The CAZyome of Phytophthora spp.: A comprehensive analysis of the gene complement coding for carbohydrate-active enzymes in species of the genus Phytophthora

<p>Abstract</p> <p>Background</p> <p>Enzymes involved in carbohydrate metabolism include Carbohydrate esterases (CE), Glycoside hydrolases (GH), Glycosyl transferases (GT), and Polysaccharide lyases (PL), commonly referred to as carbohydrate-active enzymes (CAZymes). The CE, GH, and PL superfamilies are also known as cell wall degrading enzymes (CWDE) due to their role in the disintegration of the plant cell wall by bacterial and fungal pathogens. In <it>Phytophthora infestans</it>, penetration of the plant cells occurs through a specialized hyphal structure called appressorium; however, it is likely that members of the genus <it>Phytophthora </it>also use CWDE for invasive growth because hyphal forces are below the level of tensile strength exhibited by the plant cell wall. Because information regarding the frequency and distribution of CAZyme coding genes in <it>Phytophthora </it>is currently unknown, we have scanned the genomes of <it>P. infestans, P. sojae</it>, and <it>P. ramorum </it>for the presence of CAZyme-coding genes using a homology-based approach and compared the gene collinearity in the three genomes. In addition, we have tested the expression of several genes coding for CE in cultures grown <it>in vitro</it>.</p> <p>Results</p> <p>We have found that <it>P. infestans, P. sojae </it>and <it>P. ramorum </it>contain a total of 435, 379, and 310 CAZy homologs; in each genome, most homologs belong to the GH superfamily. Most GH and PL homologs code for enzymes that hydrolyze substances present in the pectin layer forming the middle lamella of the plant cells. In addition, a significant number of CE homologs catalyzing the deacetylation of compounds characteristic of the plant cell cuticle were found. In general, a high degree of gene location conservation was observed, as indicated by the presence of sequential orthologous pairs in the three genomes. Such collinearity was frequently observed among members of the GH superfamily. On the other hand, the CE and PL superfamilies showed less collinearity for some of their putative members. Quantitative PCR experiments revealed that all genes are expressed in <it>P. infestans </it>when this pathogen grown <it>in vitro</it>. However, the levels of expression vary considerably and are lower than the expression levels observed for the constitutive control.</p> <p>Conclusions</p> <p>In conclusion, we have identified a highly complex set of CAZy homologs in the genomes of <it>P. infestans, P. sojae</it>, and <it>P. ramorum</it>, a significant number of which could play roles critical for pathogenicity, by participating in the degradation of the plant cell wall.</p

Rydberg Exciton-Polaritons in a Magnetic Field

We theoretically investigate exciton-polaritons in a two-dimensional (2D) semiconductor heterostructure, where a static magnetic field is applied perpendicular to the plane. To explore the interplay between magnetic field and a strong light-matter coupling, we employ a fully microscopic theory that explicitly incorporates electrons, holes and photons in a semiconductor microcavity. Furthermore, we exploit a mapping between the 2D harmonic oscillator and the 2D hydrogen atom that allows us to efficiently solve the problem numerically for the entire Rydberg series as well as for the ground-state exciton. In contrast to previous approaches, we can readily obtain the real-space exciton wave functions and we show how they shrink in size with increasing magnetic field, which mirrors their increasing interaction energy and oscillator strength. We compare our theory with recent experiments on exciton-polaritons in GaAs heterostructures in an external magnetic field and we find excellent agreement with the measured polariton energies. Crucially, we are able to capture the observed light-induced changes to the exciton in the regime of very strong light-matter coupling where a perturbative coupled oscillator description breaks down. Our work can guide future experimental efforts to engineer and control Rydberg excitons and exciton-polaritons in a range of 2D materials.Comment: 17 pages, 11 figure

Rydberg exciton-polaritons in a magnetic field

We theoretically investigate exciton-polaritons in a two-dimensional (2D) semiconductor heterostructure, where a static magnetic field is applied perpendicular to the plane. To explore the interplay between the magnetic field and strong light-matter coupling, we employ a fully microscopic theory that explicitly incorporates electrons, holes, and photons in a semiconductor microcavity. Furthermore, we exploit a mapping between the 2D harmonic oscillator and the 2D hydrogen atom that allows us to efficiently solve the problem numerically for the entire Rydberg series as well as for the ground-state exciton. In contrast to previous approaches, we can readily obtain the real-space exciton wave functions and we show how they shrink in size with the increasing magnetic field, which mirrors their increasing interaction energy and oscillator strength. We compare our theory with recent experiments on exciton-polaritons in GaAs heterostructures in an external magnetic field and we find excellent agreement with the measured polariton energies. Crucially, we are able to capture the observed light-induced changes to the exciton in the regime of very strong light-matter coupling where a perturbative coupled oscillator description breaks down. Our work can guide future experimental efforts to engineer and control Rydberg excitons and exciton-polaritons in a range of 2D material

'Against the World': Michael Field, female marriage and the aura of amateurism'

This article considers the case of Katherine Bradley and Edith Cooper, an aunt and niece who lived and wrote together as ‘Michael Field’ in the fin-de-siècle Aesthetic movement. Bradley’s bold statement that she and Cooper were ‘closer married’ than the Brownings forms the basis for a discussion of their partnership in terms of a ‘female marriage’, a union that is reflected, as I will argue, in the pages of their writings. However, Michael Field’s exclusively collaborative output, though extensive, was no guarantee for success. On the contrary, their case illustrates the notion, valid for most products of co-authorship, that the jointly written work is always surrounded by an aura of amateurism. Since collaboration defied the ingrained notion of the author as the solitary producer of his or her work, critics and readers have time and again attempted to ‘parse’ the collaboration by dissecting the co-authored work into its constituent halves, a treatment that the Fields too failed to escape

Breath analysis of COVID-19 patients in a tertiary UK hospital by optical spectrometry : the E-Nose CoVal Study

Throughout the SARS-CoV-2 pandemic, diagnostic technology played a crucial role in managing outbreaks on a national and global level. One diagnostic modality that has shown promise is breath analysis, due to its non-invasive nature and ability to give a rapid result. In this study, a portable FTIR (Fourier Transform Infra-Red) spectrometer was used to detect chemical components in the breath from Covid positive symptomatic and asymptomatic patients versus a control cohort of Covid negative patients. Eighty-five patients who had a nasopharyngeal polymerase chain reaction (PCR) test for the detection of SARS-CoV-2 within the last 5 days were recruited to the study (36 symptomatic PCR positive, 23 asymptomatic PCR positive and 26 asymptomatic PCR negative). Data analysis indicated significant difference between the groups, with SARS-CoV-2 present on PCR versus the negative PCR control group producing an area under the curve (AUC) of 0.87. Similar results were obtained comparing symptomatic versus control and asymptomatic versus control. The asymptomatic results were higher than the symptomatic (0.88 vs. 0.80 AUC). When analysing individual chemicals, we found ethanol, methanol and acetaldehyde were the most important, with higher concentrations in the COVID-19 group, with symptomatic patients being higher than asymptomatic patients. This study has shown that breath analysis can provide significant results that distinguish patients with or without COVID-19 disease/carriage

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus)

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P < 0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (FST = 0.021, P < 0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei’s Hs = 0.11, reference sites Nei’s Hs = 0.11). Still, pairwise FST: s between three, out of four, pairs of polluted-reference sites were significant. A FST-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P < 0.05 level and therefore indicated to be under divergent selection. When removing 13 FST-outlier loci, significant at the P < 0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment