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.

Analyzing the ACRE Program

The new farm bill enacted by Congress in June 2008 includes a new revenue-based safety-net, the Average Crop Revenue Election (ACRE) Program, that will be available to producers beginning with the 2009 crop year. This analysis of the mechanics of ACRE and the relevant yields and prices to include in ACRE can help producers assess whether ACRE will be a good choice for this crop year and beyond.

Analyzing ACRE: Results for 2009 and Decisions for 2010

In 2009, agricultural producers participating in federal farm programs had to decide between staying in the existing Direct and Counter-Cyclical Program (DCP), and the new Average Crop Revenue Election Program (ACRE). If producers chose to keep the DCP, their farm income safety net is strictly tied to crop prices, with a combination of marketing loans, counter-cyclical payments and direct payments. If producers chose the new ACRE program, they changed their farm income safety net to a combination of price and revenue. The new ACRE component is based on revenue and replaces the counter-cyclical payment. The other parts of the safety net for ACRE participants remain tied to price, albeit at lower levels (direct payments reduced 20 percent, marketing loan rates reduced 30 percent).

Analyzing the ACRE Program

The new farm bill enacted by Congress in June 2008 includes a new revenue-based safety net, the Average Crop Revenue Election (ACRE) Program, that is available to producers beginning with the 2009 crop year. While final details and implementation of the program is yet to be announced by the USDA Farm Service Agency (FSA), an analysis of the mechanics of ACRE and the relevant yields and prices to include in ACRE can help producers assess whether ACRE will be a good choice for this crop year and beyond.

Making an ACRE Decision for 2009

The initial sign-up period for 2009 farm commodity programs and the choice between the new ACRE (Average Crop Revenue Election) program and the existing DCP (Direct and Counter-Cyclical Payment) program is quickly winding down. But as the current August 14 deadline approaches, producers know more and more about the potential safety net provided under the ACRE program, and have a better opportunity to analyze the economics of choosing ACRE versus the DCP program before visiting their USDA Farm Service Agency (FSA) office.

The Probe, Issue 210 – May/June 2000

NADCA Election in Progress Berryman Institute Announces 1999 Awards New Probe Editor to be Appointed: Larry Sullivan Ken Garner Retires Book Review: "Master Land Snaring: Canine and Coon Techniques, Effective in All Terrains." by Newt Sterling as told to Bob Noonan. 1999. 58 pages, illustrated. NPCA Gets New Name Lobster Plates: PETA (People for the Ethical Treatment of Animals) is fighting to prevent the return of the lobster to Maine's automobile license plates. Active Antis in the Northwest Animal Rights Violence on Increase Abstracts from the 6th Annual Conference of The Wildlife Society: Monitoring of Sin Nombre Hantavirus in deer mice of the Southwest, USA -- Robinson, Rhonda /., Kathryn D. Bennett, James R. Biggs, Timothy K. Haarmann, David C. Keller, and Mary E. Salisbury Predators in the classroom: A prickly paradigm for educators -- Rollins, Dale Trends in bat rabies in the U.S.: Shaping public health policy -- Rupprecht, Charles E., Sharon B. Messenger, and Jean S. Smith

The Probe, Issue 229 – July/August 2003

• Human/Wildlife Conflicts in Ethiopia -- Jeff Peter sen, Berryman Institute, Utah State University • NADCA 2004 Election • If the Norway rat (Rattus norvegicus) originated in Asia, why is this rat commonly called a Norway rat? • Book Review: When Raccoons Fall through Your Ceiling: The Handbook for Coexisting with Wildlife by Andrea Dawn Lopez. • Antarctic Scientist Dies in Seal Attack: Research scientist, Kirsty Brown was snorkelling in waters close to the Rothera Research Station as part of her studies when a Leopard seal pulled her under. • Giant Lizards Spreading Through the Gulf Coast: Cape Coral, Florida has become a haven for Nile monitor lizards, and their population, which continues to grow, has possibly reached the thousands in the Gulf Coast city. • Monkeypox Outbreak: An Alert • NADCA 2004 Ballot