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Rakwal, Randeep,Kimura, Shinzo,Shibato, Junko,Nojima, Kumie,Kim, Yeonki,Nahm, Baekhie,Jwa, Namsoo,Endo, Satoru,Tanaka, Kenichi,Iwahashi, Hitoshi Korean Society for Molecular Biology 2008 Molecules and cells Vol.25 No.2
The carbon-ion beam (CIB) generated by the heavy-ion medical accelerator in Chiba (HIMAC) was targeted to 7-day-old rice. Physiological parameters such as growth, and gene expression profiles were examined immediately after CIB irradiation. Dose-dependent growth suppression was seen three days post-irradiation (PI), and all the irradiated plants died by 15 days PI. Microarray (Agilent rice 22K) analysis of the plants immediately after irradiation (iai) revealed effects on gene expression at 270 Gy; 353 genes were up-regulated and 87 down-regulated. Exactly the same set of genes was affected at 90 Gy. Among the highly induced genes were genes involved in information storage and processing, cellular processes and signaling, and metabolism. RT-PCR analysis confirmed the microarray data.
Randeep Rakwal,Shinzo Kimura,Junko Shibato,Kumie Nojima,Yeon-Ki Kim,남백희,Nam-Soo Jwa,Satoru Endo,Kenichi Tanaka,Hitoshi Iwahashi 한국분자세포생물학회 2008 Molecules and cells Vol.25 No.2
The carbon-ion beam (CIB) generated by the heavy-ion medical accelerator in Chiba (HIMAC) was targeted to 7-day-old rice. Physiological parameters such as growth, and gene expression profiles were examined immediately after CIB irradiation. Dose-dependent growth suppression was seen three days post-irradiation (PI), and all the irradiated plants died by 15 days PI. Microarray (Agilent rice 22K) analysis of the plants immediately after irradiation (iai) revealed effects on gene expression at 270 Gy; 353 genes were up-regulated and 87 down-regulated. Exactly the same set of genes was affected at 90 Gy. Among the highly induced genes were genes involved in information storage and processing, cellular processes and signaling, and metabolism. RT-PCR analysis confirmed the microarray data.
Misato Hirano,Junko Shibato,Randeep Rakwal,Nobuo Kouyama,Yoko Katayama,Motohiro Hayashi,Yoshinori Masuo 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.2
Gamma knife surgery (GKS) is used for the treatment of various human brain disorders. However, the biological effects of gamma ray irradiation on both the target area, and the surrounding tissues are not well studied. The effects of gamma ray exposure to both targeted and untargeted regions were therefore evaluated by monitoring gene expression changes in the unilateral irradiated (60 Gy) and contralateral un-irradiated striata in the rat. Striata of irradiated and control brains were dissected 16 hours post-irradiation for analysis using a whole genome 44K DNA oligo microarray approach. The results revealed 230 induced and 144 repressed genes in the irradiated striatum and 432 induced and 239 repressed genes in the unirradiated striatum. Out of these altered genes 39 of the induced and 16 of the reduced genes were common to both irradiated and un-irradiated tissue. Results of semiquantitative, confirmatory RT-PCR and western blot analyses suggested that γ-irradiation caused cellular damage, including oxidative stress, in the striata of both hemispheres of the brains of treated animals.
Thavrak Huon,Sungkuk Jang,조경원,Randeep Rakwal,우제창,김일철,지승욱,한옥수 대한화학회 2009 Bulletin of the Korean Chemical Society Vol.30 No.4
The maize lipoxgyenase-1 is a non-traditional dual positional specific enzyme and the reaction proceeds via enzyme-initiated catalysis. Bioinformatic analysis indicated that the maize lipoxygenase-1 is structurally more similar to soybean LOX1 than pea LOXN2 in that it has an additional external loop (residues 318-351) in the carboxy-terminal catalytic domain. We analyzed the dependence of product distribution on concentration of linoleic acid and monitored the formation of hydroperoxyoctadecadienoic acid as a function of enzyme concentration. Product distribution was strongly influenced by substrate concentration, such that kinetically-controlled regioisomers were enriched and thermodynamically-controlled regioisomers were depleted at high substrate concentration. Kinetic studies indicated that the formation of hydroperoxyoctadecadienoic acid saturated rapidly in an enzyme concentration-dependent manner, which implied that reactivation by reoxidation of inactive Fe(II) failed to occur. Our results support the previously proposed enzyme-initiated catalytic mechanism of the maize lipoxgyenase-1 and reveals that a substrate molecule serves as a hydrogen atom donor in its enzyme-initiated catalysis.
Rice proteomics: Ending phase I and the beginning of phase II
Agrawal, Ganesh Kumar,Jwa, Nam-Soo,Rakwal, Randeep WILEY-VCH Verlag 2009 Proteomics Vol.9 No.4
<P>Rice is a critically important food crop plant on our planet. It is also an excellent model plant for cereal crops, and now in position to serve as a reference plant for biofuel production. Proteomics study of rice therefore is crucial to better understand “rice” as a whole. Rice proteomics has moved well beyond the initial proteome analysis in the early to late 1990s. Since the year 2000, numerous proteomic studies have been performed in rice during growth and development and against a wide variety of environmental factors. These proteomic investigations have established the high-resolution 2-D reference gels of rice tissues, organs, and organelle under normal and adverse (stressed) conditions by optimizing suitable, reproducible systems for gel, and MS-based proteomic techniques, which “rejuvenated” the rice proteome field. This constituted the “phase I” in rice proteomics, and resulted in rice being labeled as the “cornerstone” of cereal food crop proteomes. Now, we are in position to state that rice proteomics today marks the “beginning of phase II”. This is due to the fact that rice researchers are capable of digging deeper into the rice proteome, mapping PTMs (in particular reversible protein phosphorylation), performing inter- and intra-species comparisons, integrating proteomics data with other “omic” technologies-generated data, and probing the functional aspect of individual proteins. These advancements and their impact on the future of rice proteomics are the focus of this review.</P>