, Sang-Haeng,Park, Hong-Seog Korean Society for Molecular and Cellular Biology 2010 Molecules and cells Vol.29 No.2
Comprehensive analysis of the transcriptome of the P. chrysosporium is a useful approach to improve our understanding of its special and unique enzyme system and fungal evolution in molecular and industrial aspects. In order to unveil the functional diversity of this white-rot fungus in gene level and the expression patterns of its genes, in this study we carried out sequencing and annotation of 4,917 P. chrysosporium expressed sequence tags (ESTs). Through our bioinformatic ESTs analysis, we elucidated that 1,751 genes were derived from the present dataset of 4,917 ESTs, based on clustering and comparative genomic analyses of the ESTs. Of the 1,751 unique ESTs, 1,006 (57.5%) had homologues and orthologues in similarity searches. Our P. chrysosporium ESTs showed many genes for encoding 23 secreted proteins, many proteins for the degradation of cellulose and hemicelluloses, and heat shock proteins for stress resistance, which explain the reason why P. chrysosporium is very important and unique white-rot fungus in dealing with contaminated resources and in degrading lignin and in applying this organism to several industrial aspects. In addition, comparative analysis has shed the fresh light on the mystery about how its unique enzyme system and stress resistance have been evolved differently from its closest relatives.
Major chimpanzee-specific structural changes in sperm development-associated genes
Kim, Ryong Nam,Kim, Dae-Won,Choi, Sang-Haeng,Chae, Sung-Hwa,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Aeri,Kang, Aram,Park, Kun-Hyang,Lee, Yong Seok,Hirai, Momoki,Suzuki, Yutaka,Sugano, Sumio,Hashimoto, Ka Springer-Verlag 2011 Functional & integrative genomics Vol.11 No.3
Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing
Kim, Ryong Nam,Kim, Dae-Soo,Choi, Sang-Haeng,Yoon, Byoung-Ha,Kang, Aram,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Jong-Joo,Ha, Ji-Hong,Toyoda, Atsushi,Fujiyama, Asao,Kim, Aeri,Kim, Min-Young,Park, Kun-Hyan Oxford University Press 2012 DNA research Vol.19 No.3
<P>Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the <I>TCOF1</I> locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.</P>
Novel mechanism of conjoined gene formation in the human genome.
Kim, Ryong Nam,Kim, Aeri,Choi, Sang-Haeng,Kim, Dae-Soo,Nam, Seong-Hyeuk,Kim, Dae-Won,Kim, Dong-Wook,Kang, Aram,Kim, Min-Young,Park, Kun-Hyang,Yoon, Byoung-Ha,Lee, Kang Seon,Park, Hong-Seog Springer 2012 Functional & integrative genomics Vol.12 No.1
<P>Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.</P>