Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages

P>To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 1031 tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 x 104 to 6.5 x 106 ml-1, with one in 103 free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.

Breathable roofing membranes and bats: interactions, outcomes and predictions

In order to achieve sustainability it is necessary to balance the interactions between the built and natural environment. Biodiversity plays an important part towards sustainability within the built environment, especially as the construction industry comes under increasing pressure to take ecological concerns into account. Bats constitute an important component of urban biodiversity and several species are now highly dependent on buildings, making them particularly vulnerable to anthropogenic and environmental changes. As many buildings suitable for use as bat roosts age, they often require re-roofing and traditional bituminous roofing felts are frequently being replaced with breathable roofing membranes (BRMs), which are designed to reduce condensation. Whilst the current position of bats is better in many respects than 30 years ago, new building regulations and modern materials, may substantially reduce the viability of existing roosts. At the same time building regulations require that materials be fit for purpose and with anecdotal evidence that both bats and BRMs may experience problems when the two interact, it is important to know what roost characteristics are essential for house dwelling bats and how these and BRMs may be affected. This paper reviews current literature and knowledge and considers the possible ways in which bats and BRMs may interact, how this could affect existing bat roosts within buildings and the implications for BRM service life predictions and warranties. It concludes that in order for the construction and conservation sectors to work together in solving this issue, a set of clear guidelines should be developed for use on a national level.

Double jeopardy: the potential for problems when bats interact with breathable roofing membranes in the United Kingdom

In order to reduce environmental impacts and achieve sustainability, it is important to balance the interactions between the built and natural environment. The construction industry is becoming more aware of ecological concerns and the importance that biodiversity and maintenance ecosystem services has for sustainability. Bats constitute an important component of urban biodiversity and several species in the UK are highly dependent on buildings, making them particularly vulnerable to anthropogenic and environmental changes. Many buildings suitable for use as bat roosts often require re-roofing as they age and traditional bituminous roofing felts are frequently being replaced with breathable roofing membranes (BRMs). In the UK new building regulations and modern materials may substantially reduce the viability of existing roosts, yet at thesame time building regulations require that materials be fit for purpose. Reports suggest that both bats and BRMs may experience problems when the two interact. Such information makes it important to understand how house dwelling bats and BRMs may be affected. This paper considers the possible ways in which bats and BRMs may interact, how this could affect existing bat roosts within buildings and the implications for BRM service life predictions and warranties. Keywords –Breathable Roofing Membranes, Bats in Buildings, Material Deterioration, Sustainability, Conservation, Biodiversit

Multiple stationary solutions of an irradiated slab

A mathematical model describing the heat budget of an irradiated medium is introduced. The one-dimensional form of the equations and boundary conditions are presented and analysed. Heat transport at one face of the slab occurs by absorption (and reflection) of an incoming beam of short-wave radiation with a fraction of this radiation penetrating into the body of the slab, a diffusive heat flux in the slab and a prescribed incoming heat flux term. The other face of the slab is immersed in its own melt and is considered to be a free surface. Here, temperature continuity is prescribed and evolution of the surface is determined by a Stefan condition. These boundary conditions are flexible enough to describe a range of situations such as a laser shining on an opaque medium, or the natural environment of polar sea ice or lake ice. A two-stream radiation model is used which replaces the simple Beer’s law of radiation attenuation frequently used for semi-infinite domains. The stationary solutions of the governing equations are sought and it is found that there exists two possible stationary solutions for a given set of boundary conditions and a range of parameter choices. It is found that the existence of two stationary solutions is a direct result of the model of radiation absorption, due to its effect on the albedo of the medium. A linear stability analysis and numerical calculations indicate that where two stationary solutions exist, the solution corresponding to a larger thickness is always stable and the solution corresponding to a smaller thickness is unstable. Numerical simulations reveal that when there are two solutions, if the slab is thinner than the smaller stationary thickness it will melt completely, whereas if the slab is thicker than the smaller stationary thickness it will evolve toward the larger stationary thickness. These results indicate that other mechanisms (e.g. wave-induced agglomeration of crystals) are necessary to grow a slab from zero initial thickness in the parameter regime that yields two stationary solutions.

Refereed journal papers: practice and process

Research must be published, otherwise it will be lost. The most important papers for a researcher to produce are those published in international refereed journals. Good practice in writing papers is something that can be learned. The editorial process involves sending submitted papers to independent experts in the field, usually anonymously, and their comments inform the editor, who decides whether and how to progress with a paper. Much of this is as obscure to experienced researchers as it is to new ones. With forethought and planning, the success rate of getting submitted papers accepted for publication can be increased. Editors and publishers are generally very keen to help people improve their success rate.

Meteorology, air quality, and health in London: the ClearfLo project

The ClearfLo project provides integrated measurements of the meteorology, composition and particulate loading of London's urban atmosphere to improve predictive capability for air quality. Air quality and heat are strong health drivers and their accurate assessment and forecast are important in densely populated urban areas. However, the sources and processes leading to high concentrations of main pollutants such as ozone, nitrogen dioxide, and fine and coarse particulate matter in complex urban areas are not fully understood, limiting our ability to forecast air quality accurately. This paper introduces the ClearfLo project's interdisciplinary approach to investigate the processes leading to poor air quality and elevated temperatures. Within ClearfLo (www.clearflo.ac.uk), a large multi-institutional project funded by the UK Natural Environment Research Council (NERC), integrated measurements of meteorology, gaseous and particulate composition/loading within London's atmosphere were undertaken to understand the processes underlying poor air quality. Long-term measurement infrastructure installed at multiple levels (street and elevated), and at urban background, kerbside and rural locations were complemented with high-resolution numerical atmospheric simulations . Combining these (measurement/modeling) enhances understanding of seasonal variations in meteorology and composition together with the controlling processes. Two intensive observation periods (winter 2012 and summer Olympics 2012) focus upon the vertical structure and evolution of the urban boundary layer, chemical controls on nitrogen dioxide and ozone production, in particular the role of volatile organic compounds, and processes controlling the evolution, size, distribution and composition of particulate matter. The paper shows that mixing heights are deeper over London than in the rural surroundings and the seasonality of the urban boundary layer evolution controls when concentrations peak. The composition also reflects the seasonality of sources such as domestic burning and biogenic emissions.

The impacts of climate change across the globe: a multi-sectoral assessment

The overall global-scale consequences of climate change are dependent on the distribution of impacts across regions, and there are multiple dimensions to these impacts.This paper presents a global assessment of the potential impacts of climate change across several sectors, using a harmonised set of impacts models forced by the same climate and socio-economic scenarios. Indicators of impact cover the water resources, river and coastal flooding, agriculture, natural environment and built environment sectors. Impacts are assessed under four SRES socio-economic and emissions scenarios, and the effects of uncertainty in the projected pattern of climate change are incorporated by constructing climate scenarios from 21 global climate models. There is considerable uncertainty in projected regional impacts across the climate model scenarios, and coherent assessments of impacts across sectors and regions therefore must be based on each model pattern separately; using ensemble means, for example, reduces variability between sectors and indicators. An example narrative assessment is presented in the paper. Under this narrative approximately 1 billion people would be exposed to increased water resources stress, around 450 million people exposed to increased river flooding, and 1.3 million extra people would be flooded in coastal floods each year. Crop productivity would fall in most regions, and residential energy demands would be reduced in most regions because reduced heating demands would offset higher cooling demands. Most of the global impacts on water stress and flooding would be in Asia, but the proportional impacts in the Middle East North Africa region would be larger. By 2050 there are emerging differences in impact between different emissions and socio-economic scenarios even though the changes in temperature and sea level are similar, and these differences are greater in 2080. However, for all the indicators, the range in projected impacts between different climate models is considerably greater than the range between emissions and socio-economic scenarios.

