• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.38-38
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• 2015

Throughout the world, clubroot disease is one of the most damaging diseases affecting Brassica oleracea. In order to perform QTL analysis of CR (clubroot resistance) loci in B. oleracea, we constructed a map, and analyzed CR-QTLs using the mean phenotypes of F3 progenies from the cross of a resistant double-haploid cabbage line (Anju) with a susceptible double-haploid broccoli line (GC). We identified one major QTL, pb-Bo(Anju)1 in C2 from Anju and four minor QTLs; pb-Bo(GC)1 in O5 from GC, pb-Bo(Anju)2, -3, -4 in C2, C3, and C7 from Anju, respectively. Additionally, we found that the accumulation of Pb-Bo(Anju)1 allele and the minor CR-QTLs is essential for resistance against various six isolates. Our finding markers closely linked to the CR-QTLs will help marker-assisted selection for CR. At present, we are undergoing toward map-based cloning for Pb-Bo(Anju)1 gene. The preliminary experiment delimited Pb-Bo(Anju)1 locus, encompassing among 450kB.

• BMB Reports
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• v.39 no.4
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• pp.464-467
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• 2006

Recently, the nucleotide sequences of entire genomes became available. This information combined with older sequencing data discloses the exact chromosomal location of millions of nucleotide markers stored in the databases at NCBI, EMBO or DDBJ. Despite having resolved the intron/exon structures of all described genes within these genomes with a stroke of a pen, the sequencing data opens up other interesting possibilities. For example, the genomic mapping of the end sequences of the human, murine and rat BAC libraries generated at The Institute for Genomic Research (TIGR), reveals now the entire encompassed sequence of the inserts for more than a million of these clones. Since these clones are individually stored, they are now an invaluable source for experiments which depend on genomic DNA. Isolation of smaller fragments from such clones with standard methods is a time consuming process. We describe here a reliable one-step cloning technique to obtain a DNA fragment with a defined size and sequence from larger genomic clones in less than 48 hours using a standard vector with a multiple cloning site, and common restriction enzymes and equipment. The only prerequisites are the sequences of ends of the insert and of the underlying genome.

• BMB Reports
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• v.47 no.10
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• pp.563-568
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• 2014

Human genome projects have enabled whole genome mapping and improved our understanding of the genes in humans. However, many unknown genes remain to be functionally characterized. In this study, we characterized human chromosome 4 open reading frame 34 gene (hC4orf34). hC4orf34 was highly conserved from invertebrate to mammalian cells and ubiquitously expressed in the organs of mice, including the heart and brain. Interestingly, hC4orf34 is a novel ER-resident, type I transmembrane protein. Mutant analysis showed that the transmembrane domain (TMD) of hC4orf34 was involved in ER retention. Overall, our results indicate that hC4orf34 is an ER-resident type I transmembrane protein, and might play a role in ER functions including $Ca^{2+}$ homeostasis and ER stress.

• Korean Journal of Microbiology
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• v.35 no.3
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• pp.211-217
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• 1999

Effects of subsh-ate RNA configuration on the tians-splicing reactcon by group I intron ribozyme of Tetralzynzena thern\ulcornerophila were analyzed with substrate RNAs which have been generated to have very stable structures with stem-loop. RNAinapping strategy was perfo~med in vivo as well as in virro to search the mosl accessible siles to the ~irms-splicing ribozymes in the substrate RNAs. Sequences present in the loop of the target RNAs have shown to be well recognized by and reacted with group I inlron ribozymes while sequences present in the stein do not. Thesc results were confirmed with the experiments of trans-cleavage and rmnssplicing reactmn with ihe specific ribozyines recognizing those sequences. Moreover, sequence analysis of the trans-splicing products have shown that irons-splicing reaction can proceed with high fidelity. In conclusion, the secondary structure of substrate RNAs is one of the most important factors to detemine the ribozyme activity.

• Genomics & Informatics
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• v.17 no.3
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• pp.27.1-27.9
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• 2019

Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log₂FC > |10|), in which 4,059 and 3,794 were up-and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.

