Fast protonation of adenosine and of its radical anion formed by hydrated electron attack; a nanosecond optical and dc-conductivity pulse radiolysis study

The study of the reaction of the hydrated electron with adenosine by optical and dc-conductivity pulse radiolysis on nano- and microsecond timescales has been carried out in an attempt to answer the question whether the electron adduct radical becomes protonated or not. The following conclusions have been reached: (1) the reaction of the hydrated electron with adenosine is followed by a water-mediated protonation, which must be complete with 5 ns; (2) no spectral indication of a further protonation of the protonated electron adduct of adenosine of 2'-deoxyadenosine has been found between 40 and 5000 ns; (3) the equilibrium reaction between radiation produced H3O+ and adenosine with a pKa of 3.5 plays an important role in the kinetics of the conductivity transients.     

An achiral (oligo)nucleotide analog

An achiral nucleotide analog based on barbituric acid has been synthesized. The analog, which is 5,5-di(2-phosphoethyl)barbituric acid, undergoes extensive oligomerization in aqueous solution, when activated, to produce pyrophosphate-linked chains. In contrast to a number of other bisphosphorylated nucleoside analogs which have been studied, the compound has little tendency to cyclize. The possible prebiotic implications are discussed. Correspondence to: AM. Schwartz     

GPS measurement error and resource selection functions in a fragmented landscape

Advances in technology have allowed ecologists to employ remote observations of individual organism's spatial location. These data are used to model species distributions and habitat associations, which inform conservation efforts and management plans. These data are not without error. To illustrate the consequences of not considering measurement error, I introduce measurement error to a habitat selection model, using three different distributions. I show how measurement error can confound inferences made about a hypothetical organism's true habitat selection. By simulating different initial strengths of selection I show the introduction of measurement error results in the largest reduction in habitat selection strength (from truth) for very selective individuals (habitat specialists). Not surprisingly, the inclusion of error in very weakly selective individuals (habitat generalists) can result in a switching from true selection to observed avoidance. Researchers need to be aware that, first, there is measurement error in remotely observed data, and second, a tradeoff occurs between measurement error and landscape fragmentation. Landscapes with a high degree of fragmentation require spatially accurate (low measurement error) data in order to make reliable estimates of habitat selection or species distribution. The results of this study are discussed in light of the conservation of species threatened by habitat fragmentation and the management suggestions arising from selection studies.     

A simplified purification method for the analysis of abscisic acid

A fast and convenient method is given for the purification of abscisic acid (ABA) in plant extracts. Using a dual pH elution system on Sep-Pak C18 reverse phase prepacked cartridges, abscisic acid appears in the third eluent (32% methanol pH 8.0). The cartridges can be regenerated for multiple reuse.     

Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes

Restriction enzymes produced by bacteria serve as a defense against invading bacteriophages, and so phages without other protection would be expected to undergo selection to eliminate recognition sites for these enzymes from their genomes. The observed frequencies of all restriction sites in the genomes of all completely sequenced DNA phages (T7, lambda, phi X174, G4, M13, f1, fd, and IKe) have been compared to expected frequencies derived from trinucleotide frequencies. Attention was focused on 6-base palindromes since they comprise the typical recognition sites for type II restriction enzymes. All of these coliphages, with the exception of lambda and G4, exhibit significant avoidance of the particular sequences that are enterobacterial restriction sites. As expected, the sequenced fraction of the genome of phi 29, a Bacillus subtilis phage, lacks Bacillus restriction sites. By contrast, the RNA phage MS2, several viruses that infect eukaryotes (EBV, adenovirus, papilloma, and SV40), and three mitochondrial genomes (human, mouse, and cow) were found not to lack restriction sites. Because the particular palindromes avoided correspond closely with the recognition sites for host enzymes and because other viruses and small genomes do not show this avoidance, it is concluded that the effect indeed results from natural selection.