First steps in experimental cancer evolution

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research.

Using experimental evolution to explore natural patterns between bacterial motility and resistance to bacteriophages

Resistance of bacteria to phages may be gained by alteration of surface proteins to which phages bind, a mechanism that is likely to be costly as these molecules typically have critical functions such as movement or nutrient uptake. To address this potential trade-off, we combine a systematic study of natural bacteria and phage populations with an experimental evolution approach. We compare motility, growth rate and susceptibility to local phages for 80 bacteria isolated from horse chestnut leaves and, contrary to expectation, find no negative association between resistance to phages and bacterial motility or growth rate. However, because correlational patterns (and their absence) are open to numerous interpretations, we test for any causal association between resistance to phages and bacterial motility using experimental evolution of a subset of bacteria in both the presence and absence of naturally associated phages. Again, we find no clear link between the acquisition of resistance and bacterial motility, suggesting that for these natural bacterial populations, phage-mediated selection is unlikely to shape bacterial motility, a key fitness trait for many bacteria in the phyllosphere. The agreement between the observed natural pattern and the experimental evolution results presented here demonstrates the power of this combined approach for testing evolutionary trade-offs.

Ethnobiology and the evolution of the human mind

An evolutionary perspective on human thought and behaviour indicates that we should expect to find universal systems of perception, classification, and decision-making regarding the natural world. It is the interaction between these evolved aspects of the human mind, the biodiversity of the natural world, and unique historical, social, and economic contexts within which individuals develop and act that gives rise to cultural diversity. The palaeoanthropological record also indicates that language is a recently evolved phenomenon. This suggests that linguistic approaches in ethnobiology are likely to provide only a partial understanding of how humans perceive, classify, and engage with the natural world.

Hybridization between Brassica napus and B. rapa on a national scale in the United Kingdom

Measures blocking hybridization would prevent or reduce biotic or environmental change caused by gene flow from genetically modified (GM) crops to wild relatives. The efficacy of any such measure depends on hybrid numbers within the legislative region over the life-span of the GM cultivar. We present a national assessment of hybridization between rapeseed (Brassica napus) and B. rapa from a combination of sources, including population surveys, remote sensing, pollen dispersal profiles, herbarium data, local Floras, and other floristic databases. Across the United Kingdom, we estimate that 32,000 hybrids form annually in waterside B. rapa populations, whereas the less abundant weedy populations contain 17,000 hybrids. These findings set targets for strategies to eliminate hybridization and represent the first step toward quantitative risk assessment on a national scale.

Bacterial evolution by genomic island transfer occurs via DNA transformation in planta

Our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of DNA that differ from core genomes and contain determinants of virulence [1, 2]. The acquisition of genomic islands (GIs) by horizontal gene transfer (HGT) is thought to have played a major role in microbial evolution. There are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. Loss of a GI from the bean pathogen Pseudomonas syringae pv. phaseolicola (Pph) is driven by exposure to the stress imposed by the plant's resistance response [3]. Here, we show that the complete episomal island, which carries pathogenicity genes including the effector avrPphB, transfers between strains of Pph by transformation in planta and inserts at a specific att site in the genome of the recipient. Our results show that the evolution of bacterial pathogens by HGT may be achieved via transformation, the simplest mechanism of DNA exchange. This process is activated by exposure to plant defenses, when the pathogen is in greatest need of acquiring new genetic traits to alleviate the antimicrobial stress imposed by plant innate immunity [4].

Evolution of microbial virulence: the benefits of stress

Although genome sequencing of microbial pathogens has shed light on the evolution of virulence, the drivers of the gain and loss of genes and of pathogenicity islands (gene clusters), which contribute to the emergence of new disease outbreaks, are unclear. Recent experiments with the bean pathogen Pseudomonas syringae pv. phaseolicola illustrate how exposure to resistance mechanisms acts as the driving force for genome reorganization. Here we argue that the antimicrobial conditions generated by host defences can accelerate the generation of genome rearrangements that provide selective advantages to the invading microbe. Similar exposure to environmental stress outside the host could also drive the horizontal gene transfer that has led to the evolution of pathogenicity towards both animals and plants.

