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.

Gray Whales (Eschrichtius robustus) Off Sakhalin Island, Russia: Seasonal And Annual Patterns Of Occurrence

The annual return, seasonal occurrence, and site fidelity of Korean-Okhotsk or western gray whales on their feeding grounds off northeastern Sakhalin Island, Russia, were assessed by boat-based photo-identification studies in 1994-1998. A total of 262 pods were observed, ranging in size from 1 to 9 whales with an overall mean of 2.0'. Sixty-nine whales were individually identified, and a majority of all whales (71.0%) were observed in multiple years. Annual sighting frequencies ranged from 1 to 18 d, with a mean of 5.4 d. The percentage of whales re-identified from previous years showed a continuous annual increase, reaching 87.0% by the end of the study. Time between first and last sighting of identified individuals within a given year was 1-85 d, with an overall mean of 40.6 d. Annual calf proportions ranged from 4.3% (1997) to 13.2% (1998), and mother-calf separations generally occurred between July and September. The seasonal site fidelity and annual return of whales to this part of the Okhotsk Sea emphasize its importance as a primary feeding ground for this endangered population.

Preliminary report on the photo-identification of blue whales off Isla de Chiloé, Chile from 2004 to 2006

Photo identification of individual blue whales during summer and autumn off the northwestern Isla de Chiloé, southern Chile, were collected from marine surveys conducted from 2004 to 2006. Re-sightings of individual whales both within and between years may provide evidence of residency and site fidelity by blue whales in the area. These records further document the importance of the northwestern Isla de Chiloé as a feeding area for blue whales. These records also highlight the necessity of further comparisons with photographic catalogues from other areas in southern Chile, off the northwestern coast of South America and the Pacific coast of Central America to better understand seasonal movements, distribution of individuals along the eastern South Pacific, and their wintering areas.

Ecology, stable isotopes, and management of grassland songbirds at National Park Service properties on the Great Plains

Grassland ecosystems have been severely reduced and grassland bird populations have experienced consistent declines. National Park Service (NPS) properties on the Great Plains provide breeding habitat for grassland songbirds, though little is known about the quality of this habitat. A short-term study on songbirds at three NPS properties complemented current monitoring, providing an among park comparison addressing grassland bird productivity and fidelity relative to NPS property size. During 2008-2009, I assessed avian species richness, and estimated bird density and grassland songbird nest success. Bird species richness was greatest at small and medium sites, while number of nesting obligate species was greatest at the large site. Species-specific densities varied among sites, with few grassland obligates occurring at all three sites. Nest success estimates for grassland obligates were highest at the small site and lower at the large site. Another method to quantify habitat quality is assessment of breeding site fidelity. Current extrinsic markers used in monitoring site fidelity are inadequate for small birds; stable isotope analyses provide an alternative. I compared two techniques for assigning stable isotope tissue origin and measured grassland songbird site fidelity. My method of assigning origin provided site-specific variances of expected stable isotope values, an improvement over the most commonly used method. Fidelity tended to be higher at the large site, which may indicate a more robust breeding community of grassland birds. The small size of two of my sites precluded large sample sizes and made strong inferences difficult. To quantify how scientists cope with weak inference, I conducted a literature review. Strong inference was rarely observed, and most authors of weak-inference papers provided specific management recommendations. I suggest that adaptive management is an ideal method to resolve uncertainty from weak inference. Managers should consider my results within the context of regional and global management and the extent to which their unit might aide songbird conservation.

Testudines - Turtles

Chelydra serpentine serpentine (Common Snapping Turtle). Nesting Behavior and Site Selection. On May 31, 2008, we observed a ca. 36 cm CL Chelydra serpentine serpentine in unexpected nesting circumstances. Observations were made from 0908 to 1027 h on clear day with ambient temp ca 24° C. The nest site near Longmont, Colorado, USA (40.1599528°N, 105.1259861°W; WGS84) was 4.3 m from a seasonal ditch running north-south to connect two lakes, one on either side of a busy road. The intriguing aspect of the nest location was that it was immediately adjacent to a heavily traveled concrete sidewalk that bordered a road with a high volume of traffic. The frequent foot traffic on the sidewalk and virtually constant vehicle traffic on the adjacent road did not deter the turtle from the particular nest location, even though virtually identical soils, gradients, and directional aspects were available equidistant from the ditch, but away from constant human activity.