Gene transfer to plants by diverse species of bacteria

Agrobacterium is widely considered to be the only bacterial genus capable of transferring genes to plants. When suitably modified, Agrobacterium has become the most effective vector for gene transfer in plant biotechnology1. However, the complexity of the patent landscape2 has created both real and perceived obstacles to the effective use of this technology for agricultural improvements by many public and private organizations worldwide. Here we show that several species of bacteria outside the Agrobacterium genus can be modified to mediate gene transfer to a number of diverse plants. These plant-associated symbiotic bacteria were made competent for gene transfer by acquisition of both a disarmed Ti plasmid and a suitable binary vector. This alternative to Agrobacterium-mediated technology for crop improvement, in addition to affording a versatile ‘open source’ platform for plant biotechnology, may lead to new uses of natural bacteria– plant interactions to achieve plant transformation.

Estimation of travel time on urban networks with midlink sources and sinks

This paper presents a methodology for estimation of average travel time on signalized urban networks by integrating cumulative plots and probe data. This integration aims to reduce the relative deviations in the cumulative plots due to midlink sources and sinks. During undersaturated traffic conditions, the concept of a virtual probe is introduced, and therefore, accurate travel time can be obtained when a real probe is unavailable. For oversaturated traffic conditions, only one probe per travel time estimation interval—360 s or 3% of vehicles traversing the link as a probe—has the potential to provide accurate travel time.

Identification of acoustic emission wave modes for accurate source location in plate-like structures

Acoustic emission (AE) technique is a popular tool used for structural health monitoring of civil, mechanical and aerospace structures. It is a non-destructive method based on rapid release of energy within a material by crack initiation or growth in the form of stress waves. Recording of these waves by means of sensors and subsequent analysis of the recorded signals convey information about the nature of the source. Ability to locate the source of stress waves is an important advantage of AE technique; but as AE waves travel in various modes and may undergo mode conversions, understanding of the modes (‘modal analysis’) is often necessary in order to determine source location accurately. This paper presents results of experiments aimed at finding locations of artificial AE sources on a thin plate and identifying wave modes in the recorded signal waveforms. Different source locating techniques will be investigated and importance of wave mode identification will be explored.

Quantitative PCR assay of sewage-associated Bacteroides markers to assess sewage pollution in an urban lake in Dhaka, Bangladesh

This paper aimed to assess the magnitude of sewage pollution in an urban lake in Dhaka, Bangladesh by using Quantitative PCR (qPCR) of sewage-associated Bacteroides HF183 markers. PCR was also used for the quantitative detection of ruminant wastewater-associated CF128 markers along with the enumeration of traditional fecal indicator bacteria, namely, enterococci. The number of enterococci in lake water samples ranged from 1.1 x 104 to 1.9 x 105 CFU/100 ml of water. From the 20 water samples tested, 14 (70%) and 7 (35%) were PCR positive for the HF183 and CF128 markers, respectively. The numbers of the HF183 and CF128 markers in lake water samples were 3.9 x 104 to 6.3 × 107 and 9.3 x 103 to 6.3 x 105 genomic units (GU)/100 ml of water, respectively. The high numbers of enterococci and the HF183 markers indicate sewage pollution and potential health risks to those who use the lake water for non-potable purposes such as bathing and washing clothes. This is the first study that investigated the presence of microbial source tracking (MST) markers in Dhaka, Bangladesh where diarrhoeal diseases is one of the major causes of childhood mortality. The molecular assay as used in this study can provide valuable information on the extent of sewage pollution, thus facilitating the development of robust strategies to minimise potential health risks.

Human and bovine adenoviruses for the detection of source-specific fecal pollution in coastal waters in Australia

In this study, the host-specificity and -sensitivity of human- and bovine-specific adenoviruses (HS-AVs and BS-AVs) were evaluated by testing wastewater/fecal samples from various animal species in Southeast, Queensland, Australia. The overall specificity and sensitivity of the HS-AVs marker were 1.0 and 0.78, respectively. These figures for the BS-AVs were 1.0 and 0.73, respectively. Twenty environmental water samples were colleted during wet conditions and 20 samples were colleted during dry conditions from the Maroochy Coastal River and tested for the presence of fecal indicator bacteria (FIB), host-specific viral markers, zoonotic bacterial and protozoan pathogens using PCR/qPCR. The concentrations of FIB in water samples collected after wet conditions were generally higher compared to dry conditions. HS-AVs was detected in 20% water samples colleted during wet conditions and whereas BS-AVs was detected in both wet (i.e., 10%) and dry (i.e., 10%) conditions. Both, C. jejuni mapA and Salmonella invA genes were detected in 10% and 10% of samples, respectively collected during dry conditions. The concentrations of Salmonella invA ranged between 3.5 × 102 to 4.3 × 102 genomic copies per 500 ml of water G. lamblia β-giardin gene was detected only in one sample (5%) collected during the dry conditions. Weak or significant correlations were observed between FIB with viral markers and zoonotic pathogens. However, during dry conditions, no significant correlations were observed between FIB concentrations with viral markers and zoonotic pathogens. The prevalence of HS-AVs in samples collected from the study river suggests that the quality of water is affected by human fecal pollution and as well as bovine fecal pollution. The results suggest that HS-AVs and BS-AVs detection using PCR could be a useful tool for the identification of human sourced fecal pollution in coastal waters.

