Browsing by Author "Chen, Yi"

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In Vitro Selection and Characterization of a Novel Zn(II)-Dependent Phosphorothiolate Thiolesterase Ribozyme
(2012-01-10)
Wang, Tzu-Pin
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Su, Yu-Chih
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Chen, Yi
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Liou, Yi-Ming
;
Lin, Kun-Liang
Here we present the in vitro selection of a novel ribozyme specific for Zn(2+)-dependent catalysis on hydrolysis of a phosphorothiolate thiolester bond. The ribozyme, called the TW17 ribozyme, was evolved and selected from an artificial RNA pool covalently linked to a biotin-containing substrate through the phosphorothiolate thiolester bond. The secondary structure for the evolved ribozyme consisted of three major helices and three loops. Biochemical and chemical studies of ribozyme-catalyzed reaction products provided evidence that the ribozyme specifically catalyzes hydrolysis of the phosphorothiolate thiolester linkage. A successful ribozyme construct with active catalysis in trans further supported the determined ribozyme structure and indicated the potential of the ribozyme for multiple-substrate turnover. The ribozyme also requires Zn(2+) and Mg(2+) for maximal catalysis. The TW17 ribozyme, in the presence of Zn(2+) and Mg(2+), conferred a rate enhancement of at least S orders of magnitude when compared to the estimated rate of the uncatalyzed reaction. The ribozyme completely lost catalytic activity in the absence of Zn(2+), like Zn(2+)-dependent protein hydrolases. The discovery and characterization of the TW17 ribozyme suggest additional roles for Zn(2+) in ribozyme catalysts.
The Global Packing Number of a Fat-Tree Network
(2017-08-01)
Lo, Yuan-Hsun
;
Zhang, Yijin
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Chen, Yi
;
Fu, Hung-Lin
;
Wong, Wing Shing
Data centers play an important role in today's Internet development. Research to find scalable architecture and efficient routing algorithms for data center networks has gained popularity. The fat-tree architecture, which is essentially a folded version of a Clos network, has proved to be readily implementable and is scalable. In this paper, we investigate routing on a fat-tree network by deriving its global packing number and by presenting explicit algorithms for the construction of optimal, load-balanced routing solutions. Consider an optical network that employs wavelength division multiplexing in which every user node sets up a connection with every other user node. The global packing number is basically the number of wavelengths required by the network to support such a traffic load, under the restriction that each source-to-destination connection is assigned a wavelength that remains constant in the network. In mathematical terms, consider a bidirectional, simple graph, G and let N subset of V(G) be a set of nodes. A path system P of G with respect to N consists of |N|(|N|-1) directed paths, one path to connect each of the source-destination node pairs in N. The global packing number of a path system P, denoted by Phi(G, N, P), is the minimum integer k to guarantee the existence of a mapping phi : P -> {1, 2, . . . , k}, such that phi(P) not equal phi((P) over cap) if P and (P) over cap have common arc(s). The global packing number of (G, N), denoted by Phi (G, N), is defined to be the minimum Phi (G, N, P) among all possible path systems P. In additional to wavelength division optical networks, this number also carries significance for networks employing time division multiple access. In this paper, we compute by explicit route construction the global packing number of (T-n, N), where T-n denotes the topology of the n-ary fat-tree network, and N is considered to be the set of all edge switches or the set of all supported hosts. We show that the constructed routes are load-balanced and require minimal link capacity at all network links.