http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
Development of Oryza sativa Alternative Spliced Transcripts Detecting Microarray
Songhwa Chae,Kyong-Mi Jun,Joung Sug Kim,Baek-Hie Nahm,Yeon-Ki Kim 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Expression profiling was conducted with the Oryza sativa alternative splicing detecting microarray v.4 (OsASDM). Probe features are designed based on rice genome IRGSP_1.0 (http://rapdb.dna.affrc.go.jp/ ). The genome contains 37,868 genes. Among these 5,254 genes have alternative spliced sites, 11,938 transcripts. In the microarray, a total of 41,953 transcripts are covered from all the loci and 9112 alternative spliced transcripts. Four 60-nt long probes were designed from each transcript starting 60 bp ahead the end of stop codon and with shifting 30 bp so 4 probes cover 150 bp in the 3’ region of the gene. Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, he 125,956 probes were designed. To find organ specific transcripts RNA was prepared from leaf, root, panicle at 1 cm (P1cm). The signal intensity files were analyzed with limma package. Background correction and normalization were performed with libraries in the package. 13,486 genes are organ specific and 1,856 transcripts are alternatively spliced. Transcripts that specifically alternatively spliced in leaf are Os02t0197600-02_UE; Chlorophyll a-b binding protein 8, Os11t0707000-01_UE; Ribulose bisphosphate carboxylase/oxygenase, Os12t0291100-01_UE; ribulose 1,5-bisphosphate carboxylase small subunit. Transcripts that specifically alternatively spliced in root are Os03t0669100-02_UE; Deoxyuridine 5’-triphosphate nucleotidohydrolase, Transcripts that specifically alternatively spliced in tissues at P1cm are Os11t0210300-02_UE; Alcohol dehydrogenase 1, Os04t0631200-02_UE; Xyloglucan endotransglycosylase. Os03t0669100-02_UE ; Deoxyuridine 5’-triphosphate nucleotidohydrolase, Os11t0210300-02_UE ; Alcohol dehydrogenase 1, Os04t0631200-02_UE; Xyloglucan endotransglycosylase. These results show that OsASDM could be used to find alternatively spliced gene at ease.
Songhwa Chae,Joung Sug Kim,Kyong-Mi Jun,Yeon-Ki Kim,Baek-hie Nahm 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Rice is an important model species and one of the most staple crops of the world. The use of rice appropriate promoters suitable for a specific target transgene is important for the control of spatial and temporal transgene expression. To isolate rice tissue-specific promoters, we exploited the potential of whole genome microarrays in 17 stages: callus, germinating seed, leaf, root, the size of the panicles before heading (1, 3, 5, 8, 10, 15, 20, and 22 cm), and the number of days after pollination (1, 3, 5, 11, 21 DAP) using a 300 K Rice Genome Microarray, covering 31,439 genes of the rice. Eight candidate genes for tissue-specific expression were selected in various organs and stage of reproductive development in rice: Histone H4 for constitutive expression, Dehydrin DHN1 for callus-specific expression, germinating seed-specific hypothetical protein, root-specific hypothetical protein, DNA topoisomerase and Retinoblastoma for expression at panicles before heading, heading-specific profiling, and invertase for expression at seed after pollination. Promoter regions of the selected genes were isolated and fused to the β-glucoronidase (GUS) reporter gene, and the constructs were introduced into rice plants. These promoters are highly active in the tissue-specific manner of rice and can be useful for the spatial and temporal enhancement of target gene(s).
Songhwa Chae,Joung Sug Kim,Kyong-Mi Jun,Byung Hyun Dang,Yeon-Ki Kim,Baek-hie Nahm 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Gene expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the temporal expression profiles of rice genes in 13 stages of reproductive development. We could profile expression of 17,676 genes in at least one of the tissues. Differential expression analysis with compare to leaf and preceding stages of development revealed reproductive stage-preferential/-specific genes. we identified 35 genes expressing specifically during panicle and seed development. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1cm) and male meiosis (P5cm), the genes involved in jasmonic acid and gebbellin biosynthesis were significantly upregulated. F11DAP stage of seed, containing enlargement organ, exhibited enrichment of transcripts involved in starch or sucrose biosynthesis. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of two panicle-specific genes, AK072471, Os08g0538700, and AK121412, an early seed-specific gene, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
Chae, Songhwa,Kim, Joung Sug,Jun, Kyong Mi,Lee, Sang-Bok,Kim, Myung Soon,Nahm, Baek Hie,Kim, Yeon-Ki Korean Society for Molecular and Cellular Biology 2017 Molecules and cells Vol.40 No.10
Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.
