A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

Review of Deep Time and the Texas High Plains: History and Geology by Paul H. Carlson

This brief book is a history of the Lubbock Lake Landmark site, a nationally recognized archeological site located on the Texas southern High Plains on the north side of the city of Lubbock. The location has been the subject of intense investigations by archaeologists since 1939. Paul H. Carlson, a noted author and professor of history at Texas Tech University, states that his purpose was to go back through what John McPhee called "deep time" to show how the Lubbock Lake location was formed and was used by humans through time. He accomplishes this in five chapters.

Centralized vs. Distributed Connection Management Schemes under Different Traffic Patterns in Wavelength-Convertible Optical Networks

Centralized and Distributed methods are two connection management schemes in wavelength convertible optical networks. In the earlier work, the centralized scheme is said to have lower network blocking probability than the distributed one. Hence, much of the previous work in connection management has focused on the comparison of different algorithms in only distributed scheme or in only centralized scheme. However, we believe that the network blocking probability of these two connection management schemes depends, to a great extent, on the network traffic patterns and reservation times. Our simulation results reveal that the performance improvement (in terms of blocking probability) of centralized method over distributed method is inversely proportional to the ratio of average connection interarrival time to reservation time. After that ratio increases beyond a threshold, those two connection management schemes yield almost the same blocking probability under the same network load. In this paper, we review the working procedure of distributed and centralized schemes, discuss the tradeoff between them, compare these two methods under different network traffic patterns via simulation and give our conclusion based on the simulation data.