Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

<p>Abstract</p> <p>Background</p> <p>Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs) are the transcription factors that regulate the expression of auxin responsive genes. The <it>ARF </it>genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, however, to our knowledge, the <it>ARF </it>gene family from maize (<it>ZmARF </it>genes) has not been characterized in detail.</p> <p>Results</p> <p>In this study, 31 maize (<it>Zea mays </it>L.) genes that encode ARF proteins were identified in maize genome. It was shown that maize <it>ARF </it>genes fall into related sister pairs and chromosomal mapping revealed that duplication of <it>ZmARFs </it>was associated with the chromosomal block duplications. As expected, duplication of some <it>ZmARFs </it>showed a conserved intron/exon structure, whereas some others were more divergent, suggesting the possibility of functional diversification for these genes. Out of these 31 <it>ZmARF </it>genes, 14 possess auxin-responsive element in their promoter region, among which 7 appear to show small or negligible response to exogenous auxin. The 18 <it>ZmARF </it>genes were predicted to be the potential targets of small RNAs. Transgenic analysis revealed that increased miR167 level could cause degradation of transcripts of six potential targets (<it>ZmARF3</it>, <it>9</it>, <it>16</it>, <it>18</it>, <it>22 </it>and <it>30</it>). The expressions of maize <it>ARF </it>genes are responsive to exogenous auxin treatment. Dynamic expression patterns of <it>ZmARF </it>genes were observed in different stages of embryo development.</p> <p>Conclusions</p> <p>Maize <it>ARF </it>gene family is expanded (31 genes) as compared to <it>Arabidopsis </it>(23 genes) and rice (25 genes). The expression of these genes in maize is regulated by auxin and small RNAs. Dynamic expression patterns of <it>ZmARF </it>genes in embryo at different stages were detected which suggest that maize <it>ARF </it>genes may be involved in seed development and germination.</p

Physcomitrella patens DCL3 Is Required for 22–24 nt siRNA Accumulation, Suppression of Retrotransposon-Derived Transcripts, and Normal Development

Endogenous 24 nt short interfering RNAs (siRNAs), derived mostly from intergenic and repetitive genomic regions, constitute a major class of endogenous small RNAs in flowering plants. Accumulation of Arabidopsis thaliana 24 nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24 nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21 nt microRNAs (miRNAs) and 21–22 nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci that consistently produced a mixture of 21–24 nt siRNAs with a peak at 23 nt. These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5 mC) DNA modification. Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22–24 nt siRNAs, but not 21 nt siRNAs, at Pp23SR loci. The 21 nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6. Transcriptome-wide, Ppdcl3 mutants failed to accumulate 22–24 nt small RNAs from repetitive regions while transcripts from two abundant families of long terminal repeat (LTR) retrotransposon-associated reverse transcriptases were up-regulated. Ppdcl3 mutants also displayed an acceleration of leafy gametophore production, suggesting that repetitive siRNAs may play a role in the development of P. patens. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants

Pulse-Extended Excimer Laser Crystallisation of Pb(Zr,Ti)O 3 Thin Films for Integration on Low Thermal Budget Substrates.

Excimer laser annealing has been used to convert low temperature (non-ferroelectric) deposited lead zirconate titanate (PZT) to the perovskite phase without significantly heating underlying layers. A pulse-extension technique has been used to lengthen the laser pulse duration from 25 ns to 374 ns, lowering the surface temperature and improving the heat distribution in the PZT, as compared to the non-extended case, but still not significantly heating the substrate. Initial experiments are reported which have shown the technique to be capable of crystallising over half a 500 nm thick PZT film to perovskite although a melting effect limited the converted thickness. The thickness crystallised is however of the order of that used in FeRAM devices and modelled temperature profiles suggest that the technique provides a tractable solution for high temperature processing of ferroelectric thin films of thickness 200-300 nm on low thermal budget substrates

Use of the solvent chemistry for the control of the critical thickness of PbTiO3 ultrathin films

The preparation of high-quality ferroelectric PbTiO3-based ultrathin films by chemical solution deposition. using a diol-based sol-gel method, has proved to be successful. However, there is a critical thickness below which the films break up into isolated structures According to previous studies, above a certain grain size to thickness ratio a microstructural instability occurs and the coatings are no longer continuous. We explore the use of the solvent chemistry to control this phenomenon, as an alternative to the more conventional variation of the crystallization parameters. The use of diols with short C chain lengths leads to films with smaller gram sizes, whose critical thicknesses are lower. A reduction from 40 to 15 nm is achieved by reducing the number of C of the chol used from 5 to 2. A critical value of G/t < 5.0 is necessary to obtain continuous ultrathin films with the processing conditions use

Kinetics of Phase Transformations in Lead Scandium Tantalate Thin Films.

