• Genomics & Informatics
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• 제7권2호
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• Current Research on Agriculture and Life Sciences
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• 제31권1호
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• pp.30-37
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• 2013

Bacillus subtilis and Bacillus amyloliquefaciens are closely related species that share a similar genomic background, and are both known to secrete large amounts of proteins directly into a medium. The extracellular proteomes of two strains of Bacillus subtilis and two strains of Bacillus amyloliquefaciens were compared by 2-D gel electrophoresis during the late exponential growth phase. The relative abundance of some minor protein spots varied among the four strains of Bacillus. Over 123 spots of extracellular proteins were visualized on the gel for B. subtilis CH 97, 68 spots for B. subtilis 3-5, 230 spots for B. amyloliquefaciens CH 51, and 60 spotsfor B. amyloliquefaciens 86-1. 2D gel electrophoresis images of the four Bacillus strains showed significantly different protein profiles. Consistent with the 2D gel electrophoretic analysis, most of the B. subtilis proteins differed from the proteases secreted by the B. amyloliquefaciensstrains. Among the proteins identified from B. subtilis, approximately 50% were cytoplasmic and 30% were canonically extracellular proteins. The secreted protein profiles for B. subtilis CH 97 and B. subtilis 3-5 were quite different, as were the profiles for B. amyloliquefaciens CH 51 and 86-1. The four proteomes also differed in the major protein composition. The B. subtilis CH 97 and B. amyloliquefaciens CH 51 proteomes both contained large amounts of secreted hydrolytic enzymes. Among the four strains, B. subtilis 3-5 secreted the least number of proteins. Therefore, even closely related bacteria in terms of genomic sequences can still have significant differences in their physiology and proteome layout.

• Journal of Korean Neurosurgical Society
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• 제48권1호
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• pp.8-13
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• 2010

Objective : The etiology and pathogenesis of moyamoya disease remain unclear. Furthermore, the definitive diagnostic protein-biomarkers for moyamoya disease are still unknown. The present study analyzed serum proteomes from normal controls and moyamoya patients to identify novel serological biomarkers for diagnosing moyamoya disease. Methods : We compared the two-dimensional electrophoresis patterns of sera from moyamoya disease patients and normal controls and identified the differentially-expressed spots by matrix-assisted laser desorption/ionization-time-of flight mass spectrometry and electrospray ionization quadruple time-of-flight mass spectrometry. Results : We found and analyzed 22 differently-expressed proteomes. Two proteins were up-regulated. Twenty proteins were down-regulated. Complement C1 inhibitor protein and apolipoprotein C-III showed predominantly changed expressions (complement C1 inhibitor protein averaged a 7.23-fold expression in moyamoya patients as compared to controls, while apolipoprotein C-III averaged a 0.066-fold expression). Conclusion : Although our study had a small sample size, our proteomic data provide serologic clue proteins for understanding moyamoya disease.

• 유전체소식지
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• 제6권4호
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• pp.14-22
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• 2006

• Journal of Plant Biotechnology
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• 제47권4호
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• pp.273-282
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• 2020

In Vietnam, Celastrus hindsii Benth, a medicinal plant rich in secondary metabolites, has been used to alleviate distress caused by ulcers, tumors, and inflammation for generations. The occurrence of two phenotypes, Broad Leaf (BL) and Narrow Leaf (NL), has raised questions about the selection of appropriate varieties for conservation and crop improvement to enhance medicinal properties. This study examined molecular differences in C. hindsii by comparing protein profiles between the NL and BL types using 2D-PAGE and MS. Peptide sequences and proteins were identified by matching MS data against the MSPnr100 databases and verified using the MultiIdent tool on ExPASy and the Blast2GO software. Our results revealed notable variations in protein abundance between the NL and BL proteomes. Selected proteins were confidently identified from 12 protein spots, thereby highlighting the molecular variation between NL and BL proteomes. Upregulated proteins in BL were found to be associated with flavonoid and amino acid biosynthesis as well as nuclease metabolism, which probably attributed to the intraspecific variations. Several bioactive proteins identified in this study can have applications in cancer therapeutics. Therefore, the BL phenotype characterized by healthier external morphological features has higher levels of bioactive compounds and could be better suited for medicinal use.

