The expression, purification and crystallization of the epsilon subunit of the F1 portion of the ATPase of Escherichia coli.

The epsilon subunit of the F0F1-ATPase from Escherichia coli has been expressed in E. coli as a fusion protein with glutathione S-transferase from the parasitic helminth Schistosoma japonicum. The epsilon subunit released by thrombin treatment of the purified fusion protein carried two amino acid changes, A1G and M2S, and was obtained in a yield of about five milligrams per litre of cultured cells. The two amino acid changes were shown not to affect function. The protein has been crystallized in a form suitable for X-ray diffraction structure analysis. The crystals are hexagonal, space group P6(1)22 (or P6(5)22), with a = b = 94.9 A, c = 57.1 A and gamma = 120 degrees. The diffraction from small crystals extends to at least 2.9 A resolution.     

Serologic evidence of a Rickettsia akari-like infection among wild-caught rodents in Orange County and humans in Los Angeles County, California.

We detected antibodies reactive with Rickettsia akari, the etiologic agent of rickettsialpox in humans and in 83 of 359 (23%) rodents belonging to several species, collected in Orange County, CA. Reciprocal antibody titers >1:16 to R. akari were detected in native mice and rats (Peromyscus maniculatus, P. eremicus, and Neotoma fuscipes) and in Old World mice and rats (Mus musculus, Rattus rattus, and R. norvegicus), representing the first time that antibodies reactive with this agent have been detected in four of these species and the first report of these antibodies in rodents and humans west of the Mississippi River. We then tested serum samples from individuals who used a free clinic in downtown Los Angeles and found that 25 of 299 (8%) of these individuals had antibody titers >1:64 to R. akari. Serologic evidence suggested that R. akari or a closely related rickettsia is prevalent among several rodent species at these localities and that infection spills over into certain segments of the human population. Isolation or molecular confirmation of the agent is needed to conclusively state that R. akari is the etiologic agent infecting these rodents.     

The influence of diet on the growth of Stenonema vicarium (Walker) (Ephemeroptera: Heptageniidae)

Laboratory studies compared the growth rate of Stenonema vicarium (Walker) nymphs on diets of detritus and natural stream periphyton. In three consecutive runs of the experiment, growth rates were consistently higher on periphyton (mean growth rate = 2.1% wet wt. d⁻¹) than detritus (mean = 1.8% wet wt. d⁻¹). The starting date of each run also significantly influenced growth rates. In each treatment growth rates generally decreased over the course of the 3 runs, and ca. one-half of the nymphs in the last run did not molt or grow. It appeared that growth of S. vicarium may be partially controlled by seasonal factors.     

Approximate matching of regular expressions

Given a sequenceA and regular expressionR, theapproximate regular expression matching problem is to find a sequence matchingR whose optimal alignment withA is the highest scoring of all such sequences. This paper develops an algorithm to solve the problem in timeO(MN), whereM andN are the lengths ofA andR. Thus, the time requirement is asymptotically no worse than for the simpler problem of aligning two fixed sequences. Our method is superior to an earlier algorithm by Wagner and Seiferas in several ways. First, it treats real-valued costs, in addition to integer costs, with no loss of asymptotic efficiency. Second, it requires onlyO(N) space to deliver just the score of the best alignment. Finally, its structure permits implementation techniques that make it extremely fast in practice. We extend the method to accommodate gap penalties, as required for typical applications in molecular biology, and further refine it to search for substrings ofA that strongly align with a sequence inR, as required for typical data base searches. We also show how to deliver an optimal alignment betweenA andR in onlyO(N+logM) space usingO(MN logM) time. Finally, anO(MN(M+N)+N ²logN) time algorithm is presented for alignment scoring schemes where the cost of a gap is an arbitrary increasing function of its length.     

Expression and sequence analyses of serum amyloid A in the Syrian hamster

Reactive amyloidosis occurs during chronic inflammation and involves deposition of amyloid A (AA) fibrils in many organs. Amyloid A is derived by proteolysis from serum amyloid A component (SAA), a major acute-phase reactant in many species. Since spontaneous amyloidosis occurs commonly in Syrian hamsters, we have studied the structure and expression of SAA genes during inflammation in these animals. Two cDNA clones and one genomic clone were sequenced, suggesting that Syrian hamster SAA is encoded by at least two genes. Hepatic mRNA analyses showed that SAA was inducible in many hamster organs during acute inflammation. These studies also demonstrated that SAA mRNA for one isotype is maximally expressed at a site of local tissue damage.     

Dispersion population models discrete in time and continuous in space

We analyze a discrete-time model of populations that grow and disperse in separate phases. The growth phase is a nonlinear process that allows for the effects of local crowding. The dispersion phase is a linear process that distributes the population throughout its spatial habitat. Our study quantifies the issues of survival and extinction, the existence and stability of nontrivial steady states, and the comparison of various dispersion strategies. Our results show that all of these issues are tied to the global nature of various model parameters. The extreme strategies of staying-in place and going-everywhere-uniformly are compared numerically to diffusion strategies in various contexts. We approach the mathematical analysis of our model from a functional analysis and an operator theory point of view. We use recent results from the theory of positive operators in Banach lattices.