Alessandro Botton

University of Padova, Padua, Veneto, Italy

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Publications (33)86.94 Total impact

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    ABSTRACT: Tight control of cell/tissue identity is essential for a correct and functional organ patterning, an important component of overall fruit development and eventual maturation and ripening. Despite many investigations regarding the molecular determinants of cell identity in fruits of different species, a useful model able to depict the regulatory networks governing this relevant part of fruit development is still missing. Here we described the peach fruit as a system to link the phenotype of a slow ripening (SR) selection to an altered transcriptional regulation of genes involved in determination of mesocarp cell identity providing insight toward molecular regulation of fruit tissue formation. Morpho- anatomical observations and metabolomics analyses per- formed during fruit development on the reference cultivar Fantasia, compared to SR, revealed that the mesocarp of SR maintained typical immaturity traits (e.g. small cell size, high amino acid contents and reduced sucrose) throughout development, along with a strong alteration of phenylpropanoid contents, resulting in accumulation of phenylalanine and lignin. These findings suggest that the SR mesocarp is phenotypically similar to a lignifying endocarp. To test this hypothesis, the expression of genes putatively involved in the determination of drupe tissues identity was assessed. Among these, the peach HEC3-like gene FLESHY showed a strongly altered expression profile consistent with pit hardening and fruit ripening, generated at a post-transcriptional level. A double function for FLESHY in channelling the phenylpropanoid pathway to either lignin or flavour/aroma is suggested, along with its possible role in triggering auxin- ethylene cross-talk at the start of ripening.
    No preview · Article · Feb 2016 · Plant Molecular Biology
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    Full-text · Book · Jul 2015
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    ABSTRACT: Nitrate is an essential nutrient for plants, and crops depend on its availability for growth and development, but its presence in agricultural soils is far from stable. In order to overcome nitrate fluctuations in soil, plants have developed adaptive mechanisms allowing them to grow despite changes in external nitrate availability. Nitrate can act as both nutrient and signal, regulating global gene expression in plants, and the root tip has been proposed as the sensory organ. A set of genome-wide studies has demonstrated several nitrate-regulated genes in the roots of many plants, although only a few studies have been carried out on distinct root zones. To unravel new details of the transcriptomic and proteomic responses to nitrate availability in a major food crop, a double untargeted approach was conducted on a transition zone-enriched root portion of maize seedlings subjected to differing nitrate supplies. The results highlighted a complex transcriptomic and proteomic reprogramming that occurs in response to nitrate, emphasizing the role of this root zone in sensing and transducing nitrate signal. Our findings indicated a relationship of nitrate with biosynthesis and signalling of several phytohormones, such as auxin, strigolactones, and brassinosteroids. Moreover, the already hypothesized involvement of nitric oxide in the early response to nitrate was confirmed with the use of nitric oxide inhibitors. Our results also suggested that cytoskeleton activation and cell wall modification occurred in response to nitrate provision in the transition zone. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
    Full-text · Article · Apr 2015 · Journal of Experimental Botany
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    ABSTRACT: Apple (Malus x domestica) is increasingly being considered an interesting model species for studying early fruit development, during which an extremely relevant phenomenon, i.e. fruitlet abscission, may occur as a response to both endogenous and/or exogenous cues. Several studies were carried out shedding light on the main physiological and molecular events leading to the selective release of lateral fruitlets within a corymb, either occurring naturally or as a result of a thinning treatment. Several studies pointed out a clear association between a rise of ethylene biosynthetic levels in the fruitlet and its tendency to abscise. A direct mechanistic link, however, has not yet been established between this gaseous hormone and the generation of the abscission signal within the fruit. In the present research, the role of ethylene during the very early stages of abscission induction was investigated in fruitlet populations with different abscission potentials due either to the natural correlative inhibitions determining the so called "physiological fruit drop" or to a well tested thinning treatment performed with the cytokinin 6-benzyladenine. A crucial role was ascribed to the ratio between the ethylene produced by the cortex and expression of ethylene receptor genes in the seed. This ratio would determine the final probability to abscise. A working model has been proposed consistently with the differential distribution of four receptor transcripts within the seed, which resembles a spatially progressive cell-specific immune-like mechanism evolved by apple to protect the embryo from harmful ethylene. Copyright © 2015, Plant Physiology.
