Electrophysiological evidence of statistical learning of long-distance dependencies in 8-month-old preterm and full-term infants.

Using electroencephalography, we examined 8-month-old infants' ability to discover a systematic dependency between the first and third syllables of successive words, concatenated into a monotonous speech stream, and to subsequently generalize this regularity to new items presented in isolation. Full-term and preterm infants, while exposed to the stream, displayed a significant entrainment (phase-locking) to the syllabic and word frequencies, demonstrating that they were sensitive to the word unit. The acquisition of the systematic dependency defining words was confirmed by the significantly different neural responses to rule-words and part-words subsequently presented during the test phase. Finally, we observed a correlation between syllabic entrainment during learning and the difference in phase coherence between the test conditions (rule-words vs part-words) suggesting that temporal processing of the syllable unit might be crucial in linguistic learning. No group difference was observed suggesting that non-adjacent statistical computations are already robust at 8 months, even in preterm infants, and thus develop during the first year of life, earlier than expected from behavioral studies.

The application of GMOs in agriculture and in food production for a better nutrition: two different scientific points of view.

This commentary is a face-to-face debate between two almost opposite positions regarding the application of genetic engineering in agriculture and food production. Seven questions on the potential benefits of the application of genetic engineering in agriculture and on the potentially adverse impacts on the environment and human health were posed to two scientists: one who is sceptical about the use of GMOs in Agriculture, and one who views GMOs as an important tool for quantitatively and qualitatively improving food production.

Comparative determination of some phytohormones in wild-type and genetically modified plants by gas chromatography-mass spectrometry and high-performance liquid chromatography-tandem mass spectrometry.

The analytical performances of two optimized analytical methodologies used for the determination of auxins, cytokinins, and abscisic acid in plant samples were critically compared. Phytohormones were extracted from Nicotiana glauca samples using a modified Bieleski solvent and determined both by gas chromatography-mass spectrometry (GC-MS), after derivatization with N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA), and by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) on the Bieleski extract without any further treatment. HPLC-MS/MS gave better results in terms of higher coefficients of determination of the calibration curves, higher and more reproducible recoveries, lower limits of detection, faster sample preparation, and higher sample throughput. Thus, two sets of N. glauca and N. langsdorffii samples, both wild-type and genetically modified by inserting the glucocorticoid receptor (GR) gene encoding for the rat glucocorticoid receptor, were first characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis and then analyzed by HPLC-MS/MS. Significant differences in the phytohormone content between the two sample sets were found and are very important in terms of understanding the mechanisms and effects on growth processes and the development of transgenic plants.

Feedback modulates the temporal scale-free dynamics of brain electrical activity in a hypothesis testing task.

We used the electroencephalogram (EEG) to investigate whether positive and negative performance feedbacks exert different long-lasting modulations of electrical activity in a reasoning task. Nine college students serially tested hypotheses concerning a hidden rule by judging its presence or absence in triplets of digits, and revised them on the basis of an exogenous performance feedback. The scaling properties of the transition period between feedback and triplet presentation were investigated with detrended fluctuation analysis (DFA). DFA showed temporal scale-free dynamics of EEG activity in both feedback conditions for time scales larger than 150 ms. Furthermore, DFA revealed that negative feedback elicits significantly higher scaling exponents than positive feedback. This effect covers a wide network comprising parieto-occipital and left frontal regions. We thus showed that specific task demands can modify the temporal scale-free dynamics of the ongoing brain activity. Putative neural correlates of these long-lasting feedback-specific modulations are proposed.

[Evaluation of polymorphism at microsatellite loci of spring durum wheat (Triticum durum Desf.) varieties and the use of SSR-based analysis in phylogenetic studies]. / Otasenka polimorfizma po mikrosatellitnim lokusam u sortov iarovoi tverdoi pshenitsy (Triticum durum Desf.) i vozmozhnost' ssr-analiza v filogeneticheskikh issledovaniiakh.

