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A systems biology approach to shed light on apple fruit development
Get PDFThe research carried out and discussed in the present dissertation is positioned within the “TranscrApple” project (www.transcrapple.com), funded by the Provincia Autonoma di Trento (PAT) within the call “Grandi Progetti 2012”. The general objectives of this project, a significant part of which overlap with the present thesis, deal with the characterization, as wide as possible with the currently available technologies, of the transcriptional events, including those related to small RNAs (not discussed in the present dissertation), the metabolic changes, on a subset of primary and secondary metabolites, and hormones’ cross-talk, through a hormone profiling approach, occurring during apple fruit development.
The present thesis is organized in different chapters, mirroring the experimental and temporal rationale effectively pursued to develop the research herein described. The main objective of the present work deals not only with providing an overview of transcripts, metabolites and hormones and their variations during fruit development, but also with the setting up of technical and experimental solutions aimed at using the achieved information within an integrative platform, according to a “systems biology view”. In model species, all this kind of studies are extremely easier, thanks to the availability of ready-to-use bioinformatics tools that are not flexible enough to be used in other species. However, especially in tree crops, this approach is still far from being defined and standardized.
Chapter 1 introduces the theme “apple fruit development”, discussing the adoption of apple as a model system that, in the last decade, acquired great importance in terms of research among the fruit species thanks to the availability of its sequenced genome. After a brief introduction on the fundamental information available about the apple fruit growth, taking into account the technological and scientific points of view, few difficulties and gaps that hamper the achievement of a complete overview of the regulatory events coordinating the development and growth of the apple, are discussed in relation to the main quantitative and qualitative parameters characterizing the apple fruit production.
Chapter 2 enters into the apple fruit research area; the preliminary phase and the multiple validations (concerning different cultivars and seasons) of transcriptional markers during the main apple developmental stages were shown to be fundamental for choosing, on the base of the expression profiles of these genes, the most representative samples, among those collected also in different seasons. Several markers have been identified, validated and
employed, among those available from literature, allowing the selection of samples of cv Golden Delicious (herein considered as model) to be used for the subsequent transcriptional and metabolomic characterization carried out in the present research.
Chapter 3 deals with the hormonal profiling survey carried out along the apple fruit development for the first time in this species. The results have allowed not only the achievement of brand new data related to the major hormonal classes, to be employed for further researches, but also the clarification and/or confirmation of new hormonal interactions connected to the fruit development stage or the transition between stages. Moreover, the relevance of this study consists in having achieved, for the first time in apple, quantitative data of an important set of hormones concurrently on the same samples.\ud
Chapter 4 concerns the survey on the metabolites and their variations during the apple fruit development. A complete overview of the changes of the different classes of metabolites (mainly sugars, organic acids, aminoacids and polyphenols) is given during the apple developmental cycