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Comprehensive proteome analysis using quantitative proteomic technologies
Abu Hena Mostafa Kamal,최종순,조용구,김홍식,송범헌,이철원,우선희 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2
With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS),and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.
Diversity of Novel Glutenin Subunits in Bread Wheat (Triticum aestivum L.)
Abu Hena Mostafa Kamal,김기현,신광현,서형석,Hisashi Tsujimoto,허화영,최종순,Chul-Soo Park,우선희 한국식물학회 2009 Journal of Plant Biology Vol.52 No.6
Glutenin is a major determinant of baking performance and viscoelasticity, which are responsible for high-quality bread with a light porous crumb structure of a well-leavened loaf. We analyzed the diversity of glutenin genes from six wheat cultivars (Korean cvs. Keumgang and Jinpum, Chinese cvs. China-108 and Yeonnon-78, and Japanese cvs. Norin-61 and Kantou-107). Glutenins contain two types of isoforms such as high molecular weight glutenin subunit (HMW-GS) and low molecular weight glutenin subunit (LMW-GS). Glutenin fractions were extracted from wheat endosperm using Osborne solubility method. A total of 217 protein spots were separated on twodimensional gel electrophoresis with isoelectric focusing (wide range of pH 3–10). The proteins spots were subjected to tryptic digestion and identified by matrix assisted laser desorption/ionization–time of flight mass spectrometry. HMW-GS (43 isoforms) and LMW-GS (seven isoforms) are directly responsible for producing high-quality bread and noodles. Likewise, all the seed storage proteins are digested to provide nutrients for the embryo during seed germination and seedling growth. We identified the diverse glutenin subunits in wheat cultivars and compared the gluten isoforms among different wheat cultivars according to quality. This work gives an insight on the quality improvement in wheat crop.
Abu Hena Mostafa Kamal,Da-Eun Kim,Myeong-Won Oh,Young-Gu Cho,Hong-Sig Kim,Nobuyuki Uozumi,Jong-Soon Choi,Kun Cho,Sun-Hee Woo 한국작물학회 2010 한국작물학회 학술발표대회 논문집 Vol.2010 No.04
To better understanding the function of the luminal sub-organelles within the thylakoid network, we have carried out a systematical analysis and identification of the lumenal proteins in the thylakoid of wheat by using Tricine / 1D-PAGE, and LTQ-ESI-FTICR mass spectrometry followed by SWISS-PROT database searching. We isolation and fractionation these membrane from fully developed wheat leaves using a combination of differential and gradient centrifugation couple to high speed ultra-centrifuge. After collecting all proteins to eliminate possible same proteins, we estimated that there are 407 different proteins including chloroplast, chloroplast stroma, lumenal, and thylakoid membrane proteins excluding 20 proteins, which were identified in nucleus, cytoplasm and mitochondria. A combination of these three programs (PSORT, TargetP, and TMHMM) was found to provide a useful tool for evaluating chloroplast localization, transit peptide, transmembranes, and also could reveal possible alternative processing sites and dual targeting. Finally, we report also sub-cellular location specific protein interaction network using Cytoscape software, which provides further insight into the biochemical pathways of photosynthesis. The present work helps understanding photosynthesis process in wheat at the molecular level and provides a new overview of the biochemical machinery of the thylakoid in wheat.
Proteomics Analysis of Embryo and Endosperm from Mature Common Buckwheat Seeds
Abu Hena Mostafa Kamal,Ill-Dong Jang,Da-Eun Kim,Tatsuro Suzuki,Keun-Yook Chung,Jong-Soon Choi,이문순,박철호,박상언,Seong Hee Lee,정헌상,우선희 한국식물학회 2011 Journal of Plant Biology Vol.54 No.2
We used proteomics analysis to generate the profiles of proteins in the endosperm and embryo of common buckwheat grains. These differentially expressed proteins are potentially involved in seed metabolism. Extractions were done by trichloroacetic acid (TCA)precipitation. The resulting proteins were separated using SDS-PAGE coupled to LC-ESI-Q/TOF-MS/MS. This allowed us to detect and identify 67 proteins with isoforms,making this the most inclusive protein profile. The proteins were determined to be functionally involved in the central metabolic pathway of the seed, with metabolic interest being reflected in the occurrence of a tissue-specific enzyme balance. For a case in point, we found a tissuespecific and subcellular compartment-specific isoform of granule-bound starch synthase 1 in the chloroplast/amyloplast. This provided proteomic verification of the presence of a distinct regulatory mechanism for the biosynthesis of glycan and starch, which produce amylase and amylopectin. Furthermore, several previously characterized allergenic proteins such as 11S and 13S globulin seed storage protein were acknowledged in our seed samples, thus representing the potential for proteomics techniques that survey food sources for any incidence of allergens. This protein profile of common buckwheat grain is a new avenue for understanding its seed physiology in dormant stage as well as suggesting commercial applications for the buckwheat industry as buckwheat flour.
Mumta Hena Mustary,유버들,한민,양종한,Volodymyr V. Lysak,홍창희 대한전자공학회 2015 Journal of semiconductor technology and science Vol.15 No.4
Light enhancement of GaN based light emitting diodes (LEDs) have been investigated by texturing the top p-GaN surface. Nano-textured LEDs have been fabricated using self-assembled Ni nano mask during dry etching process. Experimental results were further compared with simulation data. Three types of LEDs were fabricated: Conventional (planar LED), Surface nano-porous (porous LED) and Surface nano-cluster (cluster LED). Compared to planar LED there were about 100% and 54% enhancement of light output power for porous and cluster LED respectively at an injection current of 20 mA. Moreover, simulation result showed consistency with experimental result. The increased probability of light scattering at the nano-textured GaN-air interface is the major reason for increasing the light extraction efficiency.