Understanding of Genome Duplication For SNP Marker Development in Soybean

Cai Chun-Mei,Van Kyu-Jung,Kim Moon-Young,Lee Suk-Ha 한국작물학회 2006 한국작물학회 학술발표대회 논문집 Vol.2006 No.-

Gene Duplications Revealed during the Process of SNP Discovery in Soybean[Glycine max(L.) Merr.]

Cai, Chun Mei,Van, Kyu-Jung,Lee, Suk-Ha The Korean Society of Crop Science 2007 Journal of crop science and biotechnology Vol.10 No.4

Genome duplication(i.e. polyploidy) is a common phenomenon in the evolution of plants. The objective of this study was to achieve a comprehensive understanding of genome duplication for SNP discovery by Thymine/Adenine(TA) cloning for confirmation. Primer pairs were designed from 793 EST contigs expressed in the roots of a supernodulating soybean mutant and screened between 'Pureunkong' and 'Jinpumkong 2' by direct sequencing. Almost 27% of the primer sets were failed to obtain sequence data due to multiple bands on agarose gel or poor quality sequence data from a single band. TA cloning was able to identify duplicate genes and the paralogous sequences were coincident with the nonspecific peaks in direct sequencing. Our study confirmed that heterogeneous products by the co-amplification of a gene family member were the main cause of obtaining multiple bands or poor quality sequence data in direct sequencing. Counts of amplified bands on agarose gel and peaks of sequencing trace suggested that almost 27% of nonrepetitive soybean sequences were present in as many as four copies with an average of 2.33 duplications per segment. Copy numbers would be underestimated because of the presence of long intron between primer binding sites or mutation on priming site. Also, the copy numbers were not accurately estimated due to deletion or tandem duplication in the entire soybean genome.

Optimization of SNP Genotyping Assay with Fluorescence Polarization Detection

Chun Mei Cai,반규정,김문영,이석하 한국작물학회 2005 Korean journal of crop science Vol.50 No.6

Single nucleotide polymorphisms (SNPs) are valuable DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed. In this report, one of effective and high throughput SNP genotyping assays which was named the template-directed dye-terminator incorporation with fluorescence polarization detection (FP-TDI) was described. Although the most of this assay succeed, the objective of this work was to determine the reasons for the failures, find ways to improve the assay and reduce the running cost. Ninety F2-derived soybean, Glycine max (L.) Merr., RILs from a cross between Pureunkong and Jinpumkong 2 were genotyped at four SNPs. FP measurement was done on Victor3 microplate reader (Perkinelmer Inc., Boston, MA, USA). Increasing the number of thermal cycles in the single-base extension step increased the separation of the FP values between the products corresponding to different genotypes. But in some assays, excess of heterozygous genotypes was observed with increase of PCR cycles. We discovered that the excess heterozygous was due to misincorporation of one of the dye-terminators during the primer extension reaction. After pyrophosphatase incubation and thermal cycle control, misincoporation can be effectively prevented. Using long amplicons instead of short amplicons for SNP genotyping and decreasing the amount of dye terminator and Acyclopol Taq polymerase to 1/2 or 1/3 decreased the cost of the assay. With these minor adjustments, the FP-TDI assay can be used more accurately and cost-effectively.

Sequence Divergence of Recently Duplicate Genes in Soybean (Glycine max L. Merr.)

Chun Mei Cai,Kyu Jung Van,Moon Young Kim,Suk Ha Lee 한국유전학회 2008 Genes & Genomics Vol.30 No.3

Sequence divergence of duplicate genes was investigated in soybean, a diploidized paleopolyploid. To examine gene duplication, a total of seven primers designed from expressed sequence tags (ESTs) were selected for this study because they produced (1) a single band but showed poor sequencing quality and (2) double bands on an agarose gel. After PCR amplification with genomic DNA, duplicate genes were identified by cloning and subsequent sequencing of twenty randomly-selected clones. Based on their alignment, two or three classes were identified in each amplicon. Linkage analysis confirmed that two duplicate loci were located on different chromosomes. The exon/intron structure was conserved between duplicate gene pairs. A detailed examination of the variation between duplicate pairs showed that the coding regions are highly conserved while many substitutions and insertion/deletions (indels) were identified in non-coding regions. In particular, non-homologs fragments were numerous and, on average, 82 bp in length within the non-coding region. Quantitative trait loci (QTL) for some major agronomic characters, such as seed protein and oil, seed yield, plant height, and corn earworm resistance, were positioned across duplicate loci of TC225246 and TC224550, suggesting that the gene families appear to have retained similar functions throughout genome duplication and evolution events.

