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Lee W.-P.,National Sun Yat - sen University | Tzou W.-S.,Institute of Bioscience and Biotechnology | Tzou W.-S.,National Taiwan Ocean University
Protein and Peptide Letters

In the yeast protein-protein interaction network, motif mode, a collection of motifs of special combinations of protein nodes annotated by the molecular function terms of the Gene Ontology, has revealed differences in the conservation constraints within the same topology. In this study, by employing an intelligent agent-based distributed computing method, we are able to discover motif modes in a fast and adaptive manner. Moreover, by focusing on the highly evolutionarily conserved motif modes belonging to the same biological function, we find a large downshift in the distance between nodes belonging to the same motif mode compared with the whole, suggesting that nodes with the same motif mode tend to congregate in a network. Several motif modes with a high conservation of the motif constituents were revealed, but from a new perspective, including that with a three-node motif mode engaged in the protein fate and that with three four-node motif modes involved in the genome maintenance, cellular organization, and transcription. The network motif modes discovered from this method can be linked to the wealth of biological data which require further elucidation with regard to biological functions. © 2010 Bentham Science Publishers Ltd. Source

Kim D.W.,Gangneung - Wonju National University | Lee S.H.,Lumieye Genetics Co. | Ku S.K.,Daegu Haany University | Lee J.E.,Daegu Haany University | And 10 more authors.
BMB Reports

As FK506 binding proteins (FK506BPs) are known to play an important role in the regulation of a variety of biological processes related to cell survival, this study was designed to examined the protective effects of FK506 binding protein 12 (FK506BP) on low humidity air flow induced dry eye in a rat model using transduced PEP-1-FK506BP. After the topical application of PEP-1-FK506BP, tear volumes were markedly increased and significant prevention of cornea damage was observed compared with dry eye rats. Further, immunohistochemical analysis demonstrated that PEP-1-FK506BP markedly prevented damage to the cornea, the bulbar conjunctiva, and the palpebral conjunctiva epithelial lining compared with dry eye rats. In addition, caspase-3 and PARP expression levels were found to be decreased. These results demonstrated that topical application of PEP-1-FK506BP significantly ameliorates dry eye injury in an animal model. Thus, we suggest that PEP-1-FK506BP can be developed as a new ophthalmic drop to treat dry eye diseases. © 2015 by the The Korean Society for Biochemistry and Molecular Biology. Source

Lee Y.-F.,Institute of Bioscience and Biotechnology | Nan F.-H.,National Taiwan Ocean University | Chen M.-J.,National Chiayi University | Wu H.-Y.,Institute of Bioscience and Biotechnology | And 3 more authors.
Analytical Methods

This paper describes the use of two types of bovine serum albumin (BSA)-capped 14.2 nm diameter gold nanoparticles (Au NPs) for the separate detection of mercury (Hg 2+) and lead (Pb 2+) ions in highly saline media. The BSA-capped Au NPs were stable in solutions containing up to 500 mM NaCl. Introduction of BSA to a solution of rhodamine 6G (R6G) and 3-mercaptopropionic acid (MPA)-modified Au NPs (R6G/MPA-Au NPs) provided a R6G/MPA-Au NP@BSA probe for the sensing of Hg 2+ ions. We also used BSA-capped Au NPs to detect Pb 2+ ions through a mechanism based on Pb 2+ ions accelerating the leaching rate of Au NPs in the presence of thiosulfate (S 2O 3 2-) and 2-mercaptoethanol (2-ME). The resulting deposition of Hg 2+ ions onto the Au NPs induced the release of R6G from the surfaces of the Au NPs, causing increased fluorescence from the R6G/MPA-Au NP@BSA solution. The Pb 2+ ions accelerated the dissolution of the 2-ME/S 2O 3 2--Au NPs@BSA into solution, leading to dramatic decreases in the absorption. These two Au NP-based probes were highly sensitive (LOD ≈ nM) and selective (over 100-fold against other metal ions) toward Hg 2+ or Pb 2+ ions. We validated the practicality of these two probes through analyses of seawater and urine samples. We also developed a simple gel-based membrane for removal and sensing of Hg 2+ or Pb 2+ in aqueous solutions. The agarose gel was used to trap BSA-Au NPs, leading to the preparation of a nanocomposite film of Au NPs@BSA-decorated agarose gel membrane (Au NPs@BSA/AGM) for removing Hg 2+ or Pb 2+ in solution. In addition, R6G/MPA-Au NP@BSA-trapped agarose gel membrane (R6G/MPA-Au NP@BSA/AGM) and 2-ME/S 2O 3 2--Au NPs@BSA/AGM allowed for the rapid and simple detection of Hg 2+ and Pb 2+, respectively. © 2012 The Royal Society of Chemistry. Source

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