Development of an in vitro assay to screen Agathis australis (kauri) for resistance to Phytophthora agathidicida : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science at Massey University, Manawatū, New Zealand

The iconic Agathis australis (kauri) of New Zealand, is under serious threat from kauri dieback disease caused by the soil-borne pathogen Phytophthora agathidicida. Infected kauri express symptoms of root and collar rot, bleeding resins at the base of the trunk, yellowing of foliage, canopy thinning, and tree mortality. Phytophthora agathidicida was first associated with kauri decline in 1972, where it was initially identified as P. heveae however, there was some uncertainty about its significance and taxonomy. The pathogen was officially identified as a new organism in 2008 and was called Phytophthora taxon Agathis until its formal description as Phytophthora agathidicida in 2015. This pathogen is easily vectored through root to root contact and mobile zoospores. Management and research has focused on mapping pathogen distribution, reducing spread, improving detection, ex situ conservation and clonal production using tissue culture techniques. In order to gain better understanding of the disease epidemiology and to develop better breeding programmes, a reliable in vitro resistance screening assay is required. This research focused on the development of a screening assay using detached leaves from tissue culture material as a means of accelerating screening assays compared to the more labour-intensive root inoculation assays. Foliar inoculations and assessment techniques were initially optimised on kauri leaves from tissue culture lines. The most successful inoculation method involved placing P. agathidicida-colonised agar plugs on wounded detached leaves. The assay was further tested on 2 year old kauri seedlings. Variation in susceptibility across kauri genotypes and leaf age, and variation in virulence among P. agathidicida isolates was observed. To further investigate the impact of leaf age on lesion extension, an assay was conducted on detached leaves from six rooted kauri saplings over 5 years of age, across three leaf age groups with P. agathidicida, P. multivora, and P. cinnamomi. Variation in virulence among these Phytophthora species was observed. Leaf necrosis was most severe with young tissue and susceptibility tended to decrease with increasing leaf age. Preliminary studies with 50 kauri clones identified different levels of susceptibility and tolerance across the different genotypes to P. agathidicida. The methods developed within this study have increased our understanding of the overall response of kauri to P. agathidicida foliar inoculations. This study demonstrated variation in the susceptability of kauri foliage to Phytophthora inoculation, although no complete resistance was observed. Further work is required to determine if there is a relationship between root and leaf responses which will help establish if in vitro genotypic variation can accurately predict natural genotypic variation seen within kauri forests

Dephasing of a superconducting flux qubit

In order to gain a better understanding of the origin of decoherence in superconducting flux qubits, we have measured the magnetic field dependence of the characteristic energy relaxation time ($T_1$) and echo phase relaxation time ($T_2^{\rm echo}$) near the optimal operating point of a flux qubit. We have measured $T_2^{\rm echo}$ by means of the phase cycling method. At the optimal point, we found the relation $T_2^{\rm echo}\approx 2T_1$. This means that the echo decay time is {\it limited by the energy relaxation} ($T_1$ process). Moving away from the optimal point, we observe a {\it linear} increase of the phase relaxation rate ($1/T_{2}^{\rm echo}$) with the applied external magnetic flux. This behavior can be well explained by the influence of magnetic flux noise with a $1/f$ spectrum on the qubit

A Scattered Light Echo around SN 1993J in M81

A light echo around SN 1993J was observed 8.2 years after explosion by a HST WFPC2 observation, adding to the small family of supernovae with light echoes. The light echo was formed by supernova light scattered from a dust sheet, which lies 220 parsecs away from the supernova, 50 parsecs thick along the line of sight, as inferred from radius and width of the light echo. The dust inferred from the light echo surface brightness is 1000 times denser than the intercloud dust. The graphite to silicate fraction can not be determined by our BVI photometric measurements, however, a pure graphite model can be excluded based on comparison with the data. With future observations, it will be possible to measure the expansion rate of the light echo, from which an independent distance to M81 can be obtained.Comment: 10 pages, 6 figures, in AASTeX format, submitted to ApJ Part

Non-linear echo cancellation - a Bayesian approach

Echo cancellation literature is reviewed, then a Bayesian model is introduced and it is shown how how it can be used to model and fit nonlinear channels. An algorithm for cancellation of echo over a nonlinear channel is developed and tested. It is shown that this nonlinear algorithm converges for both linear and nonlinear channels and is superior to linear echo cancellation for canceling an echo through a nonlinear echo-path channel

Revivals of Coherence in Chaotic Atom-Optics Billiards

We investigate the coherence properties of thermal atoms confined in optical dipole traps where the underlying classical dynamics is chaotic. A perturbative expression derived for the coherence of the echo scheme of [Andersen et. al., Phys. Rev. Lett. 90, 023001 (2003)] shows it is a function of the survival probability or fidelity of eigenstates of the motion of the atoms in the trap. The echo coherence and the survival probability display "system specific" features, even when the underlying classical dynamics is chaotic. In particular, partial revivals in the echo signal and the survival probability are found for a small shift of the potential. Next, a "semi-classical" expression for the averaged echo signal is presented and used to calculate the echo signal for atoms in a light sheet wedge billiard. Revivals in the echo coherence are found in this system, indicating they may be a generic feature of dipole traps