Surface Acoustic Waves Integrated with Solid-State Single Photon Sources and Superconducting Electronics

This thesis investigates the design and development of novel SAW devices combining strong piezoelectric and superconducting alloy materials with semiconductors hosting two classes of quantum emitters–self-assembled In(Ga)As quantum dots, and quantum emitters in h-BN and WSe2 layered materials. The aims of this research are to both understand the mechanism of the optomechanical coupling and engineer high-quality devices which push forward the state of the art of SAWs coupled to optically active quantum emitters

Molecular analysis of the early interaction between the grapevine flower and Botrytis cinerea reveals that prompt activation of specific host pathways leads to fungus quiescence

Grape quality and yield can be impaired by bunch rot, caused by the necrotrophic fungus Botrytis cinerea. Infection often occurs at flowering, and the pathogen stays quiescent until fruit maturity. Here, we report a molecular analysis of the early interaction between B. cinerea and Vitis vinifera flowers, using a controlled infection system, confocal microscopy and integrated transcriptomic and metabolic analysis of the host and the pathogen. Flowers from fruiting cuttings of the cultivar Pinot Noir were infected with green fluorescent protein (GFP)-labelled B. cinerea and studied at 24 and 96 hours post-inoculation (h.p.i.). We observed that penetration of the epidermis by B. cinerea coincided with increased expression of genes encoding cell-wall-degrading enzymes, phytotoxins and proteases. Grapevine responded with a rapid defence reaction involving 1193 genes associated with the accumulation of antimicrobial proteins, polyphenols, reactive oxygen species and cell wall reinforcement. At 96 h.p.i., the reaction appears largely diminished both in the host and in the pathogen. Our data indicate that the defence responses of the grapevine flower collectively are able to restrict invasive fungal growth into the underlying tissues, thereby forcing the fungus to enter quiescence until the conditions become more favourable to resume pathogenic development

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea

The circadian clock, an internal timekeeping mechanism, allows plants to anticipate regular changes in the environment, such as light and dark, and biotic challenges such as pathogens and herbivores. Here, we demonstrate that the plant circadian clock influences susceptibility to the necrotrophic fungal pathogen, Botrytis cinerea. Arabidopsis plants show differential susceptibility to B. cinerea depending on the time of day of inoculation. Decreased susceptibility after inoculation at dawn compared to night persists under constant light conditions and is disrupted in dysfunctional clock mutants, demonstrating the role of the plant clock in driving time-of-day susceptibility to B. cinerea. The decreased susceptibility to B. cinerea following inoculation at subjective dawn was associated with faster transcriptional reprogramming of the defence response with gating of infection-responsive genes apparent. Direct target genes of core clock regulators were enriched among the transcription factors that responded more rapidly to infection at subjective dawn than subjective night, suggesting an influence of the clock on the defence-signalling network. In addition, jasmonate signalling plays a crucial role in the rhythmic susceptibility of Arabidopsis to B. cinerea with the enhanced susceptibility to this pathogen at subjective night lost in a jaz6 mutant

No jacket required – new fungal lineage defies dress code

Analyses of environmental DNAs have provided tantalizing evidence for “rozellida” or “cryptomycota”, a clade of mostly undescribed and deeply diverging aquatic fungi. Here, we put cryptomycota into perspective through consideration of Rozella , the only clade member growing in culture. This is timely on account of the publication in Nature of the first images of uncultured cryptomycota from environmental filtrates, where molecular probes revealed non‐motile cyst‐like structures and motile spores, all lacking typical fungal chitinous cell walls. Current studies of Rozella can complement these fragmentary observations from environmental samples. Rozella has a fungal‐specific chitin synthase and its resting sporangia have walls that appear to contain chitin. Cryptomycota, including Rozella , lack a cell wall when absorbing food but like some other fungi, they may have lost their “dinner jacket” through convergence. Rather than evolutionary intermediates, the cryptomycota may be strange, divergent fungi that evolved from an ancestor with a nearly complete suite of classical fungal‐specific characters.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90101/1/94_ftp.pd