Beyond the environmentalist's paradox and the debate on weak versus strong sustainability

Environmentalists generally argue that ecological damage will (eventually) lead to declines in human well-being. From this perspective, the recent introduction of the “environmentalist’s paradox” in BioScience by Raudsepp-Hearne and colleagues (2010) is particularly significant. In essence, Raudsepp-Hearne and colleagues (2010) claimed that although ecosystem services have been degraded, human well-being—paradoxically—has increased. In this article, we show that this debate is in fact rooted in a broader discussion on weak sustainability versus strong sustainability(the substitutability of human-made capital for natural capital). We warn against the reductive nature of focusing only on a stock–flow framework in which a natural-capital stock produces ecosystem services. Concretely, we recommend a holistic approach in which the complexity, irreversibility, uncertainty, and ethical predicaments intrinsic to the natural environment and its connections to humanity are also considered.

The land-atmosphere water flux in the tropics

Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from X decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr(-1), but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr(-1)) is considered in discussion on the use of flux data to validate and interpolate models.

LAURENCIA MARILZAE (CERAMIALES, RHODOPHYTA) FROM THE MEXICAN CARIBBEAN: A NEW RECORD FOR THE TROPICAL WESTERN ATLANTIC

Laurencia marilzae Gil-Rodriguez, Senties & MT Fujii is recorded for the first time for the tropical western Atlantic Ocean, occurring in Isla Mujeres, Quintana Roo, Mexican Caribbean. The specimens were collected in November 2008 and June 2009, growing epilithically in the lower intertidal zone on moderately exposed rocky shores. This species is characterized by its distinctive yellow-orange color in the natural environment, four pericentral cells per vegetative axial segment, the presence of secondary pit-connections between adjacent cortical cells, which are markedly projecting at the apices, and by the presence of one ""corp en cerise"" per cell in all cells of the thallus: cortical, medullary, including pericentral and axial cells, and trichoblasts. Morphological similarities and molecular data support the determination of this material as L. marilzae. The present study expands the geographical distribution of L. marilzae to the Caribbean Sea in the tropical Western Atlantic Ocean.

Rural property size drives patterns of upland and riparian forest retention in a tropical deforestation frontier

Deforestation in Brazilian Amazonia accounts for a disproportionate global scale fraction of both carbon emissions from biomass burning and biodiversity erosion through habitat loss. Here we use field- and remote-sensing data to examine the effects of private landholding size on the amount and type of forest cover retained within economically active rural properties in an aging southern Amazonian deforestation frontier. Data on both upland and riparian forest cover from a survey of 300 rural properties indicated that 49.4% (SD = 29.0%) of the total forest cover was maintained as of 2007. and that property size is a key regional-scale determinant of patterns of deforestation and land-use change. Small properties (<= 150 ha) retained a lower proportion of forest (20.7%, SD = 17.6) than did large properties (>150 ha; 55.6%, SD = 27.2). Generalized linear models showed that property size had a positive effect on remaining areas of both upland and total forest cover. Using a Landsat time-series, the age of first clear-cutting that could be mapped within the boundaries of each property had a negative effect on the proportion of upland, riparian, and total forest cover retained. Based on these data, we show contrasts in land-use strategies between smallholders and largeholders, as well as differences in compliance with legal requirements in relation to minimum forest cover set-asides within private landholdings. This suggests that property size structure must be explicitly considered in landscape-scale conservation planning initiatives guiding agro-pastoral frontier expansion into remaining areas of tropical forest. (C) 2010 Elsevier Ltd. All rights reserved.

Germination and survival of tetraspores of Kappaphycus alvarezii var. alvarezii (Solieriaceae, Rhodophyta) introduced in subtropical waters of Brazil

The carrageenophyte Kappaphycus alvarezii was introduced in 1995 and vegetatively propagated in Ubatuba, Sao Paulo State, Brazil, for the purpose of commercial cultivation. This species produces tetraspores mainly in the austral summer and fall. Tetraspore germination and survival were studied under different conditions of temperature, photon flux density, and photoperiod in the laboratory. Field experiments were also carried out. Although tetraspores of K. alvarezii germinated, they had low survival rates, most dying after 20 days. Recruitment of K. alvarezii tetraspores did not occur in experiments conducted in the field. The results indicated that the establishment of K. alvarezii via spore production in the natural environment of the south-east coast of Brazil is rather remote.

