Metabolomic analysis of wild and transgenic Nicotiana langsdorffii plants exposed to abiotic stresses: unraveling metabolic responses.

Nicotiana langsdorffii plants, wild and transgenic for the Agrobacterium rhizogenes rol C gene and the rat glucocorticoid receptor (GR) gene, were exposed to different abiotic stresses (high temperature, water deficit, and high chromium concentrations). An untargeted metabolomic analysis was carried out in order to investigate the metabolic effects of the inserted genes in response to the applied stresses and to obtain a comprehensive profiling of metabolites induced during abiotic stresses. High-performance liquid chromatography separation (HPLC) coupled to high-resolution mass spectrometry (HRMS) enabled the identification of more than 200 metabolites, and statistical analysis highlighted the most relevant compounds for each plant treatment.

Variation and constraints in species-specific promoter sequences.

A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes.

Randomness and multilevel interactions in biology.

The dynamic instability of living systems and the "superposition" of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems' dynamics.

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 30ppm cadmium(II) or 50ppm chromium(VI).

Transgene traceability in transgenic mice: a bioanalytical approach for potential gene-doping analysis.

Background: The World Anti-Doping Agency fears the use of gene doping to enhance athletic performances. Thus, a bioanalytical approach based on end point PCR for detecting markers' of transgenesis traceability was developed.

Results: A few sequences from two different vectors using an animal model were selected and traced in different tissues and at different times.

Evolutionary trends of GC/AT distribution patterns in promoters.

Nucleotide distributions in genomes is known not to be random, showing the presence of specific motifs, long and short range correlations, periodicities, etc. Particularly, motifs are critical for the recognition by specific proteins affecting chromosome organization, transcription and DNA replication but little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA, putatively leading to differential selective pressures throughout evolution. Promoter sequences have a fundamental role in the regulation of gene activity and a vast literature suggests that their conformational landscapes may be a critical factor in gene expression dynamics.

Affinity sensing for transgenes detection in antidoping control.

Sports authorities fear that a new form of doping called gene doping, based on the misuse of gene therapy, represents an emerging important problem and so far no methods are available for detecting it. The World Anti-Doping Agency (WADA) has included since 2003 for the first time gene doping methods in the "Prohibited List of Substances and Methods", thus detection of this new form of doping is challenging for analytical chemists. In this work, we apply affinity-based biosensors (ABBs), in particular DNA piezoelectric sensing, for detection of target DNA sequences selected as transgenosis markers.

How subchronic and chronic health effects can be neglected for GMOs, pesticides or chemicals.

Chronic health effects are increasing in the world such as cancers, hormonal, reproductive, nervous, or immune diseases, even in young people. During regulatory toxicological subchronic tests to prevent these on mammalian health, prior commercialization of chemicals, including pesticides and drugs, or GMOs, some statistically significant findings may be revealed. This discussion is about the need to investigate the relevant criteria to consider those as biologically significant.

Chance vs. necessity in living systems: a false antinomy.

The concepts of order and randomness are crucial to understand 'living systems' structural and dynamical rules. In the history of biology, they lay behind the everlasting debate on the relative roles of chance and determinism in evolution. Jacques Monod [1970] built a theory where chance (randomness) and determinism (order) were considered as two complementary aspects of life.

Data compression and genomes: a two-dimensional life domain map.

We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions of different complete genomes to distinguish among genomes of different domains of life (Archaea, Bacteria and Eukarya). We shall focus on the distribution function of the complexity of non-coding regions.

Identification by suppression subtractive hybridization of genes expressed in pear (Pyrus spp.) upon infestation with Cacopsylla pyri (Homoptera: Psyllidae).

The molecular interaction between pear tree (Pyrus spp.) and the phloem-feeding psylla Cacopsylla pyri (Linnaeus) was investigated through the construction and characterization of cDNA subtracted libraries. Genes expressed upon insect infestation were identified in the susceptible pear cultivar Bartlett and in the resistant selection NY10355.

Characterisation of 3' transgene insertion site and derived mRNAs in MON810 YieldGard maize.

The construct inserted in YieldGard MON810 maize, produced by Monsanto, contains the CaMV 35S promoter, the hsp70 intron of maize, the cryI(A)b gene for resistance to lepidopterans and the NOS terminator. In a previous work a truncation event at the 3' end of the cryI(A)b gene leading to the complete loss of the NOS terminator was demonstrated. The 3' maize genome junction region was isolated in the same experiment not showing any homology with known sequences.

Detection of fragmented genomic DNA by PCR-free piezoelectric sensing using a denaturation approach.

Label-free and real-time DNA sequence detection in PCR-amplified DNA samples can now be achieved by different approaches. On the contrary, only few works have been reported dealing with direct sequence detection in nonamplified genomic DNA. Here, a piezoelectric biosensor for direct detection of sequences in nonamplified genomic DNA is described.

Functional dynamics of living systems and genetic engineering.

The discussion on Genetically Modified Organisms (GMO's) has been centred mainly on the nature and effects on economy, human health, environment, of the few transgenic plant lines present in the market in the last eight years. On the contrary, the present paper starts with a discussion of some of the relevant changes in our basic knowledge of the structure and dynamics of living systems in the last twenty years. Contemporary Biology is then compared with what may be called the "modern paradigm" of life sciences on which present day GMO's are conceptually based.

Combination of amplification and post-amplification strategies to improve optical DNA sensing.

The work evaluated a series of approaches to optimise detection of polymerase chain reaction (PCR) amplified DNA samples by an optical sensor based on surface plasmon resonance (SPR) (BiacoreX). The optimised procedure was based on an asymmetric PCR amplification system to amplify predominantly one DNA strand, containing the sequence complementary to a specific probe. The study moved into two directions, aiming to improve the analytical performance of SPR detection in PCR amplified products.

A computational model for populations of dividing cells.

A mathematical model of the cell movements due to cell division is presented. In the model we assume that every cell is a computational object with a given volume, and that the cell pushes the neighbouring cells in order to acquire the space for this volume. The Force that each cell exerts over the other cells is derived from a harmonic arbitrary Potential.