Contrasting effects of necrotrophic and biotrophic plant pathogens on the aphid Aphis fabae

Phytophagous insects have to contend with a wide variation in food quality brought about by a variety of factors intrinsic and extrinsic to the plant. One of the most important factors is infection by plant pathogenic fungi. Necrotrophic and biotrophic plant pathogenic fungi may have contrasting effects on insect herbivores due to their different infection mechanisms and induction of different resistance pathways, although this has been little studied and there has been no study of their combined effect. We studied the effect of the biotrophic rust fungus Uromyces viciae-fabae (Pers.) Schroet (Basidiomycota: Uredinales: Pucciniaceae) and the necrotrophic fungus Botrytis cinerea Pers. (Ascomycota: Helotiales: Sclerotiniaceae) singly and together on the performance of the aphid Aphis fabae Scop. (Hemiptera: Aphididae) on Vicia faba (L.) (Fabaceae). Alone, botrytis had an inhibitory effect on individual A. fabae development, survival and fecundity, while rust infection consistently enhanced individual aphids’ performance. These effects varied in linear relation to lesion or pustule density. However, whole-plant infection by either pathogen resulted in a smaller aphid population of smaller aphids than on uninfected plants, indicating a lowering of aphid carrying capacity with infection. When both fungi were applied simultaneously to a leaf they generally cancelled the effect of each other out, resulting in most performance parameters being similar to the controls, although fecundity was reduced. However, sequential plant infection (pathogens applied five days apart) led to a 70% decrease in fecundity and 50% reduction in intrinsic rate of increase. The application of rust before botrytis had a greater inhibitory effect on aphids than applying botrytis before rust. Rust infection increased leaf total nitrogen concentration by 30% while infection by botrytis with or without rust led to a 38% decrease. The aphids’ responses to the two plant pathogens individually is consistent with the alteration in plant nutrient content by infection and also the induction of different plant defence pathways and the possible cross-talk between them. This is the first demonstration of the complex effects of the dual infection of a plant by contrasting pathogens on insect herbivores. Key words: Vicia faba, Botrytis cinerea, Uromyces viciae-fabae, tripartite interactions, induced resistanc

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

This is the final version of the article. Available from the publisher via the DOI in this record.Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.The Sclerotinia sclerotiorum genome project was supported by the USDA Cooperative State Research, Education and Extension Service (USDA-NRI 2004). Sclerotinia sclerotiorum ESTs were funded by a grant to JA Rollins from USDA specific cooperative agreement 58-5442-4-281. The genome sequence of Botrytis cinerea strain T4 was funded by Genoscope, CEA, France. M Viaud was funded by the “Projet INRA Jeune-Equipe”. PM Coutinho and B Henrissat were funded by the ANR to project E-Tricel (grant ANR-07-BIOE-006). The CAZy database is funded in part by GIS-IBiSA. DM Soanes and NJ Talbot were partly funded by the UK Biotechnology and Biological Sciences Research Council. KM Plummer was partially funded by the New Zealand Bio-Protection Research Centre, http://bioprotection.org.nz/. BJ Howlett and A Sexton were partially funded by the Australian Grains Research and Development Corporation, www.grdc.com.au. L Kohn was partially funded by NSERC Discovery Grant (Natural Sciences and Engineering Research Council of Canada) - Grant number 458078. M Dickman was supported by the NSF grant MCB-092391 and BARD grant US-4041-07C. O Yarden was supported by BARD grant US-4041-07C. EG Danchin obtained financial support from the European Commission (STREP FungWall grant, contract: LSHB - CT- 2004 - 511952). A Botrytis Genome Workshop (Kaiserslautern, Germany) was supported by a grant from the German Science Foundation (DFG; HA1486) to M Hahn

Still Working With “Involuntary Clients” In Youth Justice

A lack of active participation from children and young people in the design and delivery of youth justice services has culminated in the effectiveness of the Youth Justice System being reduced. There has been little independent scrutiny and to add to that strategic direction on how children’s voices are or should be accessed in practice. In the light of this, the paper explores the various challenges associated with promoting the active participation of young people who have offended. More specifically, the paper explores the difficulties engaging those who are disengaged as such individuals may perceive the support on offer as unnecessary and intrusive. The paper argues that in order to reconcile a lack of engagement and feelings of disempowerment the priority should be throughout the Youth Justice System to involve young people in decision-making processes. Ideas will be put forward with regard to how youth justice practice could become more participatory and engaging particularly with regard to those who are ‘involuntary clients’ or in other words difficult to engage. There is a dearth of ‘hard’ empirical evidence on the effectiveness of participatory approaches in youth justice. However if work with young people who offend is innovative and bespoke to allow for young people’s voices to be heard practice could become more effective. But there needs to be the recognition that the ideas put forward in this paper are not ‘magic bullets’

Global in situ observations of essential climate and ocean variables at the air–sea interface

The air–sea interface is a key gateway in the Earth system. It is where the atmosphere sets the ocean in motion, climate/weather-relevant air–sea processes occur, and pollutants (i.e., plastic, anthropogenic carbon dioxide, radioactive/chemical waste) enter the sea. Hence, accurate estimates and forecasts of physical and biogeochemical processes at this interface are critical for sustainable blue economy planning, growth, and disaster mitigation. Such estimates and forecasts rely on accurate and integrated in situ and satellite surface observations. High-impact uses of ocean surface observations of essential ocean/climate variables (EOVs/ECVs) include (1) assimilation into/validation of weather, ocean, and climate forecast models to improve their skill, impact, and value; (2) ocean physics studies (i.e., heat, momentum, freshwater, and biogeochemical air–sea fluxes) to further our understanding and parameterization of air–sea processes; and (3) calibration and validation of satellite ocean products (i.e., currents, temperature, salinity, sea level, ocean color, wind, and waves). We review strengths and limitations, impacts, and sustainability of in situ ocean surface observations of several ECVs and EOVs. We draw a 10-year vision of the global ocean surface observing network for improved synergy and integration with other observing systems (e.g., satellites), for modeling/forecast efforts, and for a better ocean observing governance. The context is both the applications listed above and the guidelines of frameworks such as the Global Ocean Observing System (GOOS) and Global Climate Observing System (GCOS) (both co-sponsored by the Intergovernmental Oceanographic Commission of UNESCO, IOC–UNESCO; the World Meteorological Organization, WMO; the United Nations Environment Programme, UNEP; and the International Science Council, ISC). Networks of multiparametric platforms, such as the global drifter array, offer opportunities for new and improved in situ observations. Advances in sensor technology (e.g., low-cost wave sensors), high-throughput communications, evolving cyberinfrastructures, and data information systems with potential to improve the scope, efficiency, integration, and sustainability of the ocean surface observing system are explored

Heterogeneous integration of superconducting thin films and epitaxial semiconductor heterostructures with lithium niobate

We report on scalable heterointegration of superconducting electrodes and epitaxial semiconductor quantum dots (QDs) on strong piezoelectric and optically nonlinear lithium niobate. The implemented processes combine the sputter-deposited thin film superconductor niobium nitride and III–V compound semiconductor membranes onto the host substrate. The superconducting thin film is employed as a zero-resistivity electrode material for a surface acoustic wave resonator with internal quality factors approx Q≈17,000 representing a three-fold enhancement compared to identical devices with normal conducting electrodes. Superconducting operation of ≈400MHz resonators is achieved to temperatures T>7K and electrical radio frequency powers Prf>+9dBm. Heterogeneously integrated single QDs couple to the resonant phononic field of the surface acoustic wave resonator operated in the superconducting regime. Position and frequency selective coupling mediated by deformation potential coupling is validated using time-integrated and time-resolved optical spectroscopy. Furthermore, acoustoelectric charge state control is achieved in a modified device geometry harnessing large piezoelectric fields inside the resonator. The hybrid QD—surface acoustic wave resonator can be scaled to higher operation frequencies and smaller mode volumes for quantum phase modulation and transduction between photons and phonons via the QD. Finally, the employed materials allow for the realization of other types of optoelectronic devices, including superconducting single photon detectors and integrated photonic and phononic circuits