Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants

Background We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes. Results We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs. Conclusion In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.

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.

Drying kinetics, quality changes and shrinkage of Two grape varieties of Italy

Two varieties of grapes, white grape and red grape grown in the Campania region of Italy were selected for the study of drying characteristics, moisture diffusion, quality changes (colour) and shrinkage behaviour. Comparisons were made with treated and untreated grapes under constant drying condition of 50o C in a conventional drying system. This temperature was selected to represent farm drying conditions. Grapes were purchased from a local market from the same supplier to maintain the same size of grapes and same properties. An abrasive physical treatment was used as pretreatment. The drying curves were constructed and drying kinetics was calculated using several commonly available models. It was found that treated samples shows better drying characteristics than untreated samples. The objective of this study is to obtain drying kinetics which can be used to optimize the drying operations in grape drying.

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.

Base-induced decomposition of alkyl hydroperoxides in the gas phase. Part 3. Kinetics and dynamics in HO-+CH3OOH, C2H5OOH, and tert-C4H9OOH reactions

The E-CO(2) elimination reactions of alkyl hydroperoxides proceed via abstraction of an (x-hydrogen by a base: X- + (RRHCOOH)-R-1-H-2 -> HX + (RRC)-R-1-C-2=O + HO-. Efficiencies and product distributions for the reactions of the hydroxide anion with methyl, ethyl, and tert-butyl hydroperoxides are studied in the gas phase. On the basis of experiments using three isotopic analogues, HO- + CH3OOH, HO- + CD3OOH, and H18O- + CH3OOH. the overall intrinsic reaction efficiency is determined to be 80% or greater. The E(CO)2 decomposition is facile for these methylperoxide reactions, and predominates over competing proton transfer at the hydroperoxide moiety. The CH3CH2OOH reaction displays a similar E(CO)2 reactivity, whereas proton transfer and the formation of HOO- are the exclusive pathways observed for (CH3)(3)COOH, which has no (x-hydrogen. All results are consistent with the E-CO(2) mechanism, transition state structure, and reaction energy diagrams calculated using the hybrid density functional B3LYP approach. Isotope labeling for HO- + CH3OOH also reveals some interaction between H2O and HO- within the E(CO)2 product complex [H2O center dot center dot center dot CH2=O center dot center dot center dot HO-]. There is little evidence, however. for the formation of the most exothermic products H2O + CH2(OH)O-, which would arise from nuclephilic condensation of CH2=O and HO-. The results suggest that the product dynamics are not totally statistical but are rather direct after the E-CO(2) transition state. The larger HO- + CH3CH2OOH system displays more statistical behavior during complex dissociation.

Thermal stability and decomposition kinetics of styrene-butadiene rubber nanocomposites filled with different particle sized kaolinites

A series of styrene-butadiene rubber (SBR) nanocomposites filledwith different particle sized kaolinites are prepared via a latex blending method. The thermal stabilities of these clay polymer nanocomposites (CPN) are characterized by a range of techniques including thermogravimetry (TG), digital photos, scanning electron microscopy (SEM) and Raman spectroscopy. These CPN show some remarkable improvement in thermal stability compared to that of the pure SBR. With the increase of kaolinite particle size, the residual char content and the average activation energy of kaolinite SBR nanocomposites all decrease; the pyrolysis residues become porous; the crystal carbon in the pyrolysis residues decrease significantly from 58.23% to 44.41%. The above results prove that the increase of kaolinite particle size is not beneficial in improving the thermal stability of kaolinite SBR nanocomposites.

Kinetics of low-pressure, low-temperature graphene growth : toward single-layer, single-crystalline structure

Graphene grown on metal catalysts with low carbon solubility is a highly competitive alternative to exfoliated and other forms of graphene, yet a single-layer, single-crystal structure remains a challenge because of the large number of randomly oriented nuclei that form grain boundaries when stitched together. A kinetic model of graphene nucleation and growth is developed to elucidate the effective controls of the graphene island density and surface coverage from the onset of nucleation to the full monolayer formation in low-pressure, low-temperature CVD. The model unprecedentedly involves the complete cycle of the elementary gas-phase and surface processes and shows a precise quantitative agreement with the recent low-energy electron diffraction measurements and also explains numerous parameter trends from a host of experimental reports. These agreements are demonstrated for a broad pressure range as well as different combinations of precursor gases and supporting catalysts. The critical role of hydrogen in controlling the graphene nucleation and monolayer formation is revealed and quantified. The model is generic and can be extended to even broader ranges of catalysts and precursor gases/pressures to enable the as yet elusive effective control of the crystalline structure and number of layers of graphene using the minimum amounts of matter and energy.

Kinetics of the initial stage of silicon surface oxidation : Deal–Grove or surface nucleation?

The nucleation-initiated oxidation of a Si surface at very low temperatures in plasmas is demonstrated experimentally, in contrast to the Deal-Grove mechanism, which predicts Si oxidation at a Si/SiO interface and cannot adequately describe the formation of SiO nanodots and oxidation rates at very low (several nanometers) oxide thickness. Based on the experimental results, an alternative oxidation scenario is proposed and supported by multiscale numerical simulations suggesting that saturation of micro- and nanohillocks with oxygen is a trigger mechanism for initiation of Si surface oxidation. This approach is generic and can be applied to describe the kinetics of low-temperature oxidation of other materials. © 2009 American Institute of Physics.

Growth kinetics of carbon nanowall-like structures in low-temperature plasmas

The results of a hybrid numerical simulation of the growth kinetics of carbon nanowall-like nanostructures in the plasma and neutral gas synthesis processes are presented. The low-temperature plasma-based process was found to have a significant advantage over the purely neutral flux deposition in providing the uniform size distribution of the nanostructures. It is shown that the nanowall width uniformity is the best (square deviations not exceeding 1.05) in high-density plasmas of 3.0× 1018 m-3, worsens in lower-density plasmas (up to 1.5 in 1.0× 1017 m-3 plasmas), and is the worst (up to 1.9) in the neutral gas-based process. This effect has been attributed to the focusing of ion fluxes by irregular electric field in the vicinity of plasma-grown nanostructures on substrate biased with -20 V potential, and differences in the two-dimensional adatom diffusion fluxes in the plasma and neutral gas-based processes. The results of our numerical simulations are consistent with the available experimental reports on the effect of the plasma process parameters on the sizes and shapes of relevant nanostructures.

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.