Polymorphism at 28 SSR loci was analyzed and described in 45 cultivars of spring durum wheat created in the former USSR and Russia during the last 80 years. Each cultivar was shown to have a unique allele combination. This allows SSR markers to be used to identify durum wheat varieties. Meanwhile, these markers can hardly be used to detect phylogenetic relationships among varieties and to specify their pedigrees, because genetic distances calculated on the basis of these markers do not correlate with the distance calculated by coefficient of parentage.

Pleiotropic effect of the insertion of the Agrobacterium rhizogenes rolD gene in tomato ( Lycopersicon esculentum Mill.).

The Agrobacterium rhizogenes rolD gene, coding for an ornithine cyclodeaminase involved in the biosynthesis of proline from ornithine, has been inserted in Lycopersicon esculentum cv Tondino with the aim of studying its effects on plant morphological characters including pathogen defense response. The analysis of plants transgenic for rolD did not show major morphological modifications. First generation transgenic plants however were found to flower earlier, and showed an increased number of inflorescences and higher fruit yield. Transformed plants were also analysed for parameters linked to pathogen defense response, i.e. ion leakage in the presence of the toxin produced by the fungus Fusarium oxysporum f. sp. lycopersici, and expression of the pathogenesis-related PR-1 gene. All the plants harbouring the rolD gene were shown to be more tolerant to the toxin in ion leakage experiments, with respect to the untransformed regenerated controls and the cv Tondino. PR-1 gene expression was quantitated by means of real-time PCR both at the basal level and after treatment with salicylic acid, an inducer of Systemic Acquired Resistance. In both cases the amount of PR-1 mRNA was higher in the transgenic plants. It seems therefore that the transformation of tomato plants with rolD could lead to an increased competence for defense response, as shown by toxin tolerance and increased expression of the Systemic Acquired Resistance marker gene PR-1. The results are finally discussed in view of their possible economic relevance.

Molecular variation in plant cell populations evolving in vitro in different physiological contexts.

Previous work has shown the fixation of context-specific random amplified polymorphic DNA (RAPD) patterns in tomato cell cultures grown for 2 years in different hormonal contexts. In this work, RAPD sequences were characterised and RAPD-derived molecular markers used for a further study of variation between and within auto- and auxo-trophic tomato cultures grown in different hormonal equilibria. Results were then compared with those obtained using microsatellite markers located in noncoding regions of differentiation- and hormone-related genes and with those obtained with the external transcribed spacer (ETS) from tomato rDNA. Hybridisation of RAPDs on a tomato genomic DNA bank, or on total DNA after enzymatic digestion, suggested that the markers were repetitive in nature. Sequence analysis. however, showed that the homology between different fragments was due mainly to the presence of homo-AT nucleotide stretches. Moreover, a series of computational methods, such as an information-theory algorithm coupled with AG estimates, suggested that the RAPD fragments isolated in our experiments are noncoding. The amplification of SSR-containing RAPD-derived markers, and of other SSRs located in noncoding regions of tomato functional genes, consistently showed polymorphism between auxo- and auto-trophic somaclones (the latter being either habituated or transgenic for Agrobacterium tumefaciens oncogenes) but not within these same clones. Differences were also found between auxotrophic clones and the differentiated tissue. These findings were confirmed by restriction fragment length polymorphism (RFLP) analysis with the REII repetitive element of the ETS from tomato rDNA, which was isolated during this study. The results obtained suggest a possible role for physiological context in the selection of RAPD patterns during the evolution of tomato cells with different endogenous hormonal equilibria. The results are discussed in terms of a possible role for variation in noncoding regions of hormone-related genes in the adaptation to different physiological contexts.

The living state of matter.

