The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map

Quasispecies Theory and the Behavior of RNA Viruses

A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity. This diversity allows a viral population to rapidly adapt to dynamic environments and evolve resistance to vaccines and antiviral drugs. For the last 30 years, quasispecies theory has provided a population-based framework for understanding RNA viral evolution. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. Here, we discuss basic principles of quasispecies theory and describe its relevance for our understanding of viral fitness, virulence, and antiviral therapeutic strategy

Effect of rainfall intensity on infiltration into partly saturated slopes

This paper describes the development of a model to analyse the rate of infiltration and run-off experienced by a partly saturated soil slope during rainfall. The paper first reviews some of the most popular infiltration models used in geotechnical analysis, and highlights some of the problems associated with their application. One particular model, the Horton Equation is extended to include rainfall intensity directly in its formulation. The new model is shown to predict infiltration responses, which agree with field measurements. In the final section the influence of the rainfall intensity and pattern of rainfall (variation of rainfall intensity) on the infiltration response of a soil is investigated using the new model.Other funderIarnród Éirean

Pre-informed consumers on a pre-adjusted menu had smaller nitrogen footprints during the N2013 conference, Kampala, than those on a conventional menu

International conferences are hotspots of food wastage and release of reactive nitrogen (Nr) into the environment, but there is limited data about extent of food wastage and food product-specific Nitrogen (N) Footprints of consumers from such conferences. This study was aimed at evaluating the impact of pre-information and pre-adjusted menu on food-product specific N Footprints of the 6th International Nitrogen (N2013) conference held in Kampala, Uganda (average of 140 participants). For comparison, we also computed N Footprints for a baseline conference held at the same venue (average of 180 participants). At N2013, the delegates, hotel management and chefs had been pre-informed about a pre-adjusted menu designed to substitute half of animal-based sources of protein with plant sources (demitarian diet). Average meat consumption (excluding eggs) during the N2013 conference was 118 g capita−1 day−1 on dry weight basis, while milk consumption (excluding powdered milk) was 75 g capita−1 day−1 (fresh weight basis). These values were smaller than those of the baseline conference where meat consumption (excluding eggs) averaged 234 g capita−1 day−1 on dry weight basis and milk consumption (excluding powdered milk) averaged 159 g capita−1 day−1 (fresh weight basis). The reduction in meat consumption during the N2013 conference was compensated for by eating more fruits (102 g capita−1 day−1) and vegetables (45 g capita−1 day−1) than during the baseline conference (69 and 33 g capita−1 day−1, respectively). Overall, the Nitrogen Footprint for the N2013 conference was 97 g N capita−1 day−1, representing a reduction of 40% compared with the baseline conference of 160 g N capita−1 day−1. The Nitrogen Footprint for the N2013 conference would have been even lower, had it not been for over-supply beyond demand that left a substantial amount of food wasted. We conclude that pre-information and a pre-adjusted menu with clear guidelines to actors in food procurement, preparation and consumption are critical to mitigating food wastage from international conferences. The experience demonstrates how a conference approach to cutting down Nr consumption simultaneously helps raise awareness, while allowing delegates to reduce their N footprints with environmental and health benefits

(Ground) ice in the proglacial zone

In mid-latitude mountains, most of the valley glaciers currently experience distinct and enhanced volume and area loss. In parallel with the glacier retreat, the related proglacial areas enlarge, leaving unconsolidated sediments and ground ice of different origins and thus forming a transitional landscape, as developing from a glacial to a non-glacial environment. The erosion, transport and accumulation of sediment in these proglacial areas are characterized by high spatio-temporal dynamics, which are typically highest in the direct glacier forefield and become more inactive with increasing distance to the glacier front. Glacial, periglacial, fluvial and gravitational processes occur and highly interact in space and time. The glacial history of recently deglaciated zones influences the complex thermal regime of the subsurface and determines the current ground ice occurrence. Besides the glacio-fluvial processes, low-temperature conditions, as well as the occurrence of ground ice, are the most effective drivers for geomorphic dynamics and related landform evolution in these proglacial areas. A deeper knowledge of ongoing processes as well as of the amounts of sediment and ground ice is decisive to assess the availability of unconsolidated sediment for potential hazardous processes (e.g. debris flows) and the availability of water from ground ice bodies. There is an increasing need for high-resolution data (e.g. repeated topographic data) of proglacial areas as well as the systematic monitoring of these environments. Keywords Ground ice Dead ice Permafrost Rockglaciers Geophysical measurement