María Arribas

Simultaneous isomerization of n-heptane and saturation of benzene over Pt/Beta catalysts: The influence of zeolite crystal size on product selectivity and sulfur resistance

Abstract In this work we show that decreasing the zeolite crystal size has a clear benefit on product selectivity and sulfur resistance of Pt/Beta catalysts during the simultaneous hydroisomerization of n-heptane and hydrogenation of benzene. The higher isomerization selectivity of the catalyst prepared from a nanocrystalline Beta zeolite can be ascribed to a faster diffusion of the iso-C7 products through the small crystallites preventing cracking reactions to occur, while the improved sulfur resistance can be related to a better dispersion of Pt owing to its higher surface area and mesoporosity.

Beneficial Effects of Population Bottlenecks in an RNA Virus Evolving at Increased Error Rate

RNA viruses replicate their genomes with a very high error rate and constitute highly heterogeneous mutant distributions similar to the molecular quasispecies introduced to explain the evolution of prebiotic replicators. The genetic information included in a quasispecies can only be faithfully transmitted below a critical error rate. When the error threshold is crossed, the population structure disorganizes, and it is substituted by a randomly distributed mutant spectrum. For viral quasispecies, the increase in error rate is associated with a decrease in specific infectivity that can lead to the extinction of the population. In contrast, a strong resistance to extinction has been observed in populations subjected to bottleneck events despite the increased accumulation of mutations. In the present study, we show that the mutagenic nucleoside analogue 5-azacytidine (AZC) is a potent mutagen for bacteriophage Qbeta. We have evaluated the effect of the increase in the replication error rate in populations of the bacteriophage Qbeta evolving either in liquid medium or during development of clonal populations in semisolid agar. Populations evolving in liquid medium in the presence of AZC were extinguished, while during plaque development in the presence of AZC, the virus experienced a significant increase in the replicative ability. Individual viruses isolated from preextinction populations could withstand high error rates during a number of plaque-to-plaque transfers. The response to mutagenesis is interpreted in the light of features of plaque development versus infections by free-moving virus particles and the distance to a mutation-selection equilibrium. The results suggest that clonal bacteriophage populations away from equilibrium derive replicative benefits from increased mutation rates. This is relevant to the application of lethal mutagenesis in vivo, in the case of viruses that encounter changing environments and are transmitted from cell to cell under conditions of limited diffusion that mimic the events taking place during plaque development.

Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus

BackgroundWhen beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine.ResultsThe analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics.ConclusionsInterference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.

Identification of mutations conferring 5-azacytidine resistance in bacteriophage Qβ

RNA virus replication takes place at a very high error rate, and additional increases in this parameter can produce the extinction of virus infectivity. Nevertheless, RNA viruses can adapt to conditions of increased mutagenesis, which demonstrates that selection of beneficial mutations is also possible at higher-than-standard error rates. In this study we have analysed the evolutionary behaviour of bacteriophage Qβ populations when replication proceeds in the presence of the mutagenic nucleoside analogue 5-azacytidine (AZC). We have obtained a virus population with reduced capacity to accumulate mutations in the presence of AZC and able to avoid extinction under conditions that are lethal for the wild type virus. Adapted populations fix a substitution in the readthrough protein gene and incorporate several mutations in the replicase gene that, despite having selective value, remain polymorphic after a large number of transfers in the presence of AZC.

Adaptation to fluctuating temperatures in an RNA virus is driven by the most stringent selective pressure.

The frequency of change in the selective pressures is one of the main factors driving evolution. It is generally accepted that constant environments select specialist organisms whereas changing environments favour generalists. The particular outcome achieved in either case also depends on the relative strength of the selective pressures and on the fitness costs of mutations across environments. RNA viruses are characterized by their high genetic diversity, which provides fast adaptation to environmental changes and helps them evade most antiviral treatments. Therefore, the study of the adaptive possibilities of RNA viruses is highly relevant for both basic and applied research. In this study we have evolved an RNA virus, the bacteriophage Qβ, under three different temperatures that either were kept constant or alternated periodically. The populations obtained were analyzed at the phenotypic and the genotypic level to characterize the evolutionary process followed by the virus in each case and the amount of convergent genetic changes attained. Finally, we also investigated the influence of the pre-existent genetic diversity on adaptation to high temperature. The main conclusions that arise from our results are: i) under periodically changing temperature conditions, evolution of bacteriophage Qβ is driven by the most stringent selective pressure, ii) there is a high degree of evolutionary convergence between replicated populations and also among populations evolved at different temperatures, iii) there are mutations specific of a particular condition, and iv) adaptation to high temperatures in populations differing in their pre-existent genetic diversity takes place through the selection of a common set of mutations.

Bifunctional noble metal/zeolite catalysts for upgrading low-quality diesel fractions via selective opening of naphthenic rings

Current regulations for diesel fuels primarily involve severe reductions in the concentrations of sulfur and polyaromatics and a minimum cetane number (51 according to current EU standards). Low-quality distillate fractions, such as the LCO fraction abundantly produced in fluid catalytic cracking (FCC) units, cannot be directly used as a blending diesel component due to their high polyaromatics content and consequently poor cetane number (CN < 25) and ignition quality. For such fractions, the increase in CN achieved by deep hydrogenation of the polyaromatics is not enough to meet the fuel specifications. Further upgrading through selective ring opening (SRO) of the produced naphthenes has been proposed as a suitable technological solution to bring the CN to the required values. As will be shown in this article, bifunctional catalysts based on noble metals loaded on acidic zeolites (and mesoporous molecular sieves) exhibit good prospects for the SRO of multi-ring naphthenes as those contained in hydrogenated distillates. Moreover, the high hydrogenation ability of the noble metal(s) makes these bifunctional catalysts suitable for the coupled hydrogenation of (poly)aromatics and the subsequent opening of the naphthenic rings. As will be illustrated here for model naphthenic and aromatic compounds, fine tuning of the hydrogenation and hydrogenolysis activities of the metallic function and the acidity and porous structure of the molecular sieve carrier becomes crucial for achieving optimum performance in SRO reactions. Finally, the relevant issue of the sulfur tolerance of these noble metal-based bifunctional SRO catalysts and their performance in the upgrading of sulfur-containing industrial feedstocks will also be addressed in this perspective article.