SNP Marker Development and SNP-based Genetic Map Construction in Soybean

Cai Chun-Mei,Van Kyu-Jung,Kim Moon-Young,Lee Suk-Ha 한국작물학회 2006 한국작물학회 학술발표대회 논문집 Vol.2006 No.-

Optimization of SNP Genotyping Assay with Fluorescence Polarization Detection

Cai Chun Mei,Van Kyujung,Kim Moon Young,Lee Suk-Ha The Korean Society of Crop Science 2005 Korean journal of crop science Vol.50 No.5

Single nucleotide polymorphisms (SNPs) are valuable DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed. In this report, one of effective and high throughput SNP genotyping assays, which was named the template-directed dye-terminator incorporation with fluorescence polarization detection (FP-TDI) was described. Although the most of this assay succeed, the objective of this work was to deter­mine the reasons for the failures, find ways to improve the assay and reduce the running cost. Ninety $F_2$-derived soybean, Glycine max (L.) Merr., RILs from a cross between 'Pureunkong' and 'Jinpumkong 2' were genotyped at four SNPs. FP measurement was done on $Victot^3$ microplate reader (perkinelmer Inc., Boston, MA, USA). Increasing the number of thermal cycles in the single-base extension step increased the separation of the FP values between the products corresponding to different genotypes. But in some assays, excess of heterozygous genotypes was observed with increase of PCR cycles. We discovered that the excess heterozygous was due to misincorporation of one of the dye­terminators during the primer extension reaction. After pyrophosphatase incubation and thermal cycle control, misincoporation can be effectively prevented. Using long amplicons instead of short amplicons for SNP genotyping and decreasing the amount of dye terminator and Acyclopol Taq polymerase to 1/2 or 1/3 decreased the cost of the assay. With these minor adjustments, the FP-TDI assay can be used more accurately and cost-effectively.

Optimization of SNP Genotyping Assay with Fluorescence Polarization Detection

Chun Mei Cai,Kyujung Van,Moon Young Kim,Suk-Ha Lee 韓國作物學會 2005 Korean journal of crop science Vol.50 No.5

Single nucleotide polymorphisms (SNPs) are valuable DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed. In this report, one of effective and high throughput SNP genotyping assays, which was named the template-directed dye-terminator incorporation with fluorescence polarization detection (FP-TDI) was described. Although the most of this assay succeed, the objective of this work was to deter-mine the reasons for the failures, find ways to improve the assay and reduce the running cost. Ninety F2 -derived soybean, Glycine max (L.) Merr., RILs from a cross between 'Pureunkong' and 'Jinpumkong 2' were genotyped at four SNPs. FP measurement was done on Victot3 microplate reader (perkinelmer Inc., Boston, MA, USA). Increasing the number of thermal cycles in the single-base extension step increased the separation of the FP values between the products corresponding to different genotypes. But in some assays, excess of heterozygous genotypes was observed with increase of PCR cycles. We discovered that the excess heterozygous was due to misincorporation of one of the dye-terminators during the primer extension reaction. After pyrophosphatase incubation and thermal cycle control, misincoporation can be effectively prevented. Using long amplicons instead of short amplicons for SNP genotyping and decreasing the amount of dye terminator and Acyclopol Taq polymerase to 1/2 or 1/3 decreased the cost of the assay. With these minor adjustments, the FP-TDI assay can be used more accurately and cost-effectively.

Gene Duplications Revealed during the Process of SNP Discovery in Soybean [Glycine max (L.) Merr.]