Rainforest Aerosols as Biogenic Nuclei of Clouds and Precipitation in the Amazon

The Amazon is one of the few continental regions where atmospheric aerosol particles and their effects on climate are not dominated by anthropogenic sources. During the wet season, the ambient conditions approach those of the pristine pre-industrial era. We show that the fine submicrometer particles accounting for most cloud condensation nuclei are predominantly composed of secondary organic material formed by oxidation of gaseous biogenic precursors. Supermicrometer particles, which are relevant as ice nuclei, consist mostly of primary biological material directly released from rainforest biota. The Amazon Basin appears to be a biogeochemical reactor, in which the biosphere and atmospheric photochemistry produce nuclei for clouds and precipitation sustaining the hydrological cycle. The prevailing regime of aerosol-cloud interactions in this natural environment is distinctly different from polluted regions.

Major- and trace-element composition of olivine, perovskite, clinopyroxene, Cr-Fe-Ti oxides, phlogopite and host kamafugites and kimberlites, Alto Paranaiba, Brazil

An integrated whole-rock petrographic and geochemical study has been carried out on kamafugites and kimberlites of the Late Cretaceous Alto Paranaiba igneous province, in Brazil, and their main minerals, olivine, clinopyroxene, perovskite, phlogopite, spinels and ilmenite. Perovskite is by far the dominant repository for light lanthanides, Nb, Ta, Th and U, and occasionally other elements, reaching concentrations up to 3.4 x 10(4) chondrite values for light lanthanides and 105 chondrite for Th. A very strong fractionation between light and heavy lanthanides (chondrite-normalized La/Yb from similar to 175 to similar to 2000) is also observed. This is likely the first comprehensive dataset on natural perovskite. Clinopyroxene has variable trace-element contents. likely due to the different position of this phase in the crystallization sequence; Sc reaches values as high as 200 ppm whereas the lanthanides show very variable enrichment in light over heavy REE, and commonly show a negative Eu anomaly. The olivine, phlogopite (and tetra-ferriphlogopite), Cr-Ti oxide and ilmenite are substantially barren minerals for lanthanides and most other trace elements, with the exception of Ba, Cs and Rb in mica, and V, Nb and Ta in ilmenite. Estimated mineral/whole-rock partition coefficients for lanthanides in perovskite are similar to previous determinations, though much higher than those calculated in experiments with synthetic compositions, testifying once more to the complex behavior of these elements in a natural environment. The enormous potential for exploitation of lanthanides, Th, U and high-field-strength elements in the Brazilian kamafugites, kimberlites and related rocks is clearly shown.

Predator Survival Tactics and Use of Habitat Cover in Rana Catesbeiana.

Predator-prey relationships are an important aspect of the natural world, and, because of its relevance to survival and natural selection, is an interesting relationship to study. In amphibian larvae, level of activity and landscape use are often what determines the survival as prey. I studied the anti-predator behavior of the North American bullfrog (Rana catesbeiana) tadpoles when presented with dragonfly (Aeshna) larvae, a known predator of tadpoles. Tadpoles were acclimated to four different habitats with varying degrees of habitat cover, and were transferred to a new habitat with a degree of cover equal to one of the acclimation tanks. A restrained predator, and thus its chemical cue, was introduced, and the behavior, particularly the use of the habitat cover to hide from the perceived risk of predation was observed. A significantly higher frequency of inactivity was found in tank I than in II and III, and inactivity followed a general trend of decreasing with increasing habitat cover. Difference in tank cover was not found to have a significant effect on swimming behavior, but did have a significant effect on hiding behavior, which increased with higher availability. Foraging decreased significantly with the addition of a predator, but did not vary significantly with different levels of cover. Hiding behavior and reducing conspicuous behaviors (like foraging) are probably the behaviors that afford the tadpole the most success at eluding a predator in their natural environment.