    Full-text · Article · Apr 2015 · Plant physiology
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    ABSTRACT: Abscission is the regulated process of detachment of an organ from a plant. In apple the abscission of fruits occurs during their early development to control the fruit load depending on the nutritional state of the plant. In order to control production and obtain fruits with optimal market qualities, the horticultural procedure of thinning is performed to further reduce the number of fruitlets. In this study we have conducted a transcriptomic profiling of seeds from two different types of fruitlets, according to size and position in the fruit cluster. Transcriptomic profiles of central and lateral fruit seeds were obtained by RNAseq. Comparative analysis was performed by the functional categorization of differentially expressed genes by means of Gene Ontology (GO) annotation of the apple genome. Our results revealed the overexpression of genes involved in responses to stress, hormone biosynthesis and also the response and/or transport of auxin and ethylene. A smaller set of genes, mainly related to
    Full-text · Article · Mar 2015 · PLoS ONE
  • G. Eccher · S. Ferrero · F. Populin · L. Colombo · A. Botton
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    ABSTRACT: Apple research has undergone great improvements in the last years, in both quantitative and qualitative terms. Huge amount of data are now available, especially as far as the early development and the ripening phase are concerned. Moreover, the recent release of the apple genome sequence is significantly speeding up research, allowing on one hand to shed light on the most critical aspects of fruit development with almost immediate practical implications and, on the other hand, to identify new molecular markers that will improve the future breeding programs. In this context, apple is being increasingly considered as a model for fruit development studies, although many gaps still exist in apple research. These gaps are being filled by coupling the next generation high-throughput technologies with new physiological approaches, aimed at achieving both new basic knowledge and innovative tools to improve the final quality of the fruit. In this review, the available information on the regulatory aspects of apple fruit development will be reported and discussed in the light of the future perspectives of apple research.
    No preview · Article · Mar 2014 · Plant Biosystems
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    ABSTRACT: A ripening specific bZIP gene of peach was studied by ectopically expressing it in tomato. Two lines, with either a mild or a strong phenotype, respectively, were analyzed in detail. Transgenic fruit morphology was normal, yet the time spent to proceed through the various ripening stages was longer compared to wild type. In agreement with this finding the transgenic berries produced less ethylene, and also had a modified expression of some ripening-related genes that was particularly evident in berries with a strong phenotype. In particular, in the latter fruits polygalacturonase and lipoxygenase genes, but also genes coding for transcription factors (TFs) important for tomato ripening (i.e. TAGL1, CNR, APETALA2a, NOR) did not show the expected decreased expression in the red berries. As regards the RIN gene, its expression continued to increase in both mild and strong lines, and this is in agreement with the dilated ripening times. Interestingly, a metabolomic analysis of berries at various stages of ripening showed that the longer time spent by the transgenic berries to proceed from a stage to another was not due to a slackened metabolism. In fact, the differences in amount of stage-specific marker metabolites indicated that the transgenic berries had a very active metabolism. Therefore, the dilated ripening and the enhanced metabolism of the berries over-expressing the bZIP gene suggest that such gene might regulate ripening by acting as a pacemaker for some of the ripening metabolic pathways.
    No preview · Article · Jun 2013 · Plant Physiology and Biochemistry
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    ABSTRACT: Apple (Malus domestica L. Borkh) fruitlet abscission represents an interesting model system to study the early phases of the shedding process, during which major transcriptomic changes and metabolic rearrangements occur within the fruit. In apple, the drop of fruits at different positions within the cluster can be selectively magnified through chemical thinners, such as benzyladenine and metamitron, acting as abscission enhancers. In the present research, different abscission potentials were obtained within the apple fruitlet population by means of the above cited thinners. A metabolomic study was conducted on the volatile organic compounds (VOCs) emitted by abscising fruitlets, allowing to identify isoprene as an early marker of abscission induction. A strong correlation was also observed between isoprene production and abscisic acid (ABA) levels in the fruit cortex, which were shown to increase in abscising fruitlets with respect to non-abscising ones. Transcriptomic evidence indicated that abscission-related ABA is biologically active and its increased biosynthesis is associated with the induction of a specific ABA-responsive NCED (9-cis-epoxycarotenoid dioxygenase) gene. According to a hypothetical model, ABA may transiently cooperate with other hormones and secondary messengers in the generation of an intra-fruit signal leading to the downstream activation of the abscission zone. The shedding process therefore appears to be triggered by multiple interdependent pathways, whose fine regulation, exerted within a very short temporal window by both endogenous and exogenous factors, determines the final destiny of the fruitlets.
    Preview · Article · Feb 2013 · Plant physiology
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    ABSTRACT: Specific bioinformatic analyses were carried out in peach and olive, starting with the ab initio identification of genes responsible for flower differentiation (‘ABCDE’ genes). The peach MADS-box genes involved in this process, already identified and partially characterized, were used to validate the bioinformatic approach herein adopted using the recent release of the genome. A double experimental approach including Hidden Markov Models and Blast was set up by exploiting all available genes with function validated not only in model plants but also in crop species. Since the genome sequence of olive is not available, a 454 collection recently generated from flower buds at different developmental stages was used as a target database. In peach, the list of candidates was implemented with further members, such as four AP2- and two AP3-like genes, with a putative ‘A’ and ‘B’ function, respectively. In olive, a higher number of candidates was identified compared to peach, probably due both to the larger size and the polyploid origin of its genome, as well as to the presence of different alleles of the same gene (being most loci heterozygous in olive and homozygous in peach). Phylogenetic analyses pointed out homogeneous clusters in which candidates of the same class group together with proteins already characterized in model species (i.e. Arabidopsis and Antirrhinum). Expression analyses of candidates are currently in progress in order to assess the organ specificity and the timing of expression.
    Full-text · Article · Dec 2012 · Acta horticulturae
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    ABSTRACT: Background Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison. Results The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial ‘synergism’ between auxins and ABA, although to a lesser extent. Conclusions This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network.
    Full-text · Article · Oct 2012 · BMC Plant Biology
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    ABSTRACT: Humic substances (HS), as component of soil organic matter, have been widely studied. Their positive effects on plant physiology have been further demonstrated, but there are no clear evidences about the direct as well as indirect mechanisms regulating these processes.In this paper a transcriptomic approach based on the detection of cDNA-AFLP markers was used to identify candidate genes potentially involved in the regulation of the response to HS in Arabidopsis thaliana.Using 160 primer combinations, the cDNA-AFLP enabled to identify 133 genes putatively involved in plant–HS interaction. Sequence analysis and Gene Ontology classification indicated that a large number of genes involved in developmental and metabolic processes, as well as in transcription regulation or RNA metabolism were identified as HS-regulated. Real-Time PCR analyses confirmed transcription levels of 32 HS-regulated genes.This study demonstrates that HS exert their effects on plant physiology by means of complex transcriptional networks. From the overall transcriptomic results we may hypothesize that HS exert their function through a multifaceted mechanism of action, partially connected to their well demonstrated auxin activity, but involving also IAA-independent signalling pathways.
    No preview · Article · Dec 2011 · Environmental and Experimental Botany
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    ABSTRACT: Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR) was used to study this process. A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia) throughout different developmental stages (S1, S2, S3 and S4) evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein), a PR (pathogenesis-related) protein, a prunin and LEA (Late Embryogenesis Abundant) protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively.The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin) or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on. In this research, genes were identified marking different phases of seed and mesocarp development. The selected genes behaved as good seed markers, while for mesocarp their reliability appeared to be dependent upon developmental and ripening traits. Regarding the cross-talk between seed and pericarp, possible candidate signals were identified among hormones.Further investigations relying upon the availability of whole genome platforms will allow the enrichment of a marker genes repertoire and the elucidation of players other than hormones that are involved in seed-pericarp cross-talk (i.e. hormone peptides and microRNAs).
    Full-text · Article · Jun 2011 · BMC Plant Biology
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    ABSTRACT: Mob1 genes are primarily involved in the cell cycle progression and mitosis exit in yeasts and animals. The function of a Mob1-like gene (At5g45550) from Arabidopsis thaliana was investigated using RNAi and immunological staining. AtMob1-like RNAi silenced lines showed a reduced radial expansion of the inflorescence stem and a reduced elongation zone of the primary root. Morphological features of plant organs were accompanied by a reduction in cell size. The fertility of AtMob1-like RNAi silenced lines was very low as seed production was strongly reduced. About 2% of the progeny of AtMob1-like RNAi silenced plants were tetraploid. The female and male sporogenesis was affected differentially. The ovules developed irregularly and one third of the megaspores and embryo sacs degenerated prematurely. Up to 20% of the ovules produced binucleated megaspores that failed to develop further, being their degeneration likely accompanied with a delayed programmed cell death. The anthers produced about 30% of aborted pollen grains, showing also a strong variation in their size. Together, the results show that Arabidopsis MOB1-like is required to regulate cell expansion and cell division, presumably by affecting the mitotic as well as the meiotic cell cycle.