이석하,Chun Mei Cai,반규정 한국작물학회 2007 Journal of crop science and biotechnology Vol.10 No.4

Genome duplication (i.e. polyploidy) is a common phenomenon in the evolution of plants. The objective of this study was to achieve a comprehensive understanding of genome duplication for SNP discovery by Thymine/Adenine (TA) cloning for confirmation. Primer pairs were designed from 793 EST contigs expressed in the roots of a supernodulating soybean mutant and screened between 'Pureunkong' and 'Jinpumkong 2' by direct sequencing. Almost 27% of the primer sets were failed to obtain sequence data due to multiple bands on agarose gel or poor quality sequence data from a single band. TA cloning was able to identify duplicate genes and the paralogous sequences were coincident with the nonspecific peaks in direct sequencing. Our study confirmed that heterogeneous products by the co-amplification of a gene family member were the main cause of obtaining multiple bands or poor quality sequence data in direct sequencing. Counts of amplified bands on agarose gel and peaks of sequencing trace suggested that almost 27% of nonrepetitive soybean sequences were present in as many as four copies with an average of 2.33 duplications per segment. Copy numbers would be underestimated because of the presence of long intron between primer binding sites or mutation on priming site. Also, the copy numbers were not accurately estimated due to deletion or tandem duplication in the entire soybean genome.

Randomized Control Study of Nedaplatin or Cisplatin Concomitant with Other Chemotherapy in the Treatment of Advanced Non-small Cell Lung Cancer

Li, Chun-Hong,Liu, Mei-Yan,Liu, Wei,Li, Dan-Dan,Cai, Li Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.2

Objective: To observe the short-term efficacy, long-term survival time and adverse responses with nedaplatin (NDP) or cisplatin (DDP) concomitant with other chemotherapy in treating non-small cell lung cancer. Materials and Methods: A retrospective, randomized, control study was conducted, in which 619 NSCLC patients in phases III and IV who were initially treated and re-treated were randomly divided into an NDP group (n=294) and a DDP group (n=325), the latter being regarded as controls. Chemotherapeutic protocols (CP/DP/GP/NP/TP) containing NDP or DDP were given to both groups. Patients in both groups were further divided to evaluate the clinical efficacies according to initial and re-treatment stage, pathological pattern, type of combined chemotherapeutic protocols, tumor stage and surgery. Results: The overall response rate (ORR) and disease control rate (DCR) in the NDP group were 48.6% and 95.2%, significantly higher than in the DDP group at 35.1% and 89.2%, respectively (P<0.01). In NSCLC patients with initial treatment, squamous carcinoma and phase III, there were significant differences in ORR and DCR between the groups (P<0.05), while ORR was significant in patients with adenocarcinoma, GP/TP and in phase IIIa (P<0.05). There was also a significant difference in DCR in patients in phase IIIb (P<0.05). According to the statistical analysis of survival time of all patients and of those in clinical phase III, the NDP group survived significantly longer than the DDP group (P<0.01). The rates of decreased hemoglobin and increased creatinine, nausea and vomiting in the NDP group were evidently lower than in DDP group (P<0.05). Conclusion: NDP concomitant with other chemotherapy is effective for treating NSCLC, with higher clinical efficacy than DDP concomitant with chemotherapy, with advantages in prolonging survival time and reducing toxic and adverse responses.

In situ growth of CdS spherical nanoparticles/Ti3C2 MXene nanosheet heterojunction with enhanced photocatalytic hydrogen evolution

Kai Chun-Mei,Kong Cui,Zhang Feng-Jun,Li Dong-Cai,Wang Ying-Rui,오원춘 한국세라믹학회 2022 한국세라믹학회지 Vol.59 No.3

Solar photocatalytic hydrogen production is considered as a potential solution to alleviate the current global energy situation. In this work, a novle CdS spherical nanoparticles/Ti3C2 MXene nanosheet (CM) heterostructure photocatalyst was prepared by in situ growth method, which has the characteristics of high efficiency and stability. The results showed that the CM sam- ple has regular morphology and size. When compared with pure CdS, its specific surface area increased and the hydrogen evolution performance also greatly improved. Among them, the hydrogen evolution of CM-0.06 is 1295 μmol·g−1·h−1 (λ > 420 nm), which is 7 times that of spherical CdS, and it also showed stronger stability. Tight interface contact can promote the transfer and migration of photo-generated carriers, and the effective separation of electron hole pairs can enhance the absorption of visible light. In addition, Ti3C2 MXene acts as an electron trap can further accelerate the separation of pho- togenerated electrons and holes. The synergistic effect between semiconductor CdS and Ti3C2 MXene nanosheets, which provides a new idea for the design of more stable and efficient CdS-based photocatalysts.