Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes

Background Transcription factors (TFs) co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs. In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1) leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. Results Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. Conclusion Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA, it does provide a tool to characterise cis-regulatory sequences that are necessary for transcription activation in a complex list of co-ordinately regulated genes.

A transient assay for recombination demonstrates that Arabidopsis SNM1 and XRCC3 enhance non-homologous recombination

Replacement of endogenous genes by homologous recombination is rare in plants; the majority of genetic modifications are the result of transforming DNA molecules undergoing random genomic insertion by way of non-homologous recombination. Factors that affect chromatin remodeling and DNA repair are thought to have the potential to enhance the frequency of homologous recombination in plants. Conventional tools to study the frequencies of genetic recombination often rely on stable transformation-based approaches, with these systems being rarely capable of high-throughput or combinatorial analysis. We developed a series of vectors that use chemiluminescent (LUC and REN) reporter genes to assay the relative frequency of homologous and non-homologous recombination in plants. These transient assay vectors were used to screen 14 candidategenes for their effects on recombination frequencies in Nicotiana benthamiana plants. Over-expression of Arabidopsis genes with sequence similarity to SNM1 from yeast and XRCC3 from humans enhanced the frequency of non-homologous recombination when assayed using two different donor vectors. Transient N. benthamiana leaf systems were also used in an alternative assay for preliminary measurements of homologous recombination frequencies, which were found to be enhanced by over-expression of RAD52, MIM and RAD51 from yeast, as well as CHR24 from Arabidopsis. The findings for the assays described here are in line with previous studies that analyzed recombination frequencies using stable transformation. The assays we report have revealed functions in non-homologous recombination for the Arabidopsis SNM1 and XRCC3 genes, so the suppression of these genes' expression offers a potential means to enhance the gene targeting frequency in plants. Furthermore, our findings also indicate that plant gene targeting frequencies could be enhanced by over-expression of RAD52, MIM, CHR24, and RAD51 genes.

Buffer scheme with battery energy storage capability for enhancement of network transient stability and load ride-through

This paper examines a buffer scheme to mitigate the negative impacts of power-conditioned loads on network voltage and transient stabilities. The scheme is based on the use of battery energy-storage systems in the buffers. The storage systems ensure that protected loads downstream of the buffers can ride through upstream voltage sags and swells. Also, by controlling the buffers to operate in either constant impedance or constant power modes, power is absorbed or injected by the storage systems. The scheme thereby regulates the rotor-angle deviations of generators and enhances network transient stability. A computational method is described in which the capacity of the storage systems is determined to achieve simultaneously the above dual objectives of load ride-through and stability enhancement. The efficacy of the resulting scheme is demonstrated through numerical examples.

Volatile properties of CNG and Diesel bus emissions produced during steady state and transient driving modes

An analysis of the emissions from 14 CNG and 5 Diesel buses was conducted during April & May, 2006. Studies were conducted at both steady state and transient driving modes on a vehicle dynamometer utilising a CVS dilution system. This article will focus on the volatile properties of particles from 4 CNG and 4 Diesel vehicles from within this group with a priority given to the previously un-investigated CNG emissions produced at transient loads. Particle number concentration data was collected by three CPC’s (TSI 3022, 3010 & 3782WCPC) having D50 cut-offs set to 5nm, 10nm & 20nm respectively. Size distribution data was collected using a TSI 3080 SMPS with a 3025 CPC during the steady state driving modes. During transient cycles mono-disperse “slices” of between 5nm & 25nm were measured. The volatility of these particles was determined by placing a thermodenuder before the 3022 and the SMPS and measuring the reduction in particle number concentration as the temperature in the thermodenuder was increased. This was then normalised against the total particle count given by the 3010 CPC to provide high resolution information on the reduction in particle concentration with respect to temperature.