Pseudomonas syringae pv. phaseolicola: from ‘has bean’ to supermodel

Pseudomonas syringae pv. phaseolicola causes halo blight of the common bean, Phaseolus vulgaris, worldwide and remains difficult to control. Races of the pathogen cause either disease symptoms or a resistant hypersensitive response on a series of differentially reacting bean cultivars. The molecular genetics of the interaction between P. syringae pv. phaseolicola and bean, and the evolution of bacterial virulence, have been investigated in depth and this research has led to important discoveries in the field of plant-microbe interactions. In this review, we discuss several of the areas of study that chart the rise of P. syringae pv. phaseolicola from a common pathogen of bean plants to a molecular plant-pathogen supermodel bacterium. Taxonomy: Bacteria; Proteobacteria, gamma subdivision; order Pseudomonadales; family Pseudomonadaceae; genus Pseudomonas; species Pseudomonas syringae; Genomospecies 2; pathogenic variety phaseolicola. Microbiological properties: Gram-negative, aerobic, motile, rod-shaped, 1.5 µm long, 0.7-1.2 µm in diameter, at least one polar flagellum, optimal temperatures for growth of 25-30 °C, oxidase negative, arginine dihydrolase negative, levan positive and elicits the hypersensitive response on tobacco. Host range: Major bacterial disease of common bean (Phaseolus vulgaris) in temperate regions and above medium altitudes in the tropics. Natural infections have been recorded on several other legume species, including all members of the tribe Phaseoleae with the exception of Desmodium spp. and Pisum sativum. Disease symptoms: Water-soaked lesions on leaves, pods, stems or petioles, that quickly develop greenish-yellow haloes on leaves at temperatures of less than 23 °C. Infected seeds may be symptomless, or have wrinkled or buttery-yellow patches on the seed coat. Seedling infection is recognized by general chlorosis, stunting and distortion of growth. Epidemiology: Seed borne and disseminated from exudation by water-splash and wind occurring during rainfall. Bacteria invade through wounds and natural openings (notably stomata). Weedy and cultivated alternative hosts may also harbour the bacterium. Disease control: Some measure of control is achieved with copper formulations and streptomycin. Pathogen-free seed and resistant cultivars are recommended. Useful websites: Pseudomonas-plant interaction http://www.pseudomonas-syringae.org/; PseudoDB http://xbase.bham.ac.uk/pseudodb/; Plant Associated and Environmental Microbes Database (PAMDB) http://genome.ppws.vt.edu/cgi-bin/MLST/home.pl; PseudoMLSA Database http://www.uib.es/microbiologiaBD/Welcome.html.

The European storm Kyrill in January 2007: synoptic evolution, meteorological impacts and some considerations with respect to climate change

The synoptic evolution and some meteorological impacts of the European winter storm Kyrill that swept across Western, Central, and Eastern Europe between 17 and 19 January 2007 are investigated. The intensity and large storm damage associated with Kyrill is explained based on synoptic and mesoscale environmental storm features, as well as on comparisons to previous storms. Kyrill appeared on weather maps over the US state of Arkansas about four days before it hit Europe. It underwent an explosive intensification over the Western North Atlantic Ocean while crossing a very intense zonal polar jet stream. A superposition of several favourable meteorological conditions west of the British Isles caused a further deepening of the storm when it started to affect Western Europe. Evidence is provided that a favourable alignment of three polar jet streaks and a dry air intrusion over the occlusion and cold fronts were causal factors in maintaining Kyrill's low pressure very far into Eastern Europe. Kyrill, like many other strong European winter storms, was embedded in a pre-existing, anomalously wide, north-south mean sea-level pressure (MSLP) gradient field. In addition to the range of gusts that might be expected from the synoptic-scale pressure field, mesoscale features associated with convective overturning at the cold front are suggested as the likely causes for the extremely damaging peak gusts observed at many lowland stations during the passage of Kyrill's cold front. Compared to other storms, Kyrill was by far not the most intense system in terms of core pressure and circulation anomaly. However, the system moved into a pre-existing strong MSLP gradient located over Central Europe which extended into Eastern Europe. This fact is considered determinant for the anomalously large area affected by Kyrill. Additionally, considerations of windiness in climate change simulations using two state-of-the-art regional climate models driven by ECHAM5 indicate that not only Central, but also Eastern Central Europe may be affected by higher surface wind speeds at the end of the 21st century. These changes are partially associated with the increased pressure gradient over Europe which is identified in the ECHAM5 simulations. Thus, with respect to the area affected, as well as to the synoptic and mesoscale storm features, it is proposed that Kyrill may serve as an interesting study case to assess future storm impacts.

