Genome sequences of six Phytophthora species threatening forest ecosystems

AbstractThe Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth.com/), we sequenced the genomes of six important Phytophthora species that are important invasive pathogens of trees and a serious threat to the international trade of forest products. This genomic data was used to develop highly sensitive and specific detection assays and for genome comparisons and to make evolutionary inferences and will be useful to the broader plant and tree health community. These WGS data have been deposited in the International Nucleotide Sequence Database Collaboration (DDBJ/ENA/GenBank) under the accession numbers AUPN01000000, AUVH01000000, AUWJ02000000, AUUF02000000, AWVV02000000 and AWVW02000000

Laser spectroscopy of NV- and NV0 colour centres in synthetic diamond

In this paper, we analyse the prospects for using nitrogen-vacancy centre (NV) containing diamond as a laser gain material by measuring its key laser related parameters. Synthetic chemical vapour deposition grown diamond samples with an NV concentration of ~1 ppm have been selected because of their relatively high NV concentration and low background absorption in comparison to other samples available to us. For the samples measured, the luminescence lifetimes of the NV- and NV0 centres were measured to be 8±1 ns and 20±1 ns respectively. The respective peak stimulated emission cross-sections were (3.6±0.1)×10-17 cm2 and (1.7±0.1)×10-17 cm2. These measurements were combined with absorption measurements to calculate the gain spectra for NV- and NV0 for differing inversion levels. Such calculations indicate that gains approaching those required for laser operation may be possible with one of the samples tested and for the NV- centre

Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR

Role of aetiology in the progression, regression, and parenchymal remodelling of liver disease: implications for liver biopsy interpretation

Clinicopathological concepts on acute and chronic liver disease have evolved rapidly during the last few years, with advances in general and specific treatment options and improved patient outcomes. The old paradigm of ‘irreversibility’ of cirrhosis had been challenged in major ways, and the validity of the usage of the term ‘cirrhosis’ has come into question. This paper addresses aetiology-based clinicopathological concepts and features that may deserve attention because they may determine disease outcome and, specifically, patterns of regression and remodelling. A variety of therapeutic interventions may influence remaining disease features after elimination of damaging agents (virus, alcohol, etc.), and determine the final clinical outcome including the risk of hepatocellular carcinoma (HCC). New concepts create new responsibilities and opportunities for the pathologist to contribute to the understanding of liver pathology and communicate this with clinical colleagues and researchers

Laser-related spectroscopic parameters of NV colour centres in diamond

One of the most common impurities in synthetic diamond is single substitutional nitrogen, which is incorporated in the diamond lattice substituting a carbon atom [1]. If the nitrogen is adjacent to a vacancy in the diamond lattice, it forms the nitrogen-vacancy (NV) colour centre (CC) [1]. The negatively charged state of this CC, NV-, is particularly well studied since its quantum properties are suitable for applications such as quantum information processing, single-photon sources and optical magnetometry [2]. NV CCs in the neutral state (NV0) are less widely studied. This CC exhibits broadband luminescence at slightly shorter wavelengths than NV-, and hence is also potentially of interest for tuneable and ultrafast visible laser applications. In this report, we present a detailed study of the laser-related spectroscopic properties of a diamond containing NV0 and NV- CCs

Bye-bye mummy: word comprehension in 9-month-old infants

From the little research that exists on the onset of word learning in infants under the age of 1 year, the evidence suggests an idiosyncratic comprehensive vocabulary is developing. To further this field, we tested 49 nine-month-old infants by pre-assessing their vocabularies using a UK version of the MacArthur-Bates Communicative Developmental Inventory. Intermodal preferential looking (IPL) was then used to examine word comprehension including: (a) words parents reported as understood, (b) words infants are expected to understand according to age-related frequency data, and (c) words parents had reported infants not to understand. Assuming parents are good assessors of their infant's early word knowledge, we expected a naming effect with IPL in condition (a), but not condition (c). As language research uses standard samples of words, we expected a discernible naming effect in condition (b). Results show clear IPL evidence of word comprehension for those words that parents reported their infants to understand (condition a). This agreement between methods demonstrates the usefulness of parental communicative developmental inventory in conjunction with IPL to assess infant's individual word knowledge. No naming effects were found for condition (c) and the lack of naming effects in (b) shows that pre-established word lists may not give a sufficiently clear picture of infant's true vocabulary – an important insight for researchers and practitioners alike

Feature biases in early word learning : network distinctiveness predicts age of acquisition

Do properties of a word’s features influence the order of its acquisition in early word learning? Combining the principles of mutual exclusivity and shape bias, the present work takes a network analysis approach to understanding how feature distinctiveness predicts the order of early word learning. Distance networks were built from nouns with edge lengths computed using various distance measures. Feature distinctiveness was computed as a distance measure, showing how far an object in a network is from other objects based on shared and non-shared features. Feature distinctiveness predicted order of acquisition across all measures; words that were further away from other words in the network space were learned earlier. The best distance measures were based only on non-shared features (object dissimilarity) and did not include shared features (object similarity). This indicates that shared features may play less of a role in early word learning than non-shared features. In addition, the strongest effects were found for visual form and surface features. Cluster analysis further revealed that this effect is a localized effect in the object feature space, where objects’ distances from their cluster centroid were inversely correlated with their age of acquisition. Together, these results suggest a role for feature distinctiveness in early word learning

Beyond "Cirrhosis" A Proposal From the International Liver Pathology Study Group

Cirrhosis is a moiphologic term that has been used for almost 200 years to denote the end stage of a variety of chronic liver diseases. The term implies a condition with adverse prognosis due to the well-known complications of portal hypertension, hepatocellular carcinoma, and liver failure. However, recent advances in the diagnosis and treatment of chronic liver diseases have changed the natural history of cirrhosis significantly. This consensus document by the International Liver Pathology Study Group challenges the usefulness of the word cirrhosis in modern medicine and suggests that this is an appropriate time to consider discontinuing the use of this term. The role of pathologists should evolve to the diagnosis of advanced stage of chronic liver disease, with emphasis on etiology, grade of activity, features suggestive of progression or regression, presence of other diseases, and risk factors for malignancy, within the perspective of an integrated clinicopathologic assessment

Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle