Mechanistic aspects of promoter binding and chain initiation by RNA polymerase

Summary The physicochemical properties of the interactions of RNA polymerase (RPase) with promoter and nonspecific DNA sequences have been investigated. These show that nonspecific binding is principally an ionic interaction and that promoter binding is more complex, involving nonionic interactions. Nonspecific binding has been shown to be very important in the promoter search, and one-dimensional diffusion can account for the rate at which RPase finds the promoter. Significant differences have been reported in the binding process for various promoters and in the effects of regulatory proteins. Further investigation of these differences will lead to a better understanding of the selectivity and regulation of the initiation process.The pathways of the initiation process have been outlined, by recent studies and considerable progress has been made in determining the rates of interconversion of the intermediate states. A number of questions remain about the detail of initiation and the effects of various parameters on the reactions. Of particular importance is the identification of the point at which the enzyme becomes truly processive. In addition, the step which is rate limiting has not been identified in either the productive or nonproductive process. The mechanistic features of the steps after bond formation are just beginning to yield to investigation.Use of substrate analogs with RPase has led to a picture of the polymerization site according to the ability of the enzyme to incorporate analogs. Base specificity appears to be determined primarily by interaction with the template rather than the enzyme, but the ribose moiety must interact with the site quite specifically. The orientation of the phosphate residues has been determined by NMR, which has also proved to be a valuable probe of the initiation site. At this site base specificity is resident in the enzyme and expressed through the interaction of the base and intrinsic metal, as shown by studies with the Cobalt substituted enzyme. In both initiation and polymerization, the reaction has been shown to proceed by inversion of configuration. Techniques similar to those used for initiation will probably be applied to the polymerization reaction as well, which has not recently received as much attention with respect to mechanism. Functional phenomena such as pausing make the polymerization process particularly promising for producing insight into RPase reactions.     

A MONTE CARLO SIMULATION OF CLONE GROWTH

A Monte Carlo simulation of clone growth is discussed from the point of view of clonal volume. It is shown that clone volume is a good representation of the number of cells per clone for a wide range of single cell growth equations. However, the rate at which the coefficient of variation in clonal volume approaches that of cell number per clone is strongly dependent upon the particular growth equation.     

Prevalence and intensity of Thelazia spp. (Nematoda: Thelazioidea) in a Musca autumnalis (Diptera: Muscidae) population from Central Alberta

A face fly (Musca autumnalis) population near Wetaskiwin, central Alberta, Canada, was sampled 9 times from 26 July to 29 September 1988 for the early larval stages of Thelazia spp. Of 426 female flies examined, 159 (37%) contained Thelazia spp. (almost exclusively T. skrjabini), with an average worm burden of 4.2 larvae per infected fly. Prevalence ranged from 17 to 56% over 9 collections. This is the first report of Thelazia skrjabini in flies from western North America and the highest Thelazia prevalence in face flies yet reported in North America. The face fly population was also parasitized by Heterotylenchus autumnalis, with a prevalence of 5.5%.     

The biology of pike, Esox lucius L., in a southern eutrophic lake

The biology of pike, Esox lucius L., in a southern productive lowland lake is described. Scales and opercular bones were difficult to read and interpret, and growth estimated had perforce to be based on scale readings. Growth of Slapton pike is average and intermediate between recorded extremes. Both male and female pike reached maximum condition in February, just prior to spawning. The population of pike of over 450 mm fork length in the lake was estimated at 870·6 ± 389·3 in 1975, and 950·4 ± 143.3 in 1976/77. This leads to the conclusion that the pike population has one of the highest biomasses per surface area of water ever recorded. Number of pike per unit area of surface was also high, despite the fact that a significant proportion of the population (fish under 450 mm) could not be adequately sampled. Mean instantaneous mortality rate was 0·53, and mean instantaneous survival rate was 0·59. The roach provided the main item of diet of the pike, with perch taken less readily. Immature pike ate a significant proportion of invertebrates, but roach was again a common feature of the diet of even small fish. Two spawning migrations were identified; at other times of the year, pike were non territorial. The majority of pike spawned in March. Fecundity of a sample of females was assessed. Overall sex ratio was 1:1.