    Full-text · Article · May 2011 · Gene
  • A. Botton · G. Eccher · B. Ruperti · A. Ramina · A. Boschetti
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    ABSTRACT: Benzyladenine (BA) is a well known synthetic cytokinin broadly used as a thinning agent in apple orchards. BA has numerous physiological effects, strictly dependent upon the tree developmental stage, the concentration of the chemical and the environmental conditions at the time of spraying. The enhanced ethylene evolution observed in BA-treated apple leaves and fruits may be one of the key factors that trigger the physiological processes leading to fruitlet abscission. In order to shed light on the ethylene-related events occurring during abscission, a timecourse model for BA action was developed based upon physiological data obtained by combining the use of BA either with AVG (aminoethoxyvinylglycine), or 1-MCP (1-methylcyclopropene), blocking ethylene biosynthesis and perception, respectively. The results confirm the bimodal action of BA through ethylene, acting first on shoot growth and then, most likely indirectly, promoting fruitlet abscission. Based on a 24 hours-resolution time-course, a very fast action of BA was observed within 24 h from the treatment. A parallel antagonist effect was exerted by AVG within 24-48 h. This model, currently under validation, was confirmed to be a very reliable system for studying fruitlet abscission in apple.
    No preview · Article · Dec 2010 · Acta horticulturae
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    ABSTRACT: Field observations and few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate partenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited and coming exclusively from a microarray approach. The identification of genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach seed and mesocarp throughout development using the first peach microarray (μPEACH 1.0). It has been shown that the transcription factor families (TFs) more involved were the MADS-box, AUX/IAA and bZIP. Some members of these families showed a differential expression pattern according to the organ and developmental phase, being more expressed in embryo at early development and in mesocarp at ripening. Among the isolated TFs, a bZIP, homologous to Arabidopsis ATB2, which controls transcription in seed and fruit, and similar to bZIPs highly abundant in ripe fleshy fruit of several species. Other factors deeply involved in the regulation of seed and fruit development are the plant hormones. Genes responsible for the biosynthesis and action of auxin, ethylene, ABA and jasmonates showed a differential expression pattern in seed and fruit, pointing out a possible role in the crosstalk between the two organs.
    Full-text · Article · Dec 2010 · Acta horticulturae
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    ABSTRACT: Apple (Malus × domestica) represents an interesting model tree crop for studying fruit abscission. The physiological fruitlet drop occurring in this species can be easily magnified by using thinning chemicals, such as benzyladenine (BA), to obtain fruits with improved quality and marketability. Despite the economic importance of this process, the molecular determinants of apple fruitlet abscission are still unknown. In this research, BA was used to obtain fruitlet populations with different abscission potentials to be analyzed by means of a newly released 30K oligonucleotide microarray. RNAs were extracted from cortex and seed of apple fruitlets sampled over a 4-d time course, during which BA triggers fruit drop, and used for microarray hybridization. Transcriptomic profiles of persisting and abscising fruitlets were tested for statistical association with abscission potential, allowing us to identify molecular signatures strictly related to fruit destiny. A hypothetical model for apple fruitlet abscission was obtained by putting together available transcriptomic and metabolomic data. According to this model, BA treatment would establish a nutritional stress within the tree that is primarily perceived by the fruitlet cortex whose growth is blocked by resembling the ovary growth inhibition found in other species. In weaker fruits, this stress is soon visible also at the seed level, likely transduced via reactive oxygen species/sugar and hormones signaling cross talk, and followed by a block of embryogenesis and the consequent activation of the abscission zone.