Nanoparticle emissions from a fleet of CNG buses in transient and steady state operation

Particle emission measurements from a fleet of 14 CNG and 5 Diesel buses were measured both for transient and steady state mode s on a chassis dynamometer with a CVS dilution system. Several transient DT80 cycles and 4 steady sate modes (0, 25, 50 100% of maximum load) were measured for each bus tested. Particle number concentration data was collected by three CPC’s (TSI 3022, 3010 3782WCPC) having D50 cut-offs set to 5, 10 and 20nm respectively. The size distributions were measured with a TSI 3080 SMPS with a 3025 CPC during the steady state modes. Particle mass emissions were measured with a TSI Dustrak. Particle mass emissions for Diesel buses were upto 2 orders of magnitude higher than for CNG buses. Particle number emissions during steady state modes for Diesel busses were 2 to 5 times higher than for CNG busses for all of the tested loads. On the other hand for the DT80 transient cycle particle number emissions were up to 3 times higher for the CNG buses. More detailed analysis of the transient cycles revealed that the reason for this was due to high particle number emissions from CNG busses during the acceleration parts of the cycles. Particles emitted by the CNG busses during acceleration were in the nucleation mode with the majority being smaller than 10nm. Volatility measurements have also shown that they were highly volatile.

Steady state and transient dynamometer vehicle emission measurements using a DiSC

Analysis of the particulate size and number concentration emissions from a fleet of inner city medium duty CNG buses was conducted using the newly available Diffusion Size Classifier in comparison with more traditional SMPS's and CPC's. Studies were conducted at both steady state and transient driving modes on a vehicle dynamometer utilising a CVS dilution system. Comparative analysis of the results showed that the DiSC provided equivalent information during steady state conditions and was able to provide additional information during transient conditions, namely, the modal diameter of the particle size distribution.

Excited-state dynamics in diketopyrrolopyrrole-based copolymer for organic photovoltaics investigated by transient optical spectroscopy

We investigate the photoexcited state dynamics in a donor-acceptor copolymer, poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]- pyrrole-1,4-dione-alt-naphthalene} (pDPP-TNT), by picosecond fluorescence and femtosecond transient absorption spectroscopies. Timeresolved fluorescence lifetime measurements of pDPP-TNT thin films reveal that the lifetime of the singlet excited state is 185 ± 5 ps and that singlet-singlet annihilation occurs at excitation photon densities above 6 × 1017 photons/cm3. From the results of singlet-singlet annihilation analysis, we estimate that the single-singlet annihilation rate constant is (6.0 ± 0.2) × 109cm3 s-1 and the singlet diffusion length is -7 nm. From the comparison of femtosecond transient absorption measurements and picosecond fluorescence measurements, it is found that the time profile of the photobleaching signal in the charge-transfer (CT) absorption band coincides with that of the fluorescence intensity and there is no indication of long-lived species, which clearly suggests that charged species, such as polaron pairs and triplet excitons, are not effectively photogenerated in the neat pDPP-TNT polymer.

An analytical framework for quantifying aquifer response time scales associated with transient boundary conditions

A major challenge in studying coupled groundwater and surface-water interactions arises from the considerable difference in the response time scales of groundwater and surface-water systems affected by external forcings. Although coupled models representing the interaction of groundwater and surface-water systems have been studied for over a century, most have focused on groundwater quantity or quality issues rather than response time. In this study, we present an analytical framework, based on the concept of mean action time (MAT), to estimate the time scale required for groundwater systems to respond to changes in surface-water conditions. MAT can be used to estimate the transient response time scale by analyzing the governing mathematical model. This framework does not require any form of transient solution (either numerical or analytical) to the governing equation, yet it provides a closed form mathematical relationship for the response time as a function of the aquifer geometry, boundary conditions, and flow parameters. Our analysis indicates that aquifer systems have three fundamental time scales: (i) a time scale that depends on the intrinsic properties of the aquifer; (ii) a time scale that depends on the intrinsic properties of the boundary condition, and; (iii) a time scale that depends on the properties of the entire system. We discuss two practical scenarios where MAT estimates provide useful insights and we test the MAT predictions using new laboratory-scale experimental data sets.

Design of a nonlinear excitation controller using inverse filtering for transient stability enhancement

This paper proposes a nonlinear excitation controller to improve transient stability, oscillation damping and voltage regulation of the power system. The energy function of the predicted system states is used to obtain the desired flux for the next time step, which in turn is used to obtain a supplementary control input using an inverse filtering method. The inverse filtering technique enables the system to provide an additional input for the excitation system, which forces the system to track the desired flux. Synchronous generator flux saturation model is used in this paper. A single machine infinite bus (SMIB) test system is used to demonstrate the efficacy of the proposed control method using time-domain simulations. The robustness of the controller is assessed under different operating conditions.

