In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called Non-Stationarity Entropic Index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation

Phytochrome A as a functional marker of phyletic relationships in Nicotiana genus

Nicotiana is a small and well characterized genus of Solanaceae and in this study we have used polymorphisms in phytochrome A coding sequence (phyA) and promoter to asses the phylogenetic relationships among species representative of all the sections of the genus. Allopolyploid species kept the two copies of the gene derived from each of the progenitors as resulted from the analyses of the coding region and promoter. Moreover, both copies of phyA present in tetraploids are transcribed, indicating that are properly regulated and do not undergo silencing

The rat glucocorticoid receptor integration in Nicotiana langsdorffii genome affects plant responses to abiotic stresses and to arbuscular mycorrhizal symbiosis

The present study reports evidence of the pleiotropic effects caused by the insertion of the rat glucocorticoid receptor (GR) into the genome of Nicotiana langsdorffii. Transgenic N. langsdorffii-GR plants and the wild-type genotypes were analysed for their phenotypic and physiological characteristics. The integration of the GR gene affected flowering, growth habit, leaf morphology and stomatal pattern. Furthermore, GR plants showed an increased tolerance to heavy metal, drought and heat stress as evidenced by electrolyte leakage and by cell dedifferentiation and differentiation capability after recovery from stress treatments. We also monitored the establishment of the beneficial symbiosis between transgenic plants and the mycorrhizal fungus Funneliformis mosseae whose presymbiotic growth was significantly reduced by root exudates of N. langsdorffii-GR plants. The observed pleiotropic responses of transgenic plants may be a consequence of the hormonal imbalance, putatively due to the interaction of the GR receptor with the host genetic background. Our findings suggest that N. langsdorffii-GR plants can be used as a functional model system for the study of plant responses to a series of environmental stimuli

A framework for a European network for a systematic environmental impact assessment of genetically modified organisms (GMO)

The assessment of the impacts of growing genetically modified (GM) crops remains a major political and scientific challenge in Europe. Concerns have been raised by the evidence of adverse and unexpected environmental effects and differing opinions on the outcomes of environmental risk assessments (ERA). The current regulatory system is hampered by insufficiently developed methods for GM crop safety testing and introduction studies. Improvement to the regulatory system needs to address the lack of well designed GM crop monitoring frameworks, professional and financial conflicts of interest within the ERA research and testing community, weaknesses in consideration of stakeholder interests and specific regional conditions, and the lack of comprehensive assessments that address the environmental and socio economic risk assessment interface. To address these challenges, we propose a European Network for systematic GMO impact assessment (ENSyGMO) with the aim directly to enhance ERA and post-market environmental monitoring (PMEM) of GM crops, to harmonize and ultimately secure the long-term socio-political impact of the ERA process and the PMEM in the EU. These goals would be achieved with a multi-dimensional and multi-sector approach to GM crop impact assessment, targeting the variability and complexity of the EU agro-environment and the relationship with relevant socio-economic factors. Specifically, we propose to develop and apply methodologies for both indicator and field site selection for GM crop ERA and PMEM, embedded in an EU-wide typology of agro-environments. These methodologies should be applied in a pan-European field testing network using GM crops. The design of the field experiments and the sampling methodology at these field sites should follow specific hypotheses on GM crop effects and use state-of-the art sampling, statistics and modelling approaches. To address public concerns and create confidence in the ENSyGMO results, actors with relevant specialist knowledge from various sectors should be involved

Response to metal stress of Nicotiana langsdorffii plants wild-type and transgenic for the rat glucocorticoid receptor gene

Recently our findings have shown that the integration of the gene coding for the rat gluco-corticoid receptor (GR receptor) in Nicotiana langsdorffii plants induced morphophysiological effects in transgenic plants through the modification of their hormonal pattern. Phytohormones play a key role in plant responses to many different biotic and abiotic stresses since a modified hormonal profile up-regulates the activation of secondary metabolites involved in the response to stress. In this work transgenic GR plants and isogenic wild type genotypes were exposed to metal stress by treating them with 30 ppm cadmium(II) or 50 ppm chromium(VI). Hormonal patterns along with changes in key response related metabolites were then monitored and compared. Heavy metal up-take was found to be lower in the GR plants. The transgenic plants exhibited higher values of S-abscisic acid (S-ABA) and 3-indole acetic acid (IAA), salicylic acid and total polyphenols, chlorogenic acid and antiradical activity, compared to the untransformed wild type plants. Both Cd and Cr treatments led to an increase in hormone concentrations and secondary metabolites only in wild type plants. Analysis of the results suggests that the stress responses due to changes in the plant's hormonal system may derive from the interaction between the GR receptor and phytosteroids, which are known to play a key role in plant physiology and development. (C) 2013 Elsevier GmbH. All rights reserved

Ingegneria genetica ed etica

1. Il termine Etica deriva come è noto dal greco Ethikòs e si può definire come una dottrina o indagine speculativa intorno al comportamento pratico dell’uomo di fronte ai due concetti del bene e del male. Questa definizione tuttavia è relativamente vaga perché si riferisce a tutti i comportamenti umani che sono molto diversi gli uni dagli altri sia perché la concezione stessa del bene e del male si va modificando con quelli che chiamo «gli spiriti dei tempi» e cioè i modi di vedere collettiv..