Molecular biology techniques as a tool for detection and characterisation of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is the causative agent of paratuberculosis, also known as Johne’s disease, a chronic intestinal infection in cattle and other ruminants. Paratuberculosis is characterised by diarrhea and weight loss that occurs after a period of a few months up to several years without any clinical signs. The considerable economic losses to dairy and beef cattle producers are caused by reduced milk production and poor reproduction performance in subclinically infected animals. Early diagnosis of infected cattle is essential to prevent the spread of the disease. Efforts have been made to eradicate paratuberculosis by using a detection and cull strategy, but eradication is hampered by the lack of suitable and sensitive diagnostic methods. This thesis, based on five scientific investigations, describes the development of different DNA amplification strategies for detection and characterisation of M. paratuberculosis. Various ways to pre-treat bacterial cultures, tissue specimens and fecal samples prior to PCR analysis were investigated. Internal positive PCR control molecules were developed and used in PCR analyses to improve the reliability and to facilitate the interpretation of the results. The sensitivity of the ultimate methods was found to be approximate that of culture and allowed detection of low numbers of M. paratuberculosis expected to be found in subclinically infected animals. Genomic DNA of a Swedish mycobacterial isolate, incorrectly identified by PCR as M. paratuberculosis was characterised. The isolate was closely related to M. cookii and harboured one copy of a DNA segment with 94% similarity to IS900, the target sequence used in diagnostic PCR for detection of M. paratuberculosis. This finding highlighted the urgency of developing or evaluating PCR systems based on genes other than IS900. A PCR-based fingerprinting method using primers targeting the enterobacterial intergenic consensus sequence (ERIC) and the IS900 sequence was developed and successfully used to distinguish M. paratuberculosis from closely related mycobacteria, including the above mentioned mycobacterial isolate. In conclusion, the molecular biology techniques developed in these studies have proved useful for accelerating the diagnostic detection and characterisation of M. paratuberculosis

Nonlinear Temporal Dynamics of Strongly Coupled Quantum Dot-Cavity System

We theoretically analyze and simulate the temporal dynamics of strongly coupled quantum dot-cavity system driven by a resonant laser pulse. We observe the signature of Rabi oscillation in the time resolved response of the system (i.e., in the numerically calculated cavity output), derive simplified linear and non-linear semi-classical models that approximate well the system's behavior in the limits of high and low power drive pulse, and describe the role of quantum coherence in the exact dynamics of the system. Finally, we also present experimental data showing the signature of the Rabi oscillation in time domain

A quantum photonics model for non-classical light generation using integrated nanoplasmonic cavity-emitter systems

The implementation of non-classical light sources is becoming increasingly important for various quantum applications. A particularly interesting approach is to integrate such functionalities on a single chip as this could pave the way towards fully scalable quantum photonic devices. Several approaches using dielectric systems have been investigated in the past. However, it is still not understood how on-chip nanoplasmonic antennas, interacting with a single quantum emitter, affect the quantum statistics of photons reflected or transmitted in the guided mode of a waveguide. Here we investigate a quantum photonic platform consisting of an evanescently coupled nanoplasmonic cavity-emitter system and discuss the requirements for non-classical light generation. We develop an analytical model that incorporates quenching due to the nanoplasmonic cavity to predict the quantum statistics of the transmitted and reflected guided waveguide light under weak coherent pumping. The analytical predictions match numerical simulations based on a master equation approach. It is moreover shown that for resonant excitation the degree of anti-bunching in transmission is maximized for an optimal cavity modal volume $V_{c}$ and cavity-emitter distance $s$. In reflection, perfectly anti-bunched light can only be obtained for specific $(V_{c},s)$ combinations. Finally, our model also applies to dielectric cavities and as such can guide future efforts in the design and development of on-chip non-classical light sources using dielectric and nanoplasmonic cavity-emitter systems

Research sensors

The program described covers development of sensors and sensing techniques for research applications on aeropropulsion systems. In general, the sensors are used in-situ to measure the environment at a given location within a turbine engine, or to measure the response of an engine component to the imposed environment. Locations of concern are generally in the gas path and, for the most part, are within the hot section. Specific parameters of concern are dynamic gas temperature, heat flux, airfoil surface temperature, and strain on airfoils and combustor liners. In order to minimize the intrusiveness of surface-mounted sensors, a considerable effort was expended to develop thin-film sensors for surface temperature, strain, and heat flux measurements. Most of the work described is sufficiently advanced that sensors were used and useful data were obtained. The notable exception is the work to develop a high-temperature static strain measuring capability; this work is still in progress

Progress on a PdCr wire strain gage

The principal activity under the HOST effort to improve the state of the art in high temperature static strain measurement has been a contract under which a palladium-chromium (PdCr) alloy was developed. The contract effort is continuing with the goal of developing a thin film high temperature static strain gage system. In addition to this effort, researchers contracted with Battelle-Columbus Laboratories to draw the PdCr allow into wire while researchers at Lewis worked to gain experience with this alloy as a wire strain gage

HOST instrumentation R and D program overview

The HOST Instrumentation R and D program is focused on two categories of instrumentation. One category is that required to characterize the environment imposed on the hot section components of turbine engines. This category includes instruments for measuring gas flow, gas temperature, and heat flux. The second category is that for measuring the effect of the environment on the hot section components. This category includes strain measuring instruments and an optical system for viewing the interior of an operating combustor to detect cracks, buckling, carbon buildup, etc

Research instrumentation for hot section components of turbine engines

Programs to develop research instrumentation for use on hot section components of turbine engines are discussed. These programs can be separated into two categories: one category includes instruments which can measure the environment within the combustor and turbine components, the other includes instruments which measure the response of engine components to the imposed environment. Included in the first category are instruments to measure total heat flux and fluctuating gas temperature. High temperature strain measuring systems, thin film sensors (e.g., turbine blade thermocouples) and a system to view the interior of a combustor during engine operation are programs which comprise the second category. The paper will describe the state of development of these sensors and measuring systems and, in some cases, show examples of measurements made with this instrumentation. The discussion will cover work done at NASA Lewis and at various contractor facilities

Research sensors

The LeRC program in research sensors is directed at development of sensors and sensing techniques for research applications on turbine engines and propulsion systems. In general, the sensors are used either to measure to response of an engine component to the imposed environment. Locations of concern are generally within the gas path and, for the most part, are within the hot section of the engine. Since these sensors are used for research testing as opposed to operational use, a sensor lifetime of the order of 50 hr is considered sufficient. The following discussion presents a sample of this work, describing programs to develop a dynamic gas temperature measuring system, total heat flux sensors, a variety of thin-film sensors, and high-temperature strain measuring systems