• Interdisciplinary Bio Central
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• v.2 no.4
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• pp.15.1-15.5
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• 2010

RIKEN BioResource Center (BRC) has collected, preserved, conducted quality control of, and distributed mouse resources since 2002 as the core facility of the National BioResource Project by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. Our mouse resources include over 5,000 strains such as humanized disease models, fluorescent reporters, and knockout mice. We have developed novel mouse strains such as tissue-specific Cre-drivers and optogenetic strains that are in high demand by the research community. We have removed all our specified pathogens from the deposited mice and used our quality control tests to examine their genetic modifications and backgrounds. RIKEN BRC is a founding member of the Federation of International Mouse Resources and the Asian Mouse Mutagenesis and Resource Association, and provides mouse resources to the one-stop International Mouse Strain Resource database. RIKEN BRC also participates in the International Gene Trap Consortium, having registered 713 gene-trap clones and their sequences in a public library, and is an advisory member of the CREATE (Coordination of resources for conditional expression of mutated mouse alleles) consortium which represents major European and international mouse database holders for the integration and dissemination of Cre-driver strains. RIKEN BRC provides training courses in the use of advanced technologies for the quality control and cryopreservation of mouse strains to promote the effective use of mouse resources worldwide.

• Journal of Microbiology
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• v.40 no.3
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• pp.245-247
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• 2002

A genomic DNA library of the fungus Trametes versicolor was constructed in a yeast integration vector which contains the URA3 gene of the budding yeast Saccharomyces cerevisiae and the gene responsible for hygromycin B resistance, and fragments acting as autonomously replicating sequences (ARSes) in the budding yeast were identified from the genomic DNA library. Sixteen recombinant plasmids from the library transformed the budding yeast Saccharomyces cerevisiae to Ura+ at high frequencies. They were maintained stably under selective conditions, but were gradually lost from yeast cells at different rates under nonselective conditions, indicating that they contain eukaryotic origins of DNA replication and exist as extrachromosomal plasmids. Base sequences of four ARS DNAs among the 16 cloned fragments revealed that all or the four contain at least one 11 bp ［(A/T)TTTA(T/C)(A/G)TTT(A/T)］consensus sequence of the budding yeast ARS.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.66-75
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• 2016

Agrobacterium-mediated gene transfer has recently been developed to improve rice transformation. In this study, 3 different transformation methods were tested including soaking, co-cultivation, and vacuum infiltration. Agrobacterium tumefaciens GV3101 harboring the binary vector pGreen:: LeGSNOR was used in this experiment. This study aimed to identify the most appropriate method for transferring LeGSNOR into rice. Vacuum infiltration of the embryonic calli for 5 min in Ilpum resulted in high transformation efficiency based on confirmation by PCR, RT-PCR, and qRT-PCR analyses. In conclusion, we described the development of an efficient transformation protocol for the stable integration of foreign genes into rice; furthermore, the study results confirmed that PCR is suitable for efficient detection of the integrated gene. The vacuum infiltration system is a potentially useful tool for future studies focusing on transferring important genes into rice seed calli, and may help reduce time and effort.

• Journal of The Korean Society of Grassland and Forage Science
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• v.34 no.3
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• pp.187-192
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• 2014

Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world. It has been demanded to establish the efficient transformation system in commercial varieties of alfalfa for forage molecular breeding and production of varieties possessing new characteristics. To approach this, genetic transformation techniques have been developed and modified. This work was performed to establish conditions for effective transformation of commercial alfalfa cultivars, Xinjiang Daye, ABT405, Vernal, Wintergreen and Alfagraze. GUS gene was used as a transgene and cotyledon and hypocotyl as a source of explants. Transformation efficiencies differed from 0 to 7.9% among alfalfa cultivars. Highest transformation efficiencies were observed in the cultivar Xinjiang Daye. The integration and expression of the transgenes in the transformed alfalfa plants was confirmed by polymerase chain reaction (PCR) and histochemical GUS assay. These data demonstrate highly efficient Agrobacterium transformation of diverse alfalfa cultivars Xinjiang Daye, which enables routine production of transgenic alfalfa plants.

• Food Science and Biotechnology
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• v.18 no.5
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• pp.1118-1123
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• 2009

Event-specific real-time polymerase chain reaction (PCR) detection method for genetically modified (GM) maize MIR604 was developed based on integration junction sequences between the host plant genome and the integrated transgene. In this study, 2 primer pairs and probes were designed for specific amplification of 100 and 111 bp DNA fragments from the zSSIIb gene (the maize endogenous reference gene) and MIR604. The quantitative method was validated using 3 certified reference materials (CRMs) with levels of 0.1, 1, and 10% MIR604. The method was also assayed with 14 different plants and other GM maize. No amplification signal was observed in real-time PCR assays with any of the species tested other than MIR604 maize. As a result, the bias from the true value and the relative deviation for MIR604 was within the range from 0 to 9%. Precision, expressed as relative standard deviation (RSD), varied from 2.7 to 10% for MIR604. Limits of detections (LODs) of qualitative and quantitative methods were all 0.1%. These results indicated that the event-specific quantitative PCR detection system for MIR604 is accurate and useful.