Progress in biology has been extremely fast in the second half of the twentieth century in terms of numbers and quality of data. However less attention has been paid to the revision of existing theories on living beings structure and dynamics in development and evolution. Within this frame, the discussion on the very definition of life is lagging in the sometimes ideological debate between mechanistic and holistic views often without serious trials to integrate the overwhelming amount of new data into the different theoretical frameworks. The aim of this short review is to try to define a series of parameters specific of the living state of matter on the basis of existing evidence. The analysis starts from mathematical, physical and experimental studies on DNA constraints in nucleotide distributions and the interactions with proteins in some basic processes of life. The data discussed seem to show that short and long range correlations in DNA, particularly significant in non coding regions and increasing during evolution may have been fixed because of the need of structural landscapes complementarity for DNA-protein recognition and complex dynamics. The need for highly efficient and frequent recognition between the molecules has been extended to gene expression, protein-protein, protein-ligand complex formation and to signal transduction pointing out to the relevance of plasticity on one hand, complementarity on the other. Compartmentalisation and individuality are then taken as critical conditions favouring such processes in the hierarchical networks of all levels, from the cell to organisms, populations, ecosystems, the biosphere. Finally the specific meaning in life of useful (correlated) and disruptive noise is discussed along with the dynamics of evolutionary change in terms of homeorrhetic, plastic maintenance of flexible equilibria continuously challenged by internal and external signals.

The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana.

With the aim of understanding better the distribution and evolution of Agrobacterium rhizogenes genes transferred in the genus Nicotiana, 42 species were screened for presence of rolB, rolC, ORF13, and ORF14. The transferred sequences were then compared within the genus and with current bacterial sequences. The results obtained showed the presence of at least one bacterial gene in 15 species belonging to different subgenera. Sequence analyses supported the hypothesis of coevolution of bacterial and plant sequences, thus suggesting a possible role for the transferred genes in the early events of Nicotiana species differentiation. The high level of conservation of Agrobacterium sequences and the dependence of their expression from the plant physiological context along with previous data suggesting their involvement in the determination of the plant hormonal balance were all consistent with this hypothesis. The results are finally discussed also as to their relevance for the hypothesis of mono and multi ancient infection by Agrobacterium.

Non-normal Statistics of DNA Sequences of Prokaryotes.

The √ n-rule of Schrödinger in his discussion of DNA is based onnormal statistics and equilibrium physics. Herein the kurtosis is used tomeasure the deviation from normality of the stistics of non-equilibrium DNAsequences. A pattern for this deviation from normality is identified andthis signature is found in prokaryotes. The signature is explained by atheory of DNA sequences that involves finite length DNA walks withdynamically generated long-range correlations.

Construction of a new vector conferring methotrexate resistance in Nicotiana tabacum plants.

A new binary vector encoding for Candida albicans dihydrofolate reductase (DFR1) has been constructed and used as a dominant selectable marker for plant transformation. Transgenic tobacco plants with an increased resistance to methotrexate (Mtx) were obtained by co-transformation of tobacco leaf discs with Agrobacterium tumefaciens strains carrying two new binary vectors: pTI20 and pTI18. Co-transformants of Nicotiana tabacum were directly selected for and rooted on medium containing both kanamycin (kan) and Mtx. Leaf discs of transgenic plants were assayed for capacity of regeneration at different Mtx concentrations. Analysis of transcripts was performed on total RNA extracted from two Mtx-resistant plants. The transgenic plants increased resistance to Mtx can be explained by the exceptionally low capacity of Mtx to bind C. albicans dihydrofolate reductase, accountable by the presence of two amino acid residues strategically important in Mtx binding.

A physiological and molecular analysis of the genus Nicotiana.

An analysis of the evolution of the genus Nicotiana was carried out with physiological and molecular tools. The capacity of explants from seedlings of several species of Nicotiana to differentiate roots or shoots or to habituate was used to ascertain whether the in vitro behavior of species has a nonrandom distribution in the genus. The results obtained allowed us to identify two groups of species, one root-forming prone composed of Paniculatae (subgenus Rustica) and the other composed of Alatae, Repandae, and Noctiflorae (subgenus Petunioides), with a major tendency toward the production of shoots. Habituation capacity was characteristic of species randomly distributed throughout the phylogenetic tree. These data suggest fixation throughout the evolution of coadapted gene complexes (hormone-related genes) involved in the control of developmental processes. RAPDs, on the other hand, used as molecular markers for the clustering of related species, seem entirely coherent both with classical morphological and karyological studies and with in vitro physiological methods, supporting an early subdivision of the whole genus into two diverging developmental patterns.

