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     

Stromatolitic knobs in Storr's Lake (San Salvador,Bahamas): a model system for formation and alteration of laminae

The initial lamination in young, metabolically active Scytonema knobs developing in Storr's Lake (Bahamas) results from the iterative succession of two different stages of microbial growth at the top of this microbialite. Stage 1 is dominated by vertically oriented cyanobacterial filaments and is characterized by a high porosity of the fabric. Stage 2 shows a higher microbial density with the filaments oriented horizontally and with higher carbonate content. The more developed, dense microbial community associated with Stage 2 of the Scytonema knobs rapidly degrades extracellular organic matter (EOM) and coupled to this, precipitates carbonate. The initial nucleation forms high‐Mg calcite nanospheroids that progressively replace the EOM. No precipitation is observed within the thick sheath of the Scytonema filaments, possibly because of strong cross‐linking of calcium and EOM (forming EOM‐Ca‐EOM complexes), which renders Ca unavailable for carbonate nucleation (inhibition process). Eventually, organominerals precipitate and form an initial lamina through physicochemical and microbial processes, including high rates of photosynthetic activity that lead to ¹³C‐enriched DIC available for initial nucleation. As this lamina moves downward by the iterative production of new laminae at the top of the microbialite, increased heterotrophic activity further alters the initial mineral product at depth. Although some rare relic preservation of ‘Stage 1–Stage 2’ laminae in subfossil knobs exists, the very fine primary lamination is considerably altered and almost completely lost when the knobs develop into larger and more complex morphologies due to the increased accommodation space and related physicochemical and/or biological alteration. Despite considerable differences in microstructure, the emerging ecological model of community succession leading to laminae formation described here for the Scytonema knobs can be applied to the formation of coarse‐grained, open marine stromatolites. Therefore, both fine‐ and coarse‐grained extant stromatolites can be used as model systems to understand the formation of microbialites in the fossil record.     

Autoinducers extracted from microbial mats reveal a surprising diversity of N-acylhomoserine lactones (AHLs) and abundance changes that may relate to diel pH

Microbial mats are highly structured and diverse communities, and one of the earliest-known life assemblages. Mat bacteria interact within an environment marked by strong geochemical gradients and fluctuations. We examined natural mat systems for the presence of autoinducers involved in quorum sensing, a form of cell–cell communication. Our results revealed that a diverse array of N -acylhomoserine lactones (AHLs) including C₄- to C₁₄-AHLs, were identified from mat extracts using mass spectrometry (MS), with further confirmation by MS/MS-collision-induced dissociation (CID), and additions of external standards. Microelectrode measurements showed that mats exhibited diel pH fluctuations, ranging from alkaline (pH 9.4) during daytime (net photosynthesis) to acidic (pH 6.8) during darkness (net respiration/fermentation). Under laboratory conditions, AHLs having shorter acyl-chains were degraded within the time frame that daily alkaline pH (> 8.2) conditions exist in mats. Intensive sampling of mats after full day- or night-time incubations revealed that accumulations of extractable shorter-chain AHLs (e.g. C₈- and C₁₀-AHLs) were significantly ( P  < 0.001) diminished during daytime. Our study offers evidence that stabilities of AHLs under natural conditions may be influenced by the proximal extracellular environment. We further propose that the ancient periodicity of photosynthesis/respiration in mats may potentially drive a mechanism for diel differences in activities of certain autoinducers, and hence bacterial activities mediated through quorum sensing.     

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.