• KSBB Journal
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• v.17 no.6
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• pp.577-581
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• 2002

In an attempt to produce recombinant proteins using the pollen enriched in some plant species, a 1.7 kb DNA encoding urease subunit B (UreB) amplified by PCR from Helicobacter pylori urease gene cluster in pH808 plasmid was cloned to be expressed under CaMV35S promoter in lily (Lilium longiflorum) pollen tubes elongated in vitro. Lily pollen at early germinating stage was transformed with the ureB DNA using Agrobacterium via vacuum infiltration and, incubated for a full pollen tube growth 16 - 24 h in the dark in the presence of kanamycin. DNA integration and expression in the transgenic pollen were analyzed by the standard molecular techniques and the results suggest that the pollen in vitro may be employed as a protein factory in a disposable fashion.

• Journal of Aquaculture
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• v.13 no.1
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• pp.21-27
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• 2000

The successful gene transfer and transient expression was demonstrated in olive flounder embryos using lipofected sperm. Olive flounder sperm interacted with foregn plasmid DNA encapsidated by positively charged liposome. The maximum plasmid copy number that associated with the sperm was 5 copies/sperm based on the examination of DNA blot assay. The foreign DNA was transferred into fertilized eggs without any adverse effect on fertilization and survival of embryos (P>0.05) and retained in embryos until at least 42 hours with successful expression. The maximal expression was detected in 18 hours after fertilization at 18$^{\cird}C$ and gradually decreased with development of embryo. Most of DNA transferred into embryos persisted extrachromosomally without significant sign of integration or replication.

• Journal of Aquaculture
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• v.10 no.1
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• pp.33-37
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• 1997

construct containing reporter gene(pFV4CAT) regulated by carp $\beta$-actin promoter was microinjected into the one-cell stage egg of mud loach (Misgurnus mizolepis), and was successfully expressed, possibly by the integration into the genome. Both mean hatching success and early survival of the microinjected groups were not significantly different with those of control groups (P>0.05). The incidence of transgene was ranged from 7 to 48% based on the PCR and/or Southern blot analyses with the DNA prepared from fin or blood tissue. The spatial and temporal patterns of expression of the pFV4CAT gene, measured by in situ immunohistochemical analysis peroxidase-conjugated anti-CAT antibody, were variable among the experimental individuals. These results suggest that carp $\beta$-actin promoter is effective to express other transgene in mud loach, such that this promoter can be useful in the generation of valuable transgenic mud loach.

• Plant Resources
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• v.7 no.1
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• pp.39-46
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• 2004

To demonstrate the importance of transformation efficiency in independent event, molecular and cytogenetic analysis were conducted with genomic DNA and chromosome of transgenic plants produced by Agrobacterium tumefeciens LBA4404 (pSBM-PPGN: gusA and bar). Selection ratios of putative transgenic calli were similar in independent experiments, however, transformation efficiencies were critically influenced by the type of regeneration media. MSRK5SS-Pr regeneration mediun, which contains 5 mgL$^{-1}$ kinetin, 2% (w/v) sucrose in combination with 3% (w/v) sorbitol, and 500 mgL$^{-1}$ proline, was efficient to produce transgenic plant of rice from putative transgenic callus in the presence of L-phosphinotricin (PPT). With MSRK5SS-Pr medium, transformation efficincies of Nagdongbyeo were significantly enhanced from 3.7% to 6.3% in independent callus lines arid from 7.3% to 19.7% in plants produced, respectively. Stable integration and expression of bar gene were confirmed by basta herbicide assay, PCR amplification and Southern blotting of bar gene, and fluorescence in situ hybridization (FISH) analysis using pSBM-PPGN as a probe. In Southern blot analysis, diverse band patterns were observed in total 44 transgenic plants regenerated from 20 independent PPT resistant calli showing from one to five copies of T-DNA segments, however, the transformants obtained from one callus line showed the same copy numbers with the same fractionized band patterns.

• Journal of Korea Artificial Intelligence Association
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• v.2 no.1
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• pp.7-14
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• 2024

In this paper, we explore the application of RNA-sequencing data and ensemble machine learning to predict lung cancer and treatment strategies for lung cancer, a leading cause of cancer mortality worldwide. The research utilizes Random Forest, XGBoost, and LightGBM models to analyze gene expression profiles from extensive datasets, aiming to enhance predictive accuracy for lung cancer prognosis. The methodology focuses on preprocessing RNA-seq data to standardize expression levels across samples and applying ensemble algorithms to maximize prediction stability and reduce model overfitting. Key findings indicate that ensemble models, especially XGBoost, substantially outperform traditional predictive models. Significant genetic markers such as ADGRF5 is identified as crucial for predicting lung cancer outcomes. In conclusion, ensemble learning using RNA-seq data proves highly effective in predicting lung cancer, suggesting a potential shift towards more precise and personalized treatment approaches. The results advocate for further integration of molecular and clinical data to refine diagnostic models and improve clinical outcomes, underscoring the critical role of advanced molecular diagnostics in enhancing patient survival rates and quality of life. This study lays the groundwork for future research in the application of RNA-sequencing data and ensemble machine learning techniques in clinical settings.