Development of a transient, high-level expression platform for protein production in plants

Plants are an attractive alternative to conventional expression systems for the production of recombinant proteins and useful biologics, however, the economic viability of plant made proteins is strongly yield dependent. This study aimed to improve transgene expression levels in the plant host Nicotiana benthamiana using the Agroinfiltration transient expression platform. Independent investigation of the physical, chemical and genetic features associated with Agroinfiltration identified factors that improved transformation frequencies, elevated transgene expression levels and ultimately improved protein yield. The major outcome of this research was a novel hyper-expression system for biofarming recombinant proteins in plants.

Updates in inducible transgene expression using viral vectors : from transient to stable expression

The prospect of economically producing useful biologics in plants has greatly increased with the advent of viral vectors. The ability of viral vectors to amplify transgene expression has seen them develop into robust transient platforms for the high-level, rapid production of recombinant proteins. To adapt these systems to stably transformed plants, new ways of deconstructing the virus machinery and linking its expression and replication to chemically controlled promoters have been developed. The more advanced of these stable, inducible hyper-expression vectors provide both activated and amplified heterologous transgene expression. Such systems could be deployed in broad acre crops and provide a pathway to fully exploit the advantages of plants as a platform for the manufacture of a wide spectrum of products.

Overvoltage and overloading prevention using coordinated PV inverters in distribution network

Overvoltage and overloading due to high utilization of PVs are the main power quality concerns for future distribution power systems. This paper proposes a distributed control coordination strategy to manage multiple PVs within a network to overcome these issues. PVs reactive power is used to deal with over-voltages and PVs active power curtailment are regulated to avoid overloading. The proposed control structure is used to share the required contribution fairly among PVs, in proportion to their ratings. This approach is examined on a practical distribution network with multiple PVs.

Fast unscented transformation-based transient stability margin estimation incorporating uncertainty of wind generation

Intermittent generation from wind farms leads to fluctuating power system operating conditions pushing the stability margin to its limits. The traditional way of determining the worst case generation dispatch for a system with several semi-scheduled wind generators yields a conservative solution. This paper proposes a fast estimation of the transient stability margin (TSM) incorporating the uncertainty of wind generation. First, the Kalman filter (KF) is used to provide linear estimation of system angle and then unscented transformation (UT) is used to estimate the distribution of the TSM. The proposed method is compared with the traditional Monte Carlo (MC) method and the effectiveness of the proposed approach is verified using Single Machine Infinite Bus (SMIB) and IEEE 14 generator Australian dynamic system. This method will aid grid operators to perform fast online calculations to estimate TSM distribution of a power system with high levels of intermittent wind generation.

Stress analysis of carotid atheroma in transient ischemic attack patients: Evidence for extreme stress-induced plaque rupture

Plaque rupture has been considered to be the result of its structural failure. The aim of this study is to suggest a possible link between higher stresses and rupture sites observed from in vivo magnetic resonance imaging (MRI) of transient ischemic attack (TIA) patients, by using stress analysis methods. Three patients, who had recently suffered a TIA, underwent in vivo multi-spectral MR imaging. Based on plaque geometries reconstructed from the post-rupture status, six pre-rupture plaque models were generated for each patient dataset with different reconstructions of rupture sites to bridge the gap of fibrous cap from original MRI images. Stress analysis by fluid structure interaction simulation was performed on the models, followed by analysis of local stress concentration distribution and plaque rupture sites. Furthermore, the sensitivity of stress analysis to the pre-rupture plaque geometry reconstruction was examined. Local stress concentrations were found to be located at the plaque rupture sites for the three subjects studied. In the total of 18 models created, the locations of the stress concentration regions were similar in 17 models in which rupture sites were always associated with high stresses. The local stress concentration region moved from circumferential center to the shoulder region (slightly away from the rupture site) for a case with a thick fibrous cap. Plaque wall stress level in the rupture locations was found to be much higher than the value in non-rupture locations. The good correlation between local stress concentrations and plaque rupture sites, and generally higher plaque wall stress level in rupture locations in the subjects studied could provide indirect evidence for the extreme stress-induced plaque rupture hypothesis. Local stress concentration in the plaque region could be one of the factors contributing to plaque rupture.