• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2023년도 임시총회 및 춘계학술대회
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• pp.15-15
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• 2023

The chloroplast (cp) is an autonomous plant organelle with an individual genome that codes for essential cellular functions. The architecture and gene content of the cp genome is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. In addition, the protein-coding genes accD and the ndh gene loss events occurred in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The gene ndh lost in the Corydalis-sub clade species is distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The molecular clock analysis suggests that the divergence time of all the ndh gene lost Corydalis sub-clade species occurred in the 44.31 - 15.71 mya. These results coincide very well with the uplift of the Qinghai-Tibet Plateau in the Oligocene and Miocene periods, and maybe during this period, it probably triggered the radiation of the Corydalis species. To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.

• Asian Pacific Journal of Cancer Prevention
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• 제16권16호
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• pp.7343-7350
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• 2015

Genetic changes associated with acute lymphoblastic leukemia (ALL) provide very important diagnostic and prognostic information with a direct impact on patient management. Detection of chromosome abnormalities by conventional cytogenetics combined with fluorescence in situ hybridization (FISH) play a very significant role in assessing risk stratification. Identification of specific chromosome abnormalities has led to the recognition of genetic subgroups based on reciprocal translocations, deletions and modal number in B or T-cell ALL. In the last twelve years 102 newly diagnosed childhood/adult ALL bone marrow samples were analysed for chromosomal abnormalities with conventional G-banding, and FISH (selected cases) using specific probes in our hospital. G-banded karyotype analysis found clonal numerical and/or structural chromosomal aberrations in 74.2% of cases. Patients with pseudodiploidy represented the most frequent group (38.7%) followed by high hyperdiploidy group (12.9%), low hyperdiploidy group (9.7%), hypodiploidy (<46) group (9.7%) and high hypertriploidy group (3.2%). The highest observed numerical chromosomal alteration was high hyperdiploidy (12.9%) with abnormal karyotypes while abnormal 12p (7.5%) was the highest observed structural abnormality followed by t(12;21)(p13.3;q22) resulting in ETV6/RUNX1 fusion (5.4%) and t(9;22)(q34.1;q11.2) resulting in BCR/ABL1 fusion (4.3%). Interestingly, we identified 16 cases with rare and complex structural aberrations. Application of the FISH technique produced major improvements in the sensitivity and accuracy of cytogenetic analysis with ALL patients. In conclusion it confirmed heterogeneity of ALL by identifying various recurrent chromosomal aberrations along with non-specific rearrangements and their association with specific immunophenotypes. This study pool is representative of paediatric/adult ALL patients in Oman.

• Asian Pacific Journal of Cancer Prevention
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• 제16권16호
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• pp.7219-7229
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• 2015

Background: Chromosomal aberrations identified in acute lymphoblastic leukemia (ALL) have an important role in disease diagnosis, prognosis and management. Information on karyotype and associated clinical parameters are essential to physicians for planning cancer control interventions in different geographical regions. Materials and Methods: In this study, we present the overall frequency and distribution patterns of chromosomal aberrations in both children and adult de novo B lineage ALL Indian patients using conventional cytogenetics, interphase FISH and multiplex RT-PCR. Results: Among the 215 subjects, cytogenetic results were achieved in 172 (80%) patients; normal karyotype represented 37.2% and abnormal 62.8% with a distribution as follows: 15.3% hypodiploidy; 10.3% hyperdiploidy; 15.8% t(9;22); 9.8% t(1;19); 3.7% t(12;21); 2.8% t(4;11); 2.8% complex karyotypes. Apart from these, we observed several novel, rare and common chromosomal rearrangements. Also, FISH studies using LSI extra-signal dual-color probes revealed additional structural or numerical changes. Conclusions: These results demonstrate cytogenetic heterogeneity of ALL and confirm that the incidence of chromosomal abnormalities varies considerably. To the best of our knowledge, this is one of the largest reported series of cytogenetic investigations in Indian B-lineage ALL cases. In addition, ongoing cytogenetic studies are warranted in larger groups of B-lineage ALL cases to identify newly acquired chromosomal abnormalities that may contribute to disease diagnosis and management.

• Molecules and Cells
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• 제43권5호
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• pp.448-458
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• 2020

T-DNA insertional mutations in Arabidopsis genes have conferred huge benefits to the research community, greatly facilitating gene function analyses. However, the insertion process can cause chromosomal rearrangements. Here, we show an example of a likely rearrangement following T-DNA insertion in the Anti-Silencing Function 1B (ASF1B) gene locus on Arabidopsis chromosome 5, so that the phenotype was not relevant to the gene of interest, ASF1B. ASF1 is a histone H3/H4 chaperone involved in chromatin remodeling in the sporophyte and during reproduction. Plants that were homozygous for mutant alleles asf1a or asf1b were developmentally normal. However, following self-fertilization of double heterozygotes (ASF1A/asf1a ASF1B/asf1b, hereafter AaBb), defects were visible in both male and female gametes. Half of the AaBb and aaBb ovules displayed arrested embryo sacs with functional megaspore identity. Similarly, half of the AaBb and aaBb pollen grains showed centromere defects, resulting in pollen abortion at the bi-cellular stage of the male gametophyte. However, inheritance of the mutant allele in a given gamete did not solely determine the abortion phenotype. Introducing functional ASF1B failed to rescue the AaBb- and aaBb-mediated abortion, suggesting that heterozygosity in the ASF1B gene causes gametophytic defects, rather than the loss of ASF1. The presence of reproductive defects in heterozygous mutants but not in homozygotes, and the characteristic all-or-nothing pollen viability within tetrads, were both indicative of commonly-observed T-DNA-mediated translocation activity for this allele. Our observations reinforce the importance of complementation tests in assigning gene function using reverse genetics.

• Journal of Genetic Medicine
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• 제2권1호
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• pp.23-26
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• 1998

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder which has been clinically shown to cause progressive weakness and result in atrophy of the facial muscles, shoulder girdle and upper arm muscles. The responsible gene for the FSHD has been located on chromosome 4q35-qter. The probes p13E-11 and pFR-1 detect DNA rearrangements associated with FSHD as under 28 kb DNA fragment in genomic southern analysis digested with EcoRI and the fragment contains 3.3 kb Kpn I tandem repeats. In this study, 4 fetuses with a family history of FSHD were analysed by genomic southern hybridization analysis with probes to determine whether they carried the deleted region. Of the 4 fetuses, three of them had mothers who were FSHD patients and the other one had a father affected with FSHD. After 10-11 weeks of gestation, we performed chorionic villi sampling and extracted DNA from uncultured and cultured tissue cells for the direct DNA analysis. The result of the southern analysis showed two fetuses having received about 15-18 kb of deleted genes from the father and the mother respectively, and found to be FSHD patients. The other two fetuses were shown to have two normal alleles from the parents and found to be normal. Two pregnancies which were determined to be normal were carried to term delivering two healthy babies.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.183-192
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• 2003

With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.

• 대한전기학회:학술대회논문집
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• 대한전기학회 1992년도 하계학술대회 논문집 B
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• pp.843-846
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• 1992

This thesis was investigated on optical-and ion-induced characteristics in positive(a-$Se_{75}Ge_{25}$) and negative (Ag/a-$Se_{75}Ge_{25}$) resists for focused-ion-beam microlithogaphy. The a-$Se_{75}Ge_{25}$ inorganic thin film shows an increase in optical absorption after exposure to$\sim$$10^{16}$ dose(ions/$cm^{2}$) of Ga ions. The observed shift in the absorption edge toward longer wavelengths is consistent with that in films exposed to band-gap photons ($\sim$$10^{20}$ photons/$cm^{2}$). But, ion induced shift is twice as much as that in film exposed to optical radiation. This result may be related with microstructural rearrangements with in the short range of SeGe network. Due to changes in the short range order, the chemical bonding may be affected, which results in increased chemical dissolution in ion-induced film. Also, this resist exhibits good thermal stability because of its high Tg(~220$^{\circ}C$). The composition of deposited film measured by AES is consistent with that of bulk.