• Journal of Microbiology and Biotechnology
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• 제22권4호
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• pp.470-478
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• 2012

Recent genome comparisons of E. coli B and K-12 strains have indicated that the makeup of the cell envelopes in these two strains is quite different. Therefore, we analyzed and compared the envelope proteomes of E. coli BL21(DE3) and MG1655. A total of 165 protein spots, including 62 nonredundant proteins, were unambiguously identified by two-dimensional gel electrophoresis and mass spectrometry. Of these, 43 proteins were conserved between the two strains, whereas 4 and 16 strain-specific proteins were identified only in E. coli BL21(DE3) and MG1655, respectively. Additionally, 24 proteins showed more than 2-fold differences in intensities between the B and K-12 strains. The reference envelope proteome maps showed that E. coli envelope mainly contained channel proteins and lipoproteins. Interesting proteomic observations between the two strains were as follows: (i) B produced more OmpF porin with a larger pore size than K-12, indicating an increase in the membrane permeability; (ii) B produced higher amounts of lipoproteins, which facilitates the assembly of outer membrane ${\beta}$-barrel proteins; and (iii) motility- (FliC) and chemotaxis-related proteins (CheA and CheW) were detected only in K-12, which showed that E. coli B is restricted with regard to migration under unfavorable conditions. These differences may influence the permeability and integrity of the cell envelope, showing that E. coli B may be more susceptible than K-12 to certain stress conditions. Thus, these findings suggest that E. coli K-12 and its derivatives will be more favorable strains in certain biotechnological applications, such as cell surface display or membrane engineering studies.

• Molecules and Cells
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• 제40권4호
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• pp.243-253
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• 2017

Eukaryotic cilia are organelles that project from the surface of cells to fulfill motility and sensory functions. In vertebrates, the functions of both motile and immotile cilia are critical for embryonic development and adult tissue homeostasis. Importantly, a multitude of human diseases is caused by abnormal cilia biogenesis and functions which rely on the compartmentalization of the cilium and the maintenance of its protein composition. The transition zone (TZ) is a specialized ciliary domain present at the base of the cilium and is part of a gate that controls protein entry and exit from this organelle. The relevance of the TZ is highlighted by the fact that several of its components are coded by ciliopathy genes. Here we review recent developments in the study of TZ proteomes, the mapping of individual components to the TZ structure and the establishment of the TZ as a lipid gate.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.746-749
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• 2003

Alignment of 2D-gel images of biological samples can visualize the difference of expression profiles and also inform us candidates of protein spots to be further analyzed. However, comparison of two proteome images between case and control does not always successfully identify differentially expressed proteins due to sample-to-sample variation. Because of poor reproducibility of 2D-gel electrophoresis, sample-by-sample variations and inconsistent electrophoresis conditions, multiple number of 2D-gel image must be processed to align each other to visualize the difference of expression profiles and to deduce the protein spots differentially expressed with reliability. Alignment of multiple 2D-Gel images and their clustering were carried out by applying various algorithms and statistical methods. In order to align multiple images, multiresolution-multilevel algorithm was found out to be suitable for fast alignment and for distorted images. Clustering of 12 different images implementing a k-means algorithm gives a phylogenetic tree of distance map of the proteomes. Microsoft Visual C++ was used to implement the algorithms in this work.

• Genomics & Informatics
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• 제10권2호
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• pp.74-80
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• 2012

Most genes are processed by alternative splicing for gene expression, resulting in the complexity of the transcriptome in eukaryotes. It allows a limited number of genes to encode various proteins with intricate functions. Alternative splicing is regulated by genetic mutations in cis-regulatory factors and epigenetic events. Furthermore, splicing events occur differently according to cell type, developmental stage, and various diseases, including cancer. Genome instability and flexible proteomes by alternative splicing could affect cancer cells to grow and survive, leading to metastasis. Cancer cells that are transformed by aberrant and uncontrolled mechanisms could produce alternative splicing to maintain and spread them continuously. Splicing variants in various cancers represent crucial roles for tumorigenesis. Taken together, the identification of alternative spliced variants as biomarkers to distinguish between normal and cancer cells could cast light on tumorigenesis.

• BMB Reports
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• 제37권1호
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• pp.133-138
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• 2004

Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular proteomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).