A. Camussi

Expression of a metallothionein A1 gene of Pisum sativum in white poplar enhances tolerance and accumulation of zinc and copper.

Metallothioneins (MT) play an important role in heavy metal detoxification and homeostasis of intracellular metal ions in plant. In this study, two transgenic lines expressing MT type 2 gene (PsMT(A1)) from Pisum sativum, a regenerated non transformed line NT and clone AL22, selected as heavy metal tolerant, were characterized in presence of the heavy metals for the ability to accumulate zinc and copper and to activate antioxidative enzyme defences: superoxide dismutase, catalase, ascorbate peroxidase. The levels of expression of MT type 2 gene assessed by RT-qPCR confirmed the gene over-expression in transgenic lines and evidenced in NT and AL22 the up-regulation of gene transcription by zinc and copper. Transgenic poplar lines during heavy metal stress displayed increased ability to translocate and accumulate zinc and copper compared with NT and AL22. The antioxidant enzyme defence was differently activated in response to metals in the transgenic lines without a significant increase of ROS. These results suggested that PsMT(A1) could play a role in ROS scavenging leading to enhanced metal tolerance and increased zinc and copper sequestration in root and leaf.

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO(2) assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.

The reduction of large molecular profiles to informative components using a Genetic Algorithm

MOTIVATION Molecular profiles (DNA fingerprints) may be used to allocate an individual of unknown membership to one among the known groups of a reference population. Time and costs of profile assessment may be reduced by identifying informative profile components (markers). RESULTS A genetic algorithm (GA) is proposed to identify promising candidate markers from a pilot experiment in which observations are supposed to be without measurement error. The analysis of simulated datasets suggests reasonable values for GA parameters and confirms that the GA finds components of the profile showing association with the considered groups. Our GA may be used to perform a first screening of candidate markers to be included in subsequent experiments. AVAILABILITY The 32-bit executable (Windows 95, 98 and NT) is available at http://www.ds.unifi.it/ approximately stefanin/bioinformatics.htm.

Effect of Water Deficit on Expression of Stress-related Genes in the Cambial Region of Two Contrasting Poplar Clones

In this study we investigated the effect of prolonged water shortage in the cambial region of two poplar clones, Dvina (Populus deltoides) and I-214 (Populus x canadensis) that differ in their response to water deficit. For this purpose we monitored growth parameters in Dvina and I-214 plants under well-watered and water-stress conditions and after rewatering and analyzed the content of malondialdehyde (MDA) and proline and the expression level of genes coding for antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; ascorbate peroxidase, APX; glutathione reductase, GR) and metallothioneins (MT) by quantitative real-time RT-PCR (RT-qPCR). Water deficit resulted in a significant increase of osmotically active solutes in both clones. No significant increase of MDA level was observed in Dvina, whereas a significant enhancement of lipid peroxidation was detected in I-214, in which also a strong fivefold increase of proline was detected. Transcript analysis of stress-related genes indicated a different ability of the two clones to modulate antioxidant genes under stress. In particular, MT3b was strongly upregulated by water deficit in Dvina thus suggesting an important role for this gene in the maintenance of cellular redox homeostasis in the clone. On the whole, the two clones exhibited changes at the transcription and physiological levels in the cambial region that suggest the occurrence of different strategies of plant protection from prolonged water deficit.

SSCP intron marker system is a convenient tool for clonal fingerprinting of poplar (Populus) cultivars of different species and interspecific hybrids

In this study, we evaluate the effectiveness of SSCP analysis of intron markers, as a routine tool for fingerprinting of clones of different poplar species and interspecific hybrids. Exon primed intron crossing primers were designed on two catalase genes. Analysis of these fragments on SSCP gels revealed that catalase introns exhibit substantial sequence variation within poplar species and cultivars. SSCP analysis resulted effective in detecting intra and interspecific polymorphisms among the 119 poplar cultivars obtaining 110 different individual profiles. A hierarchical clustering process showed the high level of divergence among clones reflecting in most cases the section and the species the clones belongs to. This marker system was also proved with high transferability within Salicaceae. SSCP intron analysis represents a powerful tool in detecting DNA sequence polymorphism, in screening diversity and an effective method for clonal fingerprinting.

APLOGEN: an object-oriented genetic algorithm performing Monte Carlo optimization.

Problem-solving and modelling within a biological context often need a level of descriptive accuracy that is unlikely to be capable of analytical treatment, especially if the mathematical background of the biologist is poor. Furthermore solver-model maintenance is often difficult without the availability of trained specialists. Better prospects are found in the genetic algorithm field. Genetic algorithms are a set of procedures formulated to solve complex problems without specifying rules for intermediate steps. This approach becomes feasible performing a Monte Carlo simulation of the natural evolution process, in which population improvement (search for solutions) in a considered environment (the specific problem domain) is achieved by following the genetic paradigm. Starting with a randomly constituted sample of individuals, drawn from the population of admissible values and expressed as binary strings, random mating brings about individuals of the next generation. Parents are chosen with a greater probability as the number of constraints violated by each individual becomes smaller. During the constitution of each generation the presence of some genetic operators causes the improvement of population diversity and its maintenance. Genetic operators are simple string transformation rules, generally independent of a specific context. We have developed the constant core of a minimal genetic algorithm, from which can be derived genetic problem-solvers in specific domains. An applicative example--a constrained matrix equation on signed integers--is also realized to show graphically the algorithm dynamics.

An APL procedure to estimate genotype by environment interaction when two environments are considered

Genotype by environment interaction (GEI) is a relevant topic in many fields of applied biology. Normal parametric approaches following analysis of variance are not suitable when large differences between error variances within environments are present. We illustrate an APL program following Yamadas approach to estimate GEIs and ancillary statistics when two environments are considered. The choice of APL environment is based on its value as a useful tool in algorithm implementation and problem-solving. Its use is suggested in biological applications where matrix algebra is involved and an understanding of the computing complexity of problems is generally not required.

Date Palm Status and Perspective in Libya

Libyan date palm germplasm represents a heritage of great value both for agriculture and the environment. This chapter analyzes all the aspects of the date palm status in Libya starting from the historical aspect to the current status as well as the results of the recent International Union for the Protection of New Varieties of Plants cooperative program between Italy and Libya for improving and promoting date palm production in Libya, which at present is quite low. All the production is consumed locally, and the cultivation techniques and the processing industry are outdated and need to be modernized. The program strategy was driven by two main objectives: first, identification of high-quality dates through production protocols that ensure the consistency and quality of the final product; second, protection of the agrobiodiversity by promoting local date palm cultivars and strengthening traditional oasis management systems. For this purpose 18 Libyan cultivars, representing common genotypes in the central Libyan oasis of Al Jufrah, were studied in detail both from a morphological and genetic point of view. Cultivar descriptions were carried out on the basis of passport descriptors according to international standards to facilitate germplasm passport information exchange together with genetic fingerprinting. This was performed using 16 highly polymorphic simple sequence repeat (SSR) loci, which allowed setting up an efficient and unambiguous identification system. Clonal fingerprinting and cultivar identification are important elements for promoting typical local products and for linking a product to its place of origin. In this context, the Libyan germplasm represents an enormous richness that deserves to be exploited. Its characterization and valorization open new prospects for date palm breeding.