Antenatal sonographic features of persistent extrahepatic vitelline vein aneurysm
( Songhwa Chae ),( Ilwoon Gi ),( Hyeonkyeong Yeon ),( Jihun Kim ) 대한산부인과학회 2018 대한산부인과학회 학술대회 Vol.104 No.-
Introduction: The vitelline veins are developmental vessels passing between the yolk sac and the sinus venosus of the heart during embryonic development. The splenic vein and SMV drain into the left vitelline vein and distal part of the right vitelline vein regresses. The presence of a persistent vitelline vein after birth is very rare and can be confused with umbilical vein varix. We present a rare case of a fetal persistent vitelline vein with thrombus in a neonate. Case report: A 24-years old nulliparous woman was referred at 28 weeks gestation because of fetal cystic abdominal mass near the umbilicus. Color Doppler showed venous-type turbulent flow inside the mass. It was initially thought to be the umbilical vein varix. A 2965 g female neonate was born by spontaneous vaginal delivery at 39+5weeks. Postnatal sonographic evaluation verified as Fusiform aneurysmal dilatation of extrahepatic persistent vitelline vein without internal thrombus. SMV meets persistent vitelline vein and fast flow of SMV makes blood whirling. After 4 days, Echogenic thrombus at persistent distal viltelline vein aneurysm found and the newborn was transferred to other hospital for early surgical thrombectomy. Discussion: Abnormalities of the umbilical-portal-hepatic venous system are rare congenital vascular anomalies. The first diagnosis to be considered in the abdominal midline vascular structure is umbilical vein varix. The aneurysmal vitelline vein can be distinguished from the umbilical vein varix in the course of the vessel. It is running downward and below the gallbladder in the sagittal plane. Though vitelline vein aneurysm is an extremely rare anomaly, it rapidly progresses to portal vein thrombosis that requires prompt diagnosis and treatment. Therefore, if an abnormal abdominal vascular structure is found during prenatal ultrasonography, persistent vitelline vein should be included in the differential diagnosis.
지진 데이터를 이용한 건물 피해 예측 모델의 성능 분석
채송화 ( Songhwa Chae ),임유진 ( Yujin Lim ) 한국정보처리학회 2023 한국정보처리학회 학술대회논문집 Vol.30 No.2
내진 설계가 되어있지 않은 건물의 경우, 지진으로 인해 건물 붕괴 가능성이 높아지며 이로 인해 많은 인명 피해가 발생할 수 있다. 지진으로 인한 건물의 피해를 예측하고 이를 기반으로 취약점을 보완한다면 인명 피해를 줄일 수 있으므로 건물 피해 예측 모델에 대한 연구가 필요하다. 본 논문에서는 2015 년 네팔 대지진으로 인해 손상된 건물 데이터를 활용하여 Random Forest 와 Extreme Gradient Boosting 기계학습 분류 알고리즘을 사용하여 지진 피해 예측 모델의 정확도를 비교하였다.
Joung Sug Kim,Songhwa Chae,Kyong-Mi Jun,Yoon Mok Pahk,Yeon-Ki Kim,Baek-hie Nahm 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Rice, as a model system of monocotyledon plants for genomic studies, is a main staple food for over half of the world population. A rice retrotransposon, Tos17, is active during tissue culture and its ability was wildly used in insertional mutagenesis. In this study we have produced 2,000 non-GM mutants induced by Tos17 in rice. We analyzed >2,000 flanking sequences of newly transposed Tos17 copies by the adaptor-ligation PCR method. The frequencies of Tos17 insertions in the genic and intergenic regions were 60.3% and 36.6%, respectively. We also selected four Tos17 insertion mutant lines for three TF genes which can be considered to be considered to be involved in rice seed development based on expression microarray data: osrem3, osta1, osbhlh1-1, and osbhlh1-2 mutant lines. According to Quadruple 9-mer-based protein binding microarray (Q9-UPBM) experiment, we found that the OsREM3, OsTA1, and OsbHLH1 bound to the ACACCAC, CACGTG, and GTAACA motifs, respectively. In combination of Q9-UPBM, RiceArrayNet analysis, and expression microarray data, we identified 8, 20, and 9 putative target genes of OsREM3, OsTA1, and OsbHLH1, respectively. We have been screening and characterizing the mutations by extensive phenotypic analysis as well as the functional analysis of genes.