Impact of increased mutagenesis on adaptation to high temperature in bacteriophage Qβ.

RNA viruses replicate with very high error rates, which makes them more sensitive to additional increases in this parameter. This fact has inspired an antiviral strategy named lethal mutagenesis, which is based on the artificial increase of the error rate above a threshold incompatible with virus infectivity. A relevant issue concerning lethal mutagenesis is whether incomplete treatments might enhance the adaptive possibilities of viruses. We have addressed this question by subjecting an RNA virus, the bacteriophage Qβ, to different transmission regimes in the presence or the absence of sublethal concentrations of the mutagenic nucleoside analogue 5-azacytidine (AZC). Populations obtained were subsequently exposed to a non-optimal temperature and analyzed to determine their consensus sequences. Our results show that previously mutagenized populations rapidly fixed a specific set of mutations upon propagation at the new temperature, suggesting that the expansion of the mutant spectrum caused by AZC has an influence on later evolutionary behavior.

Differences in adaptive dynamics determine the success of virus variants that propagate together

Abstract Virus fitness is a complex parameter that results from the interaction of virus-specific characters (e.g. intracellular growth rate, adsorption rate, virion extracellular stability, and tolerance to mutations) with others that depend on the underlying fitness landscape and the internal structure of the whole population. Individual mutants usually have lower fitness values than the complex population from which they come from. When they are propagated and allowed to attain large population sizes for a sufficiently long time, they approach mutation-selection equilibrium with the concomitant fitness gains. The optimization process follows dynamics that vary among viruses, likely due to differences in any of the parameters that determine fitness values. As a consequence, when different mutants spread together, the number of generations experienced by each of them prior to co-propagation may determine its particular fate. In this work we attempt a clarification of the effect of different levels of population diversity in the outcome of competition dynamics. To this end, we analyze the behavior of two mutants of the RNA bacteriophage Qβ that co-propagate with the wild-type virus. When both competitor viruses are clonal, the mutants rapidly outcompete the wild type. However, the outcome in competitions performed with partially optimized virus populations depends on the distance of the competitors to their clonal origin. We also implement a theoretical population dynamics model that describes the evolution of a heterogeneous population of individuals, each characterized by a fitness value, subjected to subsequent cycles of replication and mutation. The experimental results are explained in the framework of our theoretical model under two non-excluding, likely complementary assumptions: (1) The relative advantage of both competitors changes as populations approach mutation-selection equilibrium, as a consequence of differences in their growth rates and (2) one of the competitors is more robust to mutations than the other. The main conclusion is that the nearness of an RNA virus population to mutation-selection equilibrium is a key factor determining the fate of particular mutants arising during replication.

Evolutionary adaptation of an RNA bacteriophage to the simultaneous increase in the within-host and extracellular temperatures

Bacteriophages are the most numerous biological entities on Earth. They are on the basis of most ecosystems, regulating the diversity and abundance of bacterial populations and contributing to the nutrient and energy cycles. Bacteriophages have two well differentiated phases in their life cycle, one extracellular, in which they behave as inert particles, and other one inside their hosts, where they replicate to give rise to a progeny. In both phases they are exposed to environmental conditions that often act as selective pressures that limit both their survival in the environment and their ability to replicate, two fitness traits that frequently cannot be optimised simultaneously. In this study we have analysed the evolutionary ability of an RNA bacteriophage, the bacteriophage Qβ, when it is confronted with a temperature increase that affects both the extracellular and the intracellular media. Our results show that Qβ can optimise its survivability when exposed to short-term high temperature extracellular heat shocks, as well as its replicative ability at higher-than-optimal temperature. Mutations responsible for simultaneous adaptation were the same as those selected when adaptation to each condition proceeded separately, showing the absence of important trade-offs between survival and reproduction in this virus.

Chapter 10:Application of Zeolites in the Production of Light Olefins and BTX Petrochemical Intermediates

In this chapter we present the main achievements in the development of catalysts based on microporous and mesoporous molecular sieves for the production of light olefins and BTX aromatics as the main basic building blocks for the manufacture of petrochemicals. The first part of the chapter covers the relevant aspects of processes aimed at producing light olefins from crude oil via catalytic cracking of gasoil and naphtha fractions, oxidative dehydrogenation (ODH) of short-chain alkanes, and from oil-alternative carbon sources such as natural gas or biomass as offered in methanol-to-olefins (MTO) processes. In the second part, we discuss the salient features of zeolites in the production of BTX aromatics via aromatization of LPG, naphtha reforming, and methane dehydroaromatization (MDA). Finally, given the industrial relevance of para-xylene as petrochemical intermediate, processes for its production from less valuable aromatics, including isomerization of xylenes and ethylbenzene, disproportionation/transalkylation of toluene, and alkylation of toluene with methanol, using zeolites with enhanced shape-selective properties are also reviewed. As highlighted in this chapter, catalysts relying on micro- and mesoporous molecular sieves are pivotal to improving the efficiency of already commercialized processes, and to the successful implementation of new technologies that are currently at different stages of development.