Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

<p>Abstract</p> <p>Background</p> <p>Accurate computational identification of <it>cis</it>-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of <it>cis</it>-regulatory motifs.</p> <p>Results</p> <p>We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely <it>Brassicaceae </it>(mustards), <it>Fabaceae </it>(legumes) and <it>Poaceae </it>(grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (<it>Arabidopsis thaliana </it>(L.) Heynh.), soybean (<it>Glycine max </it>(L.) Merr.) and rice (<it>Oryza sativa </it>L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in <it>Brassicaceae </it>and <it>Fabaceae </it>SSP gene promoters that are similar to experimentally characterized seed-specific <it>cis</it>-regulatory elements. <it>Fabaceae </it>SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in <it>Poaceae </it>SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins.</p> <p>Conclusion</p> <p>Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs. The majority of discovered motifs match experimentally characterized <it>cis</it>-regulatory elements. These results provide a good starting point for further experimental analysis of plant seed-specific promoters and our methodology can be used to unravel more transcriptional regulatory mechanisms in plants and other eukaryotes.</p

Consistency between three different ways of administering the Short Form 6 Dimension version 2

Background The Short Form 6 Dimension (SF-6D) is a multi-attribute utility instrument derived from the Short-Form 36 Health Survey Version 2 (SF-36v2) quality of life questionnaire and is used to calculate quality-adjusted life years (QALYs) on a scale 0 to 1. The SF-6Dv2 is a new version of the SF-6D. Objective The aim of this study was to assess the consistency of respondents’ answers to 3 different methods to administer this new version. Methods SF-6Dv2 utility values were generated from the SF-36v2 using the following: (1) full questionnaire with 36 items (SF-6Dv2SF-36); (2) subset questionnaire with 10 items (SF-6Dv2ind-10); (3) SF-6Dv2 administered as an independent instrument (rephrased questionnaire with only 6 items [SF-6Dv2ind-6]). The order of the 3 instruments was randomly allocated between respondents. Results A total of 782 respondents from Quebec, Canada, were interviewed, out of whom 697 fully completed the survey. Very few deviations in respondents’ answers were observed between the 3 instruments, with mean weighted kappa of 0.79 (range 0.61-0.91) and mean global consistency index of 70% (range 54-83). Maximal difference in utility values generated was found between SF-6Dv2ind-10 and SF-6Dv2ind-6 (mean difference 0.016, P < .01), whereas minimal difference was found between SF-6Dv2SF-36 and SF-6Dv2ind-10 (0.002, P = .38). No ceiling effect was observed. Conclusions The SF-6Dv2 was designed to derive utilities from the SF-36v2, and our results indicate that it is still preferable to use the full questionnaire, although the difference with other variants of the questionnaire is very small. To use the SF-6Dv2 as an independent instrument will thus introduce minimal bias in utility values generated

Seeder: discriminative seeding DNA motif discovery

Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches

Role of Conserved Non-Coding Regulatory Elements in LMW Glutenin Gene Expression

Transcriptional regulation of LMW glutenin genes were investigated in-silico, using publicly available gene sequences and expression data. Genes were grouped into different LMW glutenin types and their promoter profiles were determined using cis-acting regulatory elements databases and published results. The various cis-acting elements belong to some conserved non-coding regulatory regions (CREs) and might act in two different ways. There are elements, such as GCN4 motifs found in the long endosperm box that could serve as key factors in tissue-specific expression. Some other elements, such as the AACA/TA motifs or the individual prolamin box variants, might modulate the level of expression. Based on the promoter sequences and expression characteristic LMW glutenin genes might be transcribed following two different mechanisms. Most of the s- and i-type genes show a continuously increasing expression pattern. The m-type genes, however, demonstrate normal distribution in their expression profiles. Differences observed in their expression could be related to the differences found in their promoter sequences. Polymorphisms in the number and combination of cis-acting elements in their promoter regions can be of crucial importance in the diverse levels of production of single LMW glutenin gene types

Influence of solution parameters for the fast growth of ZnO nanostructures by laser-induced chemical liquid deposition

ABSTRACT: ZnO nanorods, nanoneedles, nanoparticles and nanoballs were synthesized on fused quartz substrates upon irradiation of a droplet of methanolic zinc acetate dihydrate solution by an infrared continuous wave CO₂ laser for a few seconds. The addition of monoethanolamine and water to the solution improved the alignment of the nanorods and had a significant effect on the volume and morphology of the deposits. An increase of the zinc acetate concentration was found to lead to an increase of the thickness and area covered by the initial ZnO seed layer on which the nanostructures grew. By investigating the crystal structure of the deposits using x-ray and electron diffraction, we were able to show that the nanorods grow along the c axis with a high crystalline quality. Raman and photoluminescence spectroscopy confirmed the high-quality of the grown ZnO nanostructures. As a matter of fact, their photoluminescence spectra are dominated by an intense UV emission around 390 nm