Analysis of genomic patchiness of Haemophilus influenzae and Saccharomyces cerevisiae chromosomes.

We have analysed some aspects of the primary structure of the chromosome of the prokaryote Haemophilus influenzae and of the eukaryote Saccharomyces cerevisiae that share the same G + C content. In particular, we have investigated genomic patchiness over the gene size level (10 Kb) and that patchiness due to long homogenous tracts. Long polypurine and polypyrmidine tracts that are largely over-represented in S. cerevisiae chromosomes and under-represented in H. influenzae, are responsible for a large fraction of long correlation signals. Generating mechanisms of long homogenous tracts are DNA replication slippage and duplication events that appear to be linked processes driving chromosome primary structure evolution.

Genome flux in tomato cell clones cultured in vitro in different physiological equilibria. II. A RAPD analysis of variability.

An analysis of the effect of changing physiological conditions on genome evolution in tomato cell populations has been carried out on long-term in vitro cultured clones grown on different auxin-cytokinin equilibria or selected for low-high competence for active defense against Fusarium oxysporum f.sp. lycopersici. RAPD analysis, confirmed through pattern rehybridization, was used as a random tool to measure the genetic variability. Through the use of a modified ANOVA, variation was shown to depend on both the initial genotype and the physiological conditions. Pattern correlation analysis through a mutual information algorithm suggested the fixation of RAPD patterns specific to physiological equilibria. The results are discussed in view of the possible relevance for evolution at hierarchical levels higher than cell populations. Key words : tomato clones, somaclonal variation, RAPD, coadaptation.

High statistics block entropy measures of DNA sequences.

We have used an improved block-entropy measure in order to gain some further insights into the short-range correlations present in whole chromosomes of S. cerevisiae, viruses and organelles and very large genomic regions of E. coli. Although DNA sequences are largely inhomogeneous and word frequencies are unevenly distributed, the comparison of entire chromosomes and large genomic regions show a "bulk" composition homogeneity. This property suggests that biases in selection, directional mutational pressure and recombination processes act in homogenizing the base composition of the DNA molecules within a genome but their mode of action, relative impact and direction may vary in different organisms. The most interesting results appear to be the differences between the SW (C,G/A,T) and RY (A,G/C,T) two-letter alphabet entropies. Deviations from randomness in E. coli and S. cerevisiae sequences particularly concern SW dinucleotide frequencies and RY tetranucleotide frequencies.

Genome flux in tomato auto- and auxo-trophic cell clones cultured in different auxin/cytokinin equilibria. I. DNA multiplicity and methylation levels.

An analysis of the effect of changing physiological conditions on genetic stability, in terms of epigenetic changes, such as DNA, methylation patterns, and multiplicity of repetitive DNA, was carried out on tomato cell clones grown on media supplemented with different auxin/cytokinin ratios. The effect of endogenous variation in phytohormone equilibria was also indirectly analysed through a comparison of auxotrophic or habituated (autotrophic) cell clones and the differentiated leaf tissue. The data obtained showed significant variation in methylation and multiplicity levels both between clones and between treatments, clearly suggesting a contemporary influence of exogenous hormonal treatments and of the initial/endogenous physiological state of the treated tissue on both phenomena studied.

Third codon G + C periodicity as a possible signal for an "internal" selective constraint.

Quasi-local analysis methods, such as window Fast Fourier Transform and an information theoretical quantity known as mutual information, have allowed us to gain some further insights on the importance and the contextual dependence of a pattern found in DNA sequences showing a periodicity of three with a G or C base in the third position. We have screened for such a periodicity, in terms of the alternative "strong" (S = C or G) versus "weak" (W = A or T) base, a large sample of DNA coding and non-coding sequences from both prokaryotes and eukaryotes, with the aim of testing whether this pattern could be considered as a significant signal for past or present constraints regarding DNA organization and/or function. This periodicity was indeed found in a number of sequences always associated with open reading frames, generally confined in prokaryotes living in extreme environments or in highly conserved eukaryotic genes. Moreover, codon usage was found to be very similar even in genes coding for very different functions. The data are discussed in view of their possible implications for an adaptive value of such a periodicity, in terms of more accurate translation processing and better overall stability.