• Molecules and Cells
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• v.38 no.11
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• pp.1007-1012
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• 2015

EphA7 is a key molecule in regulating the development of the dien- and mesencephalon. To get insight into the mechanism of how EphA7 gene expression is regulated during the dorsal specification of the dien- and mesencephalon, we investigated the cis-acting regulatory sequence driving EphA7 to the dorsal midline of the dien- and mesencephalon. Transgenic LacZ reporter analysis, using overlapping EphA7 BACs, was used to narrow down the dorsal midline-specific enhancer, revealing the 25.3 kb genomic region as the enhancer candidate. Strikingly, this genomic DNA was located far downstream of the EphA7 transcription start site, +302.6 kb to +327.9 kb. Further enhancer mapping, using comparative genomic analysis and transgenic methods, showed that the 187 bp genomic DNA alone, approximately 305 kb downstream of the EphA7 transcription start site, was sufficient to act as the dorsal midline-specific enhancer of EphA7. Importantly, our results indicate that the 187 bp dorsal midline-specific enhancer is critically regulated by homeobox transcription factors during the development of the dien- and mesencephalon.

• Clinical and Experimental Reproductive Medicine
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• v.26 no.2
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• pp.293-296
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• 1999

Different Y mutation in Yq11 occurring de novo in sterile males were first described 19 years ago. Since the phenotype of the patients was always associated with azoospermia or severe oligospermia, it was postulated that these mutations interrupt a Y spermatogenesis locus in the euchromatic Y region (Yq11) called azoospermia factor (AZF). Recently, it became possible to map AZF mutations to different subregions in Yq11by molecular deletion mapping. This indicated that azoospermia is possibly caused by more than one Y gene in Yq11 and the Yq11 chromatin structure. The frequency of AZF mutations in idiopathic sterile males $(5{\sim}20%)$ may indicate a need for a general screening programme for its analysis in infertility clinic. We have experienced a case of deletion distal to Yq11 region in azoospermic patient. So we report this case with a brief review of literatures.

• Applied Microscopy
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• v.46 no.4
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• pp.184-187
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• 2016

Neuronal connectivity determines brain function. Therefore, understanding the full map of brain connectivity with functional annotations is one of the most desirable but challenging tasks in science. Current methods to achieve this goal are limited by the resolution of imaging tools and the field of view. Macroscale imaging tools (e.g., magnetic resonance imaging, diffusion tensor images, and positron emission tomography) are suitable for large-volume analysis, and the resolution of these methodologies is being improved by developing hardware and software systems. Microscale tools (e.g., serial electron microscopy and array tomography), on the other hand, are evolving to efficiently stack small volumes to expand the dimension of analysis. The advent of mesoscale tools (e.g., tissue clearing and single plane ilumination microscopy super-resolution imaging) has greatly contributed to filling in the gaps between macroscale and microscale data. To achieve anatomical maps with gene expression and neural connection tags as multimodal information hubs, much work on information analysis and processing is yet required. Once images are obtained, digitized, and cumulated, these large amounts of information should be analyzed with information processing tools. With this in mind, post-imaging processing with the aid of many advanced information processing tools (e.g., artificial intelligence-based image processing) is set to explode in the near future, and with that, anatomic problems will be transformed into informatics problems.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.21-21
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• 2017

Severe lodging has recurrently occurred at strong typhoon's hitting in recent climate change. The identification of quantitative trait loci (QTLs) and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To identify QTLs for lodging resistance, the tropical japonica line, Chugoku 117 and the improved indica variety, Habataki were selected as the donor parent, as these had thick and strong culms compared with the temperate japonica varieties in Japan such as Koshihikari. By using chromosome segment substitution lines (CSSLs) in which chromosome segments from the japonica variety were replaced to them from Habataki, we identified the QTLs for strong culm on chrs. 1 and 6, which were designated as STRONG CULM1 (SCM1) and STRONG CULM2 (SCM2), respectively. By using recombinant inbred lines (BILs) derived from a cross between Chugoku 117 and Koshihikari and introgression lines, we also identified the other QTLs for strong culm on chrs. 3 and 2, which were designated as STRONG CULM3 (SCM3) and STRONG CULM4 (SCM4), respectively. Candidate region of SCM1 includes Gn1 related to grain number. SCM2 was identical to APO1, a gene related to the control of panicle branch number, and SCM3 was identical to FC1, a strigolactone signaling associated gene, by performing fine mapping and positional cloning of these genes. To evaluate the effects of SCM1~SCM4 on lodging resistance, the Koshihiakri near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of Habataki (NIL-SCM1, NIL-SCM2) and the another Koshihikari NIL with the introgeressed SCM3 or SCM4 locus of Chugoku 117 (NIL-SCM3, NIL-SCM4) were developed. Then, we developed the pyramiding lines with double or triple combinations derived from step-by-step crosses among NIL-SCM1 NIL-SCM4. Triple pyramiding lines (NIL-SCM1+2+3, ~ NIL-SCM1+3+4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.141-141
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• 2017

The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.