The phase transformations from amorphous to pyrochlore to perovskite in lead scandium tantalate (PST) thin films during rapid thermal annealing process (RTA) have been studied. Volume fractions for pyrochlore and perovskite were obtained from their respective X-ray diffraction intensities. Two models assuming the starting phase being pure amorphous or pyrochlore were analysed in detail. Equations have been derived and numerical calculation used to simulate the volume fractions for each phase as functions of annealing time. Transformation parameters k and n were obtained by comparing experiment with simulation using a least-squares curve fitting technique

Fabrication of continuous ultrathin ferroelectric films by chemical solution deposition methods

The integration of ferroelectrics in nanodevices requires firstly the preparation of high-quality ultrathin films. Chemical solution deposition is considered a rapid and cost-effective technique for preparing high-quality oxide films, but one that has traditionally been regarded as unsuitable, or at least challenging, for fabricating films with good properties and thickness below 100 nm. In the present work we explore the deposition of highly diluted solutions of pure and Ca-modified lead titanates to prepare ultrathin ferroelectric films, the thickness of which is controlled by the concentration of the precursor solution. The results show that we are able to obtain single crystalline phase continuous films down to 18 nm thickness, one of the lowest reported using these methods. Below that thickness, the films start to be discontinuous, which is attributed to a microstructural instability that can be controlled by an adequate tailoring of the processing conditions. The effect of the reduction of thickness on the piezoelectric behavior is studied by piezoresponse force microscopy. The results indicate that films retain a significant piezoelectric activity regardless of their low thickness, which is promising for their eventual integration in nanodevices, for example, as transducer elements in nanoelectromechanical systems

Comparative Studies of PST Thin Films as Prepared by Sol-Gel, LDCVD and Sputtering Techniques

Lead scandium tantalate (PST) thin films for pyroelectric applications have been deposited by using liquid delivery chemical vaporise deposition (LDCVD), sputtering and sol-gel techniques. These films were annealed by using rapid thermal annealing to improve their electrical properties. Their microstructures and electrical properties such as permittivity r , dielectric loss tan , pyroelectric coefficient p, and thermal detection figure of merit F d were studied. It is suggested to use a combination of methods to depositing films and then use rapid thermal annealing to producing high quality PST thin films

Direct and converse magnetoelectic effect in laminate bonded Terfenol-D-PZT composites

Results from measurements of the direct and converse magnetoelectric (ME) effect on a three-layer, epoxy-bonded, laminate composite are presented. The laminae are a single transversely polarized piezoelectric elements (PZ29) sandwiched between two longitudinal-magnetic ally polarized magnetostrictive TD elements (Terfenol-D-TX GMM). The direct ME effect was determined by measuring laminate output with a Helmholtz-generated AC field (up to 7 Oe) in the range 50 Hz-100 kHz biased by a DC field (0-1000 Oe). Peak voltage output occurred at the sample's mechanical resonant frequency, its value depending on the strength and direction of the applied magnetic field. The peak output was 3061 mV at 3 Oe AC field and 1000 Oe bias, equivalent to 74.4 V cm(-1) Oe(-1). The peak output coefficient, however, was 93.6 V cm(-1) Oe(-1) at 0.1 Oe AC field and 1000 Oe DC bias. The reduction at higher drive amplitudes was attributed to increased Young's modulus of the TD phase. Anomalous peaks in the low frequency spectrum of sample's output are explained. The converse magnetoelectric effect was measured by recording the voltage induced in a solenoid encompassing the ME while exposed to a DC bias field and the PZ phase driven by a 10 VAC source. The peak output is shown to depend on the strength of the applied DC magnetic field and developed a maximum field of 15.4 Oe at the sample's mechanical resonant frequency. This equates to a converse magnetoelectric coefficient of 55 Oe cm kV (-1) (c) 2007 Elsevier B.V. All rights reserved

Mouse Mammary Tumor Virus Carrying a Bacterial supFGene Has Wild-Type Pathogenicity and Enables Rapid Isolation of Proviral Integration Sites

Mouse mammary tumor virus (MMTV) has frequently been used as an insertional mutagen to identify provirally activated mammary proto-oncogenes. To expedite and facilitate the process of cloning MMTV insertion sites, we have introduced a bacterial supF suppressor tRNA gene into the long terminal repeat (LTR) of MMTV, thus allowing selection of clones containing it in lambda vectors bearing amber mutations. The presence of supF in the LTR should circumvent the screening process for proviral insertion sites, since only those lambda clones with supF-containing proviral-cellular junction fragments should be able to form plaques on a lawn of wild-type Escherichia coli (i.e., lacking supF). The resulting virus (MMTVsupF) induced mammary tumors at the expected rate in infected mice, deleted the appropriate T-cell population by virtue of its superantigen gene, and stably retained the supF gene after passage via the milk to female offspring. To test the selective function of the system, size-selected DNA containing two proviral-cellular junction fragments from an MMTV supF-induced mammary tumor was ligated into λgtWES.λB, packaged, and plated on a supF-deficient bacterial host for selection of supF-containing clones. All plaques tested contained the desired cloned fragments, thus demonstrating the utility of this modified provirus for the rapid cloning of MMTV insertion sites