Modification of competence for in vitro response to Fusarium oxysporum in tomato cells. II. Effect of the integration of Agrobacterium tumefaciens genes for auxin and cytokinin synthesis.

We have studied the effect of a change in the endogenous hormone equilibria on the competence of tomato (Lycopersicon esculentum) cells to defend themselves against the fungal pathogen Fusarium oxysporum f. sp. lycopersici. Calluses from cvs 'Davis' and 'Red River', respectively resistant and susceptible to Fusarium and transgenic for an auxin- or cytokinin-synthesizing gene from Agrobacterium tumefaciens, were used. The integration of Agrobacterium hormone-related genes into susceptible cv 'Red River' can bring the activation of defense processes to a stable competence as assessed by the inhibition of mycelial growth in dual culture and gem-tube elongation of Fusarium conidia, the determination of callose contents, peroxidase induction and ion leakage in the presence of fusaric acid. This is particularly true when the transformation results in a change of phytohormone equilibria towards an higher cytokin in concentration. On the contrary, in resistant cv 'Davis' the inhibition of both fungal growth in dual culture and conidia germination is higher when the hormone balance is modified in favour of the auxins. No significant effect was observed for ion leakage and peroxidase induction, probably because of a constitutive overproduction of cytokinins in 'Davis' cells.

Modification of competence for in vitro response to Fusarium oxysporum in tomato cells. I. Selection from a susceptible cultivar for high and low polysaccharide content.

Plant cell walls play a major role in the outcome of host-parasite interactions. Wall fragments released from the plant, and/or the fungal pathogen, can act respectively as endogenous and exogenous elicitors of the defence response, and other wall components, such as callose, lignin, or hydroxyproline-rich glycoproteins, can inhibit pathogen penetration and/or spreading. We have previously demonstrated that calli from tomato cultivars resistant in vivo to Fusarium oxysporum f.sp. lycopersici show a high amount of polysaccharides in vitro. The aim of the present work was to assess the possible role of polysaccharide content and/or synthetic capacity in determining the competence of plant cells for active defence. For this purpose, tomato cell clones with increased and decreased polysaccharide (FL(+), FL(-)) and callose (A(+), A(-)) content have been selected by means of specific stains as visual markers and tested for the effect of these changes on the extent of response to Fusarium. The analysis of several parameters known to be indicative of active defence (cell browning after elicitor treatment, peroxidase and ß-glucanase induction and inhibition of fungal growth in dual culture) clearly shows that FL(+) and A(+) clones have acquired an increased competence for the activation of defence response. The results are thoroughly discussed in terms of an evaluation of the relative importance of constitutive and/or inducible polysaccharide synthetic capacity for plant response to pathogens, and their possible regulation by plant physiological backgrounds.

The in vitro physiological phenotype of tomato resistance to Fusarium oxysporum f. sp. lycopersici.

With the aim of dissecting host-parasite interaction processes in the system Lycopersicon aesculentum-Fusarium oxysporum f. sp. lycopersici we have isolated plant cell mutants having single-step alterations in their defense response. A previous analysis of the physiological phenotypes of mutant cell clones suggested that recognition is the crucial event for active defence, and that polysaccharide content, fungal growth inhibition, peroxidase induction in in vitro dual culture and ion leakage induced by cultural filtrates of the pathogen can be markers of resistance. In this paper we present the results of a similar analysis carried out on cell cultures from one susceptible ('Red River'), one tolerant ('UC 105') and three resistant ('Davis UC 82', 'Heinz', 'UC 90') tomato cultivars. Our data confirm that the differences in the parameters considered are correlated with resistance versus susceptibility in vivo. Therefore, these parameters can be used for early screening in selection programmes. These data, together with those obtained on isolated cell mutants, suggest that the selection in vitro for altered fungal recognition and/or polysaccharide or callose content may lead to in vivo - resistant genotypes. The data are thoroughly discussed with particular attention paid to the importance of polysaccharides in active defense initiation.