Paralog re-emergence: a novel, historically contingent mechanism in the evolution of antimicrobial resistance

Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51, and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R. commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B, but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by horizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation.

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.

Interactive effect of floral abundance and semi-natural habitats on pollinators in field beans (Vicia faba)

Pollination services are economically important component of agricultural biodiversity which enhance the yield and quality of many crops. An understanding of the suitability of extant habitats for pollinating species is crucial for planning management actions to protect and manage these service providers. In a highly modified agricultural ecosystem, we tested the effect of different pollination treatments (open, autonomous self- and wind-pollination) on pod set, seed set, and seed weight in field beans (Vicia faba). We also investigated the effect of semi-natural habitats and flower abundance on pollinators of field beans. Pollinator sampling was undertaken in ten field bean fields along a gradient of habitat complexity; CORINE land cover classification was used to analyse the land use patterns between 500–3000 m around the sites. Total yield from open-pollination increased by 185% compared to autonomous self-pollination. There was positive interactive effect of local flower abundance and cover of semi-natural habitats on overall abundance of pollinators at 1500 and 2000 m, and abundance of bumblebees (Bombus spp.) at 1000–2000 m. In contrast, species richness of pollinators was only correlated with flower abundance and not with semi-natural habitats. We did not find a link between pod set from open-pollination and pollinator abundance, possibly due to variations in the growing conditions and pollinator communities between sites. We conclude that insect pollination is essential for optimal bean yields and therefore the maintenance of semi-natural habitats in agriculture-dominated landscapes should ensure stable and more efficient pollination services in field beans.

Ordinal judgements of depth in monocularly- and binocularly-viewed photographs of complex natural scenes

This study investigated the contribution of stereoscopic depth cues to the reliability of ordinal depth judgments in complex natural scenes. Participants viewed photographs of cluttered natural scenes, either monocularly or stereoscopically. On each trial, they judged which of two indicated points in the scene was closer in depth. We assessed the reliability of these judgments over repeated trials, and how well they correlated with the actual disparities of the points between the left and right eyes' views. The reliability of judgments increased as their depth separation increased, was higher when the points were on separate objects, and deteriorated for point pairs that were more widely separated in the image plane. Stereoscopic viewing improved sensitivity to depth for points on the same surface, but not for points on separate objects. Stereoscopic viewing thus provides depth information that is complementary to that available from monocular occlusion cues.

Does fertilizer type and method of application cause significant differences in essential oil yield and composition in rosemary (Rosmarinus officinalis L.)?

Organic fertilizers based on seaweed extract potentially have beneficial effects on many crop plants. Herewe investigate the impact of organic fertilizer on Rosmarinus officinalis measured by both yield and oilquality. Plants grown in a temperature-controlled greenhouse with a natural photoperiod and a controlledirrigation system were treated with seaweed fertilizer and an inorganic fertilizer of matching mineralcomposition but with no organic content. Treatments were either by spraying on to the foliage or wateringdirect to the compost. The essential oil was extracted by hydro-distillation with a Clevenger apparatusand analysed by gas-chromatography mass-spectrometry (GC–MS) and NMR. The chemical composi-tions of the plants were compared, and qualitative differences were found between fertilizer treatmentsand application methods. Thus sprayed seaweed fertilizer showed a significantly higher percentage of�-pinene, �-phellandrene, �-terpinene (monoterpenes) and 3-methylenecycloheptene than other treat-ments. Italicene, �-bisabolol (sesquiterpenes), �-thujene, and E-isocitral (monoterpenes) occurred insignificantly higher percentages for plants watered with the seaweed extract. Each was significantly dif-ferent to the inorganic fertilizer and to controls. The seaweed treatments caused a significant increasein oil amount and leaf area as compared with both inorganic treatments and the control regardless ofapplication method.