Stability and convergence of an effective numerical method for the time-space fractional Fokker-Planck equation with a nonlinear source term

Fractional Fokker-Planck equations (FFPEs) have gained much interest recently for describing transport dynamics in complex systems that are governed by anomalous diffusion and nonexponential relaxation patterns. However, effective numerical methods and analytic techniques for the FFPE are still in their embryonic state. In this paper, we consider a class of time-space fractional Fokker-Planck equations with a nonlinear source term (TSFFPE-NST), which involve the Caputo time fractional derivative (CTFD) of order α ∈ (0, 1) and the symmetric Riesz space fractional derivative (RSFD) of order μ ∈ (1, 2). Approximating the CTFD and RSFD using the L1-algorithm and shifted Grunwald method, respectively, a computationally effective numerical method is presented to solve the TSFFPE-NST. The stability and convergence of the proposed numerical method are investigated. Finally, numerical experiments are carried out to support the theoretical claims.

Coal Seam Gas Water from Maramarua, New Zealand: Characterisation and Comparison to United States Analogues

Groundwater from Maramarua has been identified as coal seam gas (CSG) water by studying its composition, and comparing it against the geochemical signature from other CSG basins. CSG is natural gas that has been produced through thermogenic and biogenic processes in underground coal seams; CSG extraction requires the abstraction of significant amounts of CSG water. To date, no international literature has described coal seam gas water in New Zealand, however recent CSG exploration work has resulted in CSG water quality data from a coal seam in Maramarua, New Zealand. Water quality from this site closely follows the geochemical signature associated with United States CSG waters, and this has helped to characterise the type of water being abstracted. CSG water from this part of Maramarua has low calcium, magnesium, and sulphate concentrations but high sodium (334 mg/l), chloride (146 mg/l) and bicarbonate (435 mg/l) concentrations. In addition, this water has high pH (7.8) and alkalinity (360 mg/l as CaCO3), which is a direct consequence of carbonate dissolution and biogenic processes. Different analyte ratios ('source-rock deduction' method) have helped to identify the different formation processes responsible in shaping Maramarua CSG water

Microphone array beamforming approach to blind speech separation

In this paper, we present a microphone array beamforming approach to blind speech separation. Unlike previous beamforming approaches, our system does not require a-priori knowledge of the microphone placement and speaker location, making the system directly comparable other blind source separation methods which require no prior knowledge of recording conditions. Microphone location is automatically estimated using an assumed noise field model, and speaker locations are estimated using cross correlation based methods. The system is evaluated on the data provided for the PASCAL Speech Separation Challenge 2 (SSC2), achieving a word error rate of 58% on the evaluation set.

Automatic generation of assertions to detect potential security vulnerabilities in C programs that use union and pointer types

Type unions, pointer variables and function pointers are a long standing source of subtle security bugs in C program code. Their use can lead to hard-to-diagnose crashes or exploitable vulnerabilities that allow an attacker to attain privileged access over classified data. This paper describes an automatable framework for detecting such weaknesses in C programs statically, where possible, and for generating assertions that will detect them dynamically, in other cases. Exclusively based on analysis of the source code, it identifies required assertions using a type inference system supported by a custom made symbol table. In our preliminary findings, our type system was able to infer the correct type of unions in different scopes, without manual code annotations or rewriting. Whenever an evaluation is not possible or is difficult to resolve, appropriate runtime assertions are formed and inserted into the source code. The approach is demonstrated via a prototype C analysis tool.

