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"Cooke, David"
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Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen
Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.
Journal Article
Interiors : the greatest rooms of the century
Contains over 400 global interiors organized by designer from A to Z. It features exquisite residential spaces conceived by design professionals, style icons and influencers, couturiers, artists, and film stars.--Adapted from insert.
Book
Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs
In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.
Journal Article
The World War I book
Combining authoritative, exciting text and bold images, The World War I Book explores the historical background of the war, its causes, all of the key events across the major theatres of conflict, and its aftermath. Using the original, graphic-led approach of the series, entries profile more than 90 of the key events during and surrounding the conflict -- from the growing tensions between Europe's major powers to the assassination of Archduke Franz Ferdinand, the German invasion of Belgium, the endless slaughter in the trenches, the American entry into the war, the Russian Revolution, the Armistice, and the creation of the League of Nations.
BOOK
Lithological and Hydrothermal Alteration Mapping of Epithermal, Porphyry and Tourmaline Breccia Districts in the Argentine Andes Using ASTER Imagery
The area of interest is located on the eastern flank of the Andean Cordillera, San Juan province, Argentina. The 3600 km2 area is characterized by Siluro-Devonian to Neogene sedimentary and igneous rocks and unconsolidated Quaternary sediments. Epithermal, porphyry-related, and magmatic-hydrothermal breccia-hosted ore deposits, common in this part of the Frontal Cordillera, are associated with various types of hydrothermal alteration assemblages. Kaolinite – alunite-rich argillic, quartz – illite-rich phyllic, epidote – chlorite – calcite-rich propylitic and silicic are the most common hydrothermal alteration assemblages in the study area. VNIR, SWIR and TIR ASTER data were used to characterize geological features on a portion of the Frontal Cordillera. Red-green-blue band combinations, band ratios, logical operations, mineral indices and principal component analysis were applied to successfully identify rock types and hydrothermal alteration zones in the study area. These techniques were used to enhance geological features to contrast different lithologies and zones with high concentrations of argillic, phyllic, propylitic alteration mineral assemblages and silicic altered rocks. Alteration minerals detected with portable short-wave infrared spectrometry in hand specimens confirmed the capability of ASTER to identify hydrothermal alteration assemblages. The results from field control areas confirmed the presence of those minerals in the areas classified by ASTER processing techniques and allowed mapping the same mineralogy where pixels had similar information. The current study proved ASTER processing techniques to be valuable mapping tools for geological reconnaissance of a large area of the Argentinean Frontal Cordillera, providing preliminary lithologic and hydrothermal alteration maps that are accurate as well as cost and time effective.
Journal Article
Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation
The considerable economic and social impact of the oomycete genus
Phytophthora
is well known. In response to evidence that all downy mildews (DMs) reside phylogenetically within
Phytophthora
, rendering
Phytophthora
paraphyletic, a proposal has been made to split the genus into multiple new genera. We have reviewed the status of the genus and its relationship to the DMs. Despite a substantial increase in the number of described species and improvements in molecular phylogeny the
Phytophthora
clade structure has remained stable since first demonstrated in 2000. Currently some 200 species are distributed across twelve major clades in a relatively tight monophyletic cluster. In our assessment of 196 species for twenty morphological and behavioural criteria the clades show good biological cohesion. Saprotrophy, necrotrophy and hemi-biotrophy of woody and non-woody roots, stems and foliage occurs across the clades. Phylogenetically less related clades often show strong phenotypic and behavioural similarities and no one clade or group of clades shows the synapomorphies that might justify a unique generic status. We propose the clades arose from the migration and worldwide radiation ~ 140 Mya (million years ago) of an ancestral Gondwanan
Phytophthora
population, resulting in geographic isolation and clade divergence through drift on the diverging continents combined with adaptation to local hosts, climatic zones and habitats. The extraordinary flexibility of the genus may account for its global ‘success’. The 20 genera of the obligately biotrophic, angiosperm-foliage specialised DMs evolved from
Phytophthora
at least twice via convergent evolution, making the DMs as a group polyphyletic and
Phytophthora
paraphyletic in cladistic terms. The long phylogenetic branches of the DMs indicate this occurred rather rapidly, via paraphyletic evolutionary ‘jumps’. Such paraphyly is common in successful organisms. The proposal to divide
Phytophthora
appears more a device to address the issue of the convergent evolution of the DMs than the structure of
Phytophthora
per se. We consider it non-Darwinian, putting the emphasis on the emergent groups (the DMs) rather than the progenitor (
Phytophthora
) and ignoring the evolutionary processes that gave rise to the divergence. Further, the generic concept currently applied to the DMs is narrower than that between some closely related
Phytophthora
species. Considering the biological and structural cohesion of
Phytophthora
, its historic and social impacts and its importance in scientific communication and biosecurity protocol, we recommend that the current broad generic concept is retained by the scientific community.
Journal Article
Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes
Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan ’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli , Phytophthora mirabilis , and Phytophthora ipomoeae , as well as the interspecific hybrid Phytophthora andina . We did not find support for an Andean origin of P. infestans ; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.
Journal Article
How optical excitation controls the structure and properties of vanadium dioxide
We combine ultrafast electron diffraction and time-resolved terahertz spectroscopy measurements to link structure and electronic transport properties during the photoinduced insulator–metal transitions in vanadium dioxide. We determine the structure of the metastable monoclinic metal phase, which exhibits antiferroelectric charge order arising from a thermally activated, orbital-selective phase transition in the electron system. The relative contribution of the photoinduced monoclinic and rutile metals to the time-dependent and pump-fluence–dependent multiphase character of the film is established, as is the respective impact of these two distinct phase transitions on the observed changes in terahertz conductivity. Our results represent an important example of how light can control the properties of strongly correlated materials and demonstrate that multimodal experiments are essential when seeking a detailed connection between ultrafast changes in optical-electronic properties and lattice structure.
Journal Article
Mesopore quality determines the lifetime of hierarchically structured zeolite catalysts
Deactivation due to coking limits the lifetime of zeolite catalysts in the production of chemicals and fuels. Superior performance can be achieved through hierarchically structuring the zeolite porosity, yet no relation has been established between the mesopore architecture and the catalyst lifetime. Here we introduce a top-down demetallation strategy to locate mesopores in different regions of MFI-type crystals with identical bulk porous and acidic properties. In contrast, well-established bottom-up strategies as carbon templating and seed silanization fail to yield materials with matching characteristics. Advanced characterization tools capable of accurately discriminating the mesopore size, distribution and connectivity are applied to corroborate the concept of mesopore quality. Positron annihilation lifetime spectroscopy proves powerful to quantify the global connectivity of the intracrystalline pore network, which, as demonstrated in the conversions of methanol or of propanal to hydrocarbons, is closely linked to the lifetime of zeolite catalysts. The findings emphasize the need to aptly tailor hierarchical materials for maximal catalytic advantage.
Zeolite catalysts are industrially important, but may be deactivated by coking. Here, the authors demonstrate the effectiveness of top-down demetallation approaches in controlling mesopore formation, using a range of techniques to probe the resulting structures and assess the effects on catalyst lifetime.
Journal Article