• 한국초지조사료학회지
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• 제36권3호
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• pp.237-242
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• 2016

Copper (Cu) is a necessary microelement for plants. However, high concentrations of Cu are toxic to plants that change the regulation of several stress-induced proteins. In this study, an annealing control primer (ACP) based approach was used to identify differentially expressed Cu-induced genes in alfalfa leaves. Two-week-old alfalfa plants (Medicago sativa L.) were exposed to Cu for 6 h. Total RNAs were isolated from treated and control leaves followed by ACP-based PCR technique. Using GeneFishing ACPs, we obtained several genes those expression levels were induced by Cu. Finally, we identified several genes including UDP-glucuronic acid decarboxylase, transmembrane protein, small heat shock protein, C-type cytochrome biogenesis protein, mitochondrial 2-oxoglutarate, and trans-2,3-enoyl-CoA reductase in alfalfa leaves. These identified genes have putative functions in cellular processes such as cell wall structural rearrangements, transduction, stress tolerance, heme transport, carbon and nitrogen assimilation, and lipid biosynthesis. Response of Cu-induced genes and their identification in alfalfa would be useful for molecular breeding to improve alfalfa with tolerance to heavy metals.

• Clinical and Experimental Reproductive Medicine
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• 제39권2호
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• pp.58-67
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• 2012

Objective: Previously, we identified that transketolase (Tkt), an important enzyme in the pentose phosphate pathway, is highly expressed at 2 hours of spontaneous maturation in oocytes. Therefore, this study was performed to determine the function of Tkt in meiotic cell cycle regulation, especially at the point of germinal vesicle breakdown (GVBD). Methods: We evaluated the loss-of-function of Tkt by microinjecting Tkt double-stranded RNAs (dsRNAs) into germinal vesicle-stage oocytes, and the oocytes were cultured in vitro to evaluate phenotypic changes during oocyte maturation. In addition to maturation rates, meiotic spindle and chromosome rearrangements, and changes in expression of other enzymes in the pentose phosphate pathway were determined after Tkt RNA interference (RNAi). Results: Despite the complete and specific knockdown of Tkt expression, GVBD occurred and meiosis was arrested at the metaphase I (MI) stage. The arrested oocytes exhibited spindle loss, chromosomal aggregation, and declined maturation promoting factor and mitogen-activated protein kinase activities. The modified expression of two enzymes in the pentose phosphate pathway, Prps1 and Rbks, after Tkt RNAi and decreased maturation rates were amended when ribose-5-phosphate was supplemented in the culture medium, suggesting that the Tkt and pentose phosphate pathway are important for the maturation process. Conclusion: We concluded that Tkt and its associated pentose phosphate pathway play an important role in the MI-MII transition of the oocytes' meiotic cell cycle, but not in the process of GVBD.

• Asian Pacific Journal of Cancer Prevention
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• 제17권2호
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• pp.677-684
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• 2016

Background: Acute lymphoblastic leukemia (ALL) is a heterogeneous disease which requires a risk-stratified approach for appropriate treatment. Specific chromosomal translocations within leukemic blasts are important prognostic factors that allow identification of relevant subgroups. In this study, we developed a multiplex RT-PCR assay for detection of the 4 most frequent translocations in ALL (BCR-ABL, TEL-AML1, MLL-AF4, and E2A-PBX1). Materials and Methods: A total of 214 diagnosed ALL samples from both adult and pediatric ALL and 14 cases of CML patients (154 bone marrow and 74 peripheral blood samples) were assessed for specific chromosomal translocations by cytogenetic and multiplex RT-PCR assays. Results: The results showed that 46 cases of ALL and CML (20.2%) contained the fusion transcripts. Within the positive ALL patients, the most prevalent cryptic translocation observed was mBCR-ABL (p190) at 8.41%. In addition, other genetic rearrangements detected by the multiplex PCR were 4.21% TEL-AML1 and 2.34% E2A-PBX1, whereas MLL-AF4 exhibited negative results in all tested samples. Moreover, MBCR-ABL was detected in all 14 CML samples. In 16 samples of normal karyotype ALL (n=9), ALL with no cytogentic result (n=4) and CML with no Philadelphia chromosome (n=3), fusion transcripts were detected. Conclusions: Multiplex RT-PCR provides a rapid, simple and highly sensitive method to detect fusion transcripts for prognostic and risk stratification of ALL and CML patients.