Development of a composite line source emission model for traffic interrupted microenvironments and its application in particle number emissions at a bus station

A composite line source emission (CLSE) model was developed to specifically quantify exposure levels and describe the spatial variability of vehicle emissions in traffic interrupted microenvironments. This model took into account the complexity of vehicle movements in the queue, as well as different emission rates relevant to various driving conditions (cruise, decelerate, idle and accelerate), and it utilised multi-representative segments to capture the accurate emission distribution for real vehicle flow. Hence, this model was able to quickly quantify the time spent in each segment within the considered zone, as well as the composition and position of the requisite segments based on the vehicle fleet information, which not only helped to quantify the enhanced emissions at critical locations, but it also helped to define the emission source distribution of the disrupted steady flow for further dispersion modelling. The model then was applied to estimate particle number emissions at a bi-directional bus station used by diesel and compressed natural gas fuelled buses. It was found that the acceleration distance was of critical importance when estimating particle number emission, since the highest emissions occurred in sections where most of the buses were accelerating and no significant increases were observed at locations where they idled. It was also shown that emissions at the front end of the platform were 43 times greater than at the rear of the platform. Although the CLSE model is intended to be applied in traffic management and transport analysis systems for the evaluation of exposure, as well as the simulation of vehicle emissions in traffic interrupted microenvironments, the bus station model can also be used for the input of initial source definitions in future dispersion models.

Application of chemometrics to analysis of soil pollutants

This overview focuses on the application of chemometrics techniques for the investigation of soils contaminated by polycyclic aromatic hydrocarbons (PAHs) and metals because these two important and very diverse groups of pollutants are ubiquitous in soils. The salient features of various studies carried out in the micro- and recreational environments of humans, are highlighted in the context of the various multivariate statistical techniques available across discipline boundaries that have been effectively used in soil studies. Particular attention is paid to techniques employed in the geosciences that may be effectively utilized for environmental soil studies; classical multivariate approaches that may be used in isolation or as complementary methods to these are also discussed. Chemometrics techniques widely applied in atmospheric studies for identifying sources of pollutants or for determining the importance of contaminant source contributions to a particular site, have seen little use in soil studies, but may be effectively employed in such investigations. Suitable programs are also available for suggesting mitigating measures in cases of soil contamination, and these are also considered. Specific techniques reviewed include pattern recognition techniques such as Principal Components Analysis (PCA), Fuzzy Clustering (FC) and Cluster Analysis (CA); geostatistical tools include variograms, Geographical Information Systems (GIS), contour mapping and kriging; source identification and contribution estimation methods reviewed include Positive Matrix Factorisation (PMF), and Principal Component Analysis on Absolute Principal Component Scores (PCA/APCS). Mitigating measures to limit or eliminate pollutant sources may be suggested through the use of ranking analysis and multi criteria decision making methods (MCDM). These methods are mainly represented in this review by studies employing the Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and its associated graphic output, Geometrical Analysis for Interactive Aid (GAIA).

Structural health monitoring of bridges : source localisation in acoustic emission technique

Managing the sustainability of urban infrastructure requires regular health monitoring of key infrastructure such as bridges. The process of structural health monitoring involves monitoring a structure over a period of time using appropriate sensors, extracting damage sensitive features from the measurements made by the sensors, and analysing these features to determine the current state of the structure. Various techniques are available for structural health monitoring of structures, and acoustic emission is one technique that is finding an increasing use in the monitoring of civil infrastructures such as bridges. Acoustic emission technique is based on the recording of stress waves generated by rapid release of energy inside a material, followed by analysis of recorded signals to locate and identify the source of emission and assess its severity. This chapter first provides a brief background of the acoustic emission technique and the process of source localization. Results from laboratory experiments conducted to explore several aspects of the source localization process are also presented. The findings from the study can be expected to enhance knowledge of the acoustic emission process, and to aid the development of effective bridge structure diagnostics systems.

High bandwidth voltage and current control design for voltage source converters

In this paper, two different high bandwidth converter control strategies are discussed. One of the strategies is for voltage control and the other is for current control. The converter, in each of the cases, is equipped with an output passive filter. For the voltage controller, the converter is equipped with an LC filter, while an output has an LCL filter for current controller. The important aspect that has been discussed the paper is to avoid computation of unnecessary references using high-pass filters in the feedback loop. The stability of the overall system, including the high-pass filters, has been analyzed. The choice of filter parameters is crucial for achieving desirable system performance. In this paper, the bandwidth of achievable performance is presented through frequency (Bode) plot of the system gains. It has been illustrated that the proposed controllers are capable of tracking fundamental frequency components along with low-order harmonic components. Extensive simulation results are presented to validate the control concepts presented in the paper.

