Effect of 5′UTR introns on gene expression in Arabidopsis thaliana

Background The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5′UTRs and 3′UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome. Results A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5′UTRs is similar to that in CDSs but much higher than that in 3′UTRs; (2) the 5′UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5′UTRs are, on average, longer than introns in the CDSs and 3′UTRs; and (4) 5′UTR introns have a different nucleotide composition to that of CDs and 3′UTR introns. Furthermore, we show that the 5′UTR intron of the A. thaliana EFIα-A3 gene affects the gene expression and the size of the 5′UTR intron influences the level of gene expression. Conclusion Introns within the 5′UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3′UTR. In the EFIα-A3 gene, the presence of a long intron in the 5′UTR is sufficient to enhance gene expression in plants in a size dependent manner.

Optimising ketocarotenoid production in potato tubers : effect of genetic background, transgene combinations and environment

Astaxanthin is a high value carotenoid produced by some bacteria, a few green algae, several fungi but only a limited number of plants from the genus Adonis. Astaxanthin has been industrially exploited as a feed supplement in poultry farming and aquaculture. Consumption of ketocarotenoids, most notably astaxanthin, is also increasingly associated with a wide range of health benefits,as demonstrated in numerous clinical studies. Currently astaxanthin is produced commercially by chemical synthesis or from algal production systems. Several studies have used a metabolic engineering approach to produce astaxanthin in transgenic plants. Previous attempts to produce transgenic potato tubers biofortified with astaxanthin have met with limited success. In this study we have investigated approaches to optimising tuber astaxanthin content. It is demonstrated that the selection of appropriate parental genotype for transgenic approaches and stacking carotenoid biosynthetic pathway genes with the cauliflower Or gene result in enhanced astaxanthin content, to give six-fold higher tuber astaxanthin content than has been achieved previously. Additionally we demonstrate the effects of growth environment on tuber carotenoid content in both wild type and astaxanthin-producing transgenic lines and describe the associated transcriptome and metabolome restructuring.

Removal of herbicides from aqueous solutions by modified forms of montmorillonite

This investigation for the removal of agricultural pollutants, imazaquin and atrazine was conducted using montmorillonite (MMT) exchanged with organic cations through ion exchange. The study found that the adsorption of the herbicides was affected by the degree of organic cation saturations, the size of organic cations and the different natures of the herbicides. The modified clays intercalated with the larger surfactant molecules at the higher concentrations tended to enhance the adsorption of imazaquin and atrazine. In particular, the organoclays were highly efficient for the removal of imazaquin while the adsorption of atrazine was minimal due to the different hydrophobicities. Both imazaquin and atrazine were influenced by the changes of pH. The amphoteric imazaquin exists as an anion at the pH 5–7 and the anionic imazaquin was protonated to a neutral and further a cationic form when the pH is lower. The weak base, atrazine was also protonated at lower pH values. The anionic imazaquin had a strong affinity to the organoclays on the external surface as well as in the interlayer space of the MMT through electrostatic and hydrophobic interactions. In this study, the electrostatic interaction can be the primary mechanism involved during the adsorption process. This study also investigated a comparative adsorption for the imazaquin and atrazine and the lower adsorption of atrazine was enhanced and this phenomenon was due to the synergetic effect. This work highlights a potential mechanism for the removal of specific persistence herbicides from the environment.

Effect of water management practice on pesticide behavior in paddy water

The fate and transport of three herbicides commonly used in rice production in Japan were compared using two water management practices. The herbicides were simetryn, thiobencarb and mefenacet. The first management practice was an intermittent irrigation scheme using an automatic irrigation system (AI) with a high drainage gate and the second one was a continuous irrigation and overflow drainage scheme (CI) in experimental paddy fields. Dissipation of the herbicides appeared to follow first order kinetics with the half-lives (DT₅₀) of 1.6-3.4 days and the DT₉₀ (90% dissipation) of 7.4-9.8 days. The AI scheme had little drainage even during large rainfall events thus resulting in losses of less than 4% of each applied herbicide through runoff. Meanwhile the CI scheme resulted in losses of about 37%, 12% and 35% of the applied masses of simetryn, thiobencarb and mefenacet, respectively. The intermittent irrigation scheme using an automatic irrigation system with a high drainage gate saved irrigation water and prevented herbicide runoff whereas the continuous irrigation and overflow scheme resulted in significant losses of water as well as the herbicides. Maintaining the excess water storage is important for preventing paddy water runoff during significant rainfall events. The organic carbon partition coefficient K_oc seems to be a strong indicator of the aquatic fate of the herbicide as compared to the water solubility (S_W). However, further investigations are required to understand the relation between K_oc and the agricultural practices upon the pesticide fate and transport. An extension of the water holding period up to 10 days after herbicide application based on the DT₉₀ from the currently specified period of 3-4 days in Japan is recommended to be a good agricultural practice for controlling the herbicide runoff from paddy fields. Also, the best water management practice, which can be recommended for use during the water holding period, is the intermittent irrigation scheme using an automatic irrigation system with a high drainage gate. © 2006 Elsevier B.V. All rights reserved.

Behavior of simetryn and thiobencarb in rice paddy lysimeters and the effect of excess water storage depth in controlling herbicide run-off

Eight small-scale lysimeters with different excess water storage depths (EWSDs) were used to investigate the behavior of two herbicides, simetryn and thiobencarb, under paddy conditions. The concentration of simetryn dissipated similarly in all the lysimeters, while the thiobencarb concentration varied significantly because thiobencarb can adsorb onto the dissolved organic matter in a manure slurry, which was applied to six of the lysimeters. The herbicide losses (the percentage of the applied mass) from the lysimeters were reversely proportional with the EWSD. The correlation was stronger for simetryn than for thiobencarb. An appropriate EWSD is required to effectively prevent herbicide run-off from the paddy field, especially when a rainfall event occurs soon after herbicide application.