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Year Month   
2018/11  Seminars
Seminar Title Tangling with Alzheimer's disease - discovering therapeutics and risk factors
Time Y/M/D 2018/11/1 11:00 ~ 12:00
Venue IBC R114
Speaker Dr. Min-Hao Kuo
Current Position Associate Professor, Department of Biochemistry and Molecular Biology, Michigan State University, USA
Host Dr. Rita P.-Y. Chen
Contact Ms. Nancy Liu
TEL 02-27855696#1165
E-mail liukchun@gate.sinica.edu.tw
 
Seminar Title DNA repair studies using lesion-containing oligonucleotides
Time Y/M/D 2018/11/5 11:00 ~ 12:00
Venue IBC R114
Speaker Dr. Junpei Yamamoto
Current Position Associate Professor, Department of Materials Engineering Science, Osaka University, Japan
Host Dr. Ming-Daw Tsai
Contact Ms. Nancy Liu
TEL 02-27855696#1165
E-mail liukchun@gate.sinica.edu.tw
Abstract DNA is spontaneously damaged by endogenous and exogenous factors such as reactive oxygen species, ultraviolet, ionizing radiations, metabolites of chemical substances, drugs, and so on, resulting in alteration of chemical structures of DNA. Such DNA damage is repaired by several specific DNA repair pathways, depending on the type of the lesions. For the in vitro biochemical studies, oligonucleotides containing DNA damage are indispensable. Chemical synthesis of oligonucleotides containing DNA damage is a powerful strategy that can provide a uniform, structure- and position-defined substrates without limitation of DNA lengths (up to ~100 nt) and sequence. In this talk, I would like to introduce our works on solid-phase synthesis of oligonucleotides containing UV-damaged DNA, i.e. cyclobutane pyrimidine dimers and pyrimidine(6–4)pyrimidone photoproducts (and its Dewar valence isomer), and its application to DNA repair by a Y-family polymerase and photolyases.-Dr. Junpei Yamamoto
 
Seminar Title Molecular dynamics simulations of aggregates of amyloid-β peptides
Time Y/M/D 2018/11/20 11:00 ~ 12:00
Venue IBC R114
Speaker Dr. Hisashi Okumura
Current Position Associate Professor, Institute for Molecular Science, National Institutes of Natural Sciences, Japan
Host Dr. Rita P.-Y. Chen
Contact Ms. Nancy Liu
TEL 02-27855696#1165
E-mail liukchun@gate.sinica.edu.tw
Abstract Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 40 serious human diseases. For example, amyloid-β peptides (Aβ) form amyloid fibrils that are associated with Alzheimer's disease. To investigate the oligomerization process of Aβ, we developed Hamiltonian replica-permutation molecular dynamics (MD) method and applied this method to Aβ in explicit water solvent [1, 2, 3, 4]. We will show the oligomerization process of Aβ. We also performed MD simulations of Aβ fibrils in explicit water. We discovered that molecular structure is different between two ends: The two β-sheets β1 and β2 are close to each other at the even end. On the other hand, at the odd end the Aβ fluctuates more and takes an open form, too [5]. Our theoretical prediction was proved by experiment after our MD simulations. We further performed nonequilibrium MD simulations with sinusoidal pressure and visualized this process with movies to describe the disruption of amyloid-β fibrils by ultrasonic cavitation. When the pressure is negative, a bubble was formed. When the pressure became positive, the bubble collapsed, and water molecules crashed against the hydrophilic residues to disrupt the amyloid [6].-Dr. Hisashi Okumura Reference 1.S. G. Itoh and H. Okumura, J. Comput. Chem. (2013) 34 2493. 2.S. G. Itoh and H. Okumura, J. Phys. Chem. B (2014) 118 11428. 3.S. G. Itoh and H. Okumura, J. Chem. Theory Comput. (2013) 9 570. 4.S. G. Itoh and H. Okumura, J. Phys. Chem. B (2016) 120 6555. 5.H. Okumura and S. G. Itoh, Sci. Rep. 6 (2016) 38422 (9 pages). 6.H. Okumura and S. G. Itoh, J. Am. Chem. Soc. 136 (2014) 10549-10552.
 
Seminar Title Bacterial lipid trafficking and outer membrane homeostasis
Time Y/M/D 2018/11/22 11:00 ~ 12:00
Venue IBC R114
Speaker Dr. Shu Sin Chng
Current Position Associate Professor, Department of Chemistry, National University of Singapore, Singapore
Host Dr. Yu-Ling Shih
Contact Ms. Nancy Liu
TEL 02-27855696#1165
E-mail liukchun@gate.sinica.edu.tw
Abstract Diderm bacteria, such as Gram-negative bacteria and mycobacteria, contain two lipid bilayers in their cellular envelopes – an inner membrane (IM) comprising mostly of phospholipids (PLs), and an outer membrane (OM) that additionally contains unique glycolipids (lipopolysaccharides (LPS) in Gram-negative bacteria and mycolic acids in mycobacteria). The OM is essential for growth in these organisms. Furthermore, the OM serves as an effective permeability barrier that in part allows Gram-negative bacteria and mycobacteria to survive in harsh environments, and renders them intrinsically resistant to many antibiotics. Despite the importance of the OMs in these bacteria, the processes that assemble these bilayers, in particular lipid transport, are not well understood. In this seminar, I will describe our work in understanding and characterizing lipid trafficking pathways in Escherichia coli and Mycobacterium smegmatis, and discuss how these systems function in maintaining lipid homeostasis in the OMs of these organisms.-Dr. Shu Sin Chng
 
Seminar Title Isoform-dependent regulation of endocytic trafficking, signaling and migration
Time Y/M/D 2018/11/29 11:00 ~ 12:00
Venue IBC R114
Speaker Dr. Ping-Hung Chen
Current Position Assistant Professor, Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taiwan
Host Dr. Guang-Chao Chen
Contact Ms. Nancy Liu
TEL 02-27855696#1165
E-mail liukchun@gate.sinica.edu.tw
 

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