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.

Modifying Fences to Prevent Ungulate Use of Cropland and High-Value Pastures

Big game can damage crops and compete with livestock for valuable forage. Ranchers have reported their tolerance for big game would increase if the animals could be prevented from using key areas critical for spring livestock use. Likewise, some farmers have high value areas that must be protected. Fences provide the most consistent long term control compared to other deterrent methods, but are costly to erect. Many designs of woven wire and electric fences are currently used. Costs of erecting deer proof fencing could be greatly reduced if an existing fence could be modified instead of being replaced entirely. This study investigates the possibility of modifying existing fences to prohibit deer and elk crossings. Preliminary results indicate effective modifications can be made to existing fences for $1300- $3500 per mile for materials. Traditional complete construction of game fences cost more than $10,000 per mile. These fences may be used in lieu of compensation programs for ranchers. Also, if farmers and ranchers can keep big game out of important foraging areas, their tolerance for these animals on the rest of their property may greatly increase.