The application of a profluorescent nitroxide probe to detect reactive oxygen species derived from combustion-generated particulate matter

Particulate pollution has been widely recognised as an important risk factor to human health. In addition to increases in respiratory and cardiovascular morbidity associated with exposure to particulate matter (PM), WHO estimates that urban PM causes 0.8 million premature deaths globally and that 1.5 million people die prematurely from exposure to indoor smoke generated from the combustion of solid fuels. Despite the availability of a huge body of research, the underlying toxicological mechanisms by which particles induce adverse health effects are not yet entirely understood. Oxidative stress caused by generation of free radicals and related reactive oxygen species (ROS) at the sites of deposition has been proposed as a mechanism for many of the adverse health outcomes associated with exposure to PM. In addition to particle-induced generation of ROS in lung tissue cells, several recent studies have shown that particles may also contain ROS. As such, they present a direct cause of oxidative stress and related adverse health effects. Cellular responses to oxidative stress have been widely investigated using various cell exposure assays. However, for a rapid screening of the oxidative potential of PM, less time-consuming and less expensive, cell-free assays are needed. The main aim of this research project was to investigate the application of a novel profluorescent nitroxide probe, synthesised at QUT, as a rapid screening assay in assessing the oxidative potential of PM. Considering that this was the first time that a profluorescent nitroxide probe was applied in investigating the oxidative stress potential of PM, the proof of concept regarding the detection of PM–derived ROS by using such probes needed to be demonstrated and a sampling methodology needed to be developed. Sampling through an impinger containing profluorescent nitroxide solution was chosen as a means of particle collection as it allowed particles to react with the profluorescent nitroxide probe during sampling, avoiding in that way any possible chemical changes resulting from delays between the sampling and the analysis of the PM. Among several profluorescent nitroxide probes available at QUT, bis(phenylethynyl)anthracene-nitroxide (BPEAnit) was found to be the most suitable probe, mainly due to relatively long excitation and emission wavelengths (λex= 430 nm; λem= 485 and 513 nm). These wavelengths are long enough to avoid overlap with the background fluorescence coming from light absorbing compounds which may be present in PM (e.g. polycyclic aromatic hydrocarbons and their derivatives). Given that combustion, in general, is one of the major sources of ambient PM, this project aimed at getting an insight into the oxidative stress potential of combustion-generated PM, namely cigarette smoke, diesel exhaust and wood smoke PM. During the course of this research project, it was demonstrated that the BPEAnit probe based assay is sufficiently sensitive and robust enough to be applied as a rapid screening test for PM-derived ROS detection. Considering that for all three aerosol sources (i.e. cigarette smoke, diesel exhaust and wood smoke) the same assay was applied, the results presented in this thesis allow direct comparison of the oxidative potential measured for all three sources of PM. In summary, it was found that there was a substantial difference between the amounts of ROS per unit of PM mass (ROS concentration) for particles emitted by different combustion sources. For example, particles from cigarette smoke were found to have up to 80 times less ROS per unit of mass than particles produced during logwood combustion. For both diesel and wood combustion it has been demonstrated that the type of fuel significantly affects the oxidative potential of the particles emitted. Similarly, the operating conditions of the combustion source were also found to affect the oxidative potential of particulate emissions. Moreover, this project has demonstrated a strong link between semivolatile (i.e. organic) species and ROS and therefore, clearly highlights the importance of semivolatile species in particle-induced toxicity.

Inheritance of Resistance to Rice Tungro Spherical Virus in a Near-Isogenic Line Derived from Utri Merah and in Rice Cultivar TKM6

Resistance to rice virus diseases is an important requirement in many Southeast Asian rice breeding programs. Inheritance of resistance to rice tungro spherical virus (RTSV) in TW5, a near-isogenic line derived from Indonesian rice cultivar Utri Merah, was compared to that in TKM6, an Indian rice cultivar. Both TKM6 and Utri Merah are cultivars resistant to RTSV infections. Crosses were made between TKM6 and TN1, a susceptible cultivar, and between TW5 and TN1, and F3 lines were evaluated for their resistance to RTSV using two RTSV inoculum sources and a serological assay (ELISA). In TKM6, the resistance to the mixture of RTSV-V + RTBV inoculum source was controlled by a single recessive gene, whereas in TW5, the resistance was controlled by two recessive genes. A single recessive gene, however, controlled the resistance in TW5 when another RTSV variant, RTSV-VI, was used, suggesting that the resistance in TW5 depends on the nature of the RTSV inoculum used. RT-PCR, sequence, and phylogenetic analyses confirmed that RTSV-VI inoculum differs from RTSV-V inoculum and accurate phenotyping of the resistance to RTSV requires the use of a genetic marker.