    Full-text · Article · Oct 2010 · Plant physiology
  • Alessandro Botton · Carlo Andreotti · Guglielmo Costa · Angelo Ramina
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    ABSTRACT: The fruits of Rosaceae species may frequently induce allergic reactions in both adults and children, especially in the Mediterranean area. In peach, true allergens and cross-reactive proteins may cause hypersensitive reactions involving a wide diversity of symptoms. Three known classes of allergenic proteins, namely, Pru p 1, Pru p 3, and Pru p 4, have been reported to be mostly involved, but an exhaustive survey of the proteins determining the overall allergenic potential, their biological functions, and the factors affecting the expression of the related genes is still missing. In the present study, the expression profiles of some selected genes encoding peach allergen isoforms were studied during fruit growth and development and upon different fruit load and light radiation regimens. The results indicate that the majority of allergen-encoding genes are expressed at their maximum during the ripening stage, therefore representing a potential risk for peach consumers. Nevertheless, enhancing the light radiation and decreasing the fruit load achieved a reduction of the transcription rate of most genes and a possible decrease of the overall allergenic potential at harvest. According to these data, new growing practices could be set up to obtain hypoallergenic peach fruits and eventually combined with the cultivation of hypoallergenic genotypes to obtain a significant reduction of the allergenic potential.
    No preview · Article · Jan 2009 · Journal of Agricultural and Food Chemistry
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    ALESSANDRO BOTTON · PAOLO LEZZER · ALBERTO DORIGONI
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    ABSTRACT: SUMMARY Apples can cause allergic reactions in the worldwide population because of the presence of four classes of allergens (Mal d 1, Mal d 2, Mal d 3, and Mal d 4), and their cross-reactivity with sensitising allergens in other species. Knowledge of the factors that affect the allergenic potential of apples would provide important information to apple growers and consumers for the adoption of agronomic practices to decrease the allergenic potential, and for the consumption of fruits with reduced levels of allergens. Expression studies on apple genes that encode allergens were performed by means of real-time PCR. Samples were collected from fruit in different trials set up to assess the effects of shading, elevation, storage, and water stress on the expression of apple allergen genes. Shading, elevation, and storage significantly affected the transcription of all genes encoding allergens, whereas water stress had only a slight influence on the expression of the Mal d 4 family of genes. The implications of these results for growers and consumers are critically discussed.
    Full-text · Article · Jan 2009 · Journal of Horticultural Science and Biotechnology
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    ABSTRACT: l-Aminoethoxyvinylglycine (AVG) and 1-naphthylacetic acid (NAA) are known to affect preharvest fruit drop, fruit quality and fruit maturation in Golden Delicious apples (Malus×domestica Borkh). Experiments were carried out on GD/M9 trees treated at three different developmental stages (41, 28 and 17days before the beginning of the commercial harvest) with AVG and NAA. Both chemicals significantly reduced fruit drop without significantly affecting the fruit weight. Background colour development and ripening were both delayed by AVG, whereas NAA significantly enhanced yellowing without affecting the evolution of ripening. Ethylene evolution and transcription profiles of genes involved in ethylene biosynthesis (MdACS1 and MdACO1) and action (MdETR1, MdERS1 and MdCTR1) were monitored in cortex from the date of the first treatment until the beginning of fruit drop in the control trees (21days after the beginning of commercial harvest). AVG blocked or efficiently reduced the ethylene evolution. This effect was paralleled by a down-regulation of MdACS1, MdACO1, MdETR1 and MdERS1. NAA at the second and third date of application enhanced the onset of ethylene evolution, although, at the end of the experiment, no difference was found between control and treated fruits. The chemical applied in the first date significantly down-regulated the transcription of the genes at the end of the experiment. MdCTR1 expression, basically unaffected by AVG and NAA, appeared to be transiently down-regulated. The initial down-regulation is under developmental control, whereas the late regain of transcript accumulation paralleled the ethylene evolution.
    No preview · Article · Dec 2008 · Plant Growth Regulation
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    ABSTRACT: Aspergillus carbonarius is responsible for the majority of mycotoxin contaminations in grapes and its derivatives. Most of A. carbonarius strains are ochratoxin A (OTA) producers, even though at very different levels. This broad variability was used to identify genes whose expression is linked with the ability of producing OTA. A cDNA-AFLP differential display screening was performed in two strains of A. carbonarius, antagonists for the ability of producing OTA, allowing the identification of 119 differentially expressed sequences putatively involved in the regulation of OTA biosynthesis. A likely connection was pointed out between the biosynthesis of the toxin, vegetative growth and sexual/asexual developmental progression, along with common signalling pathways involving G protein and Ca2+/calmodulin dependent phosphorylation and dephoshorylation cascades.
    Full-text · Article · Oct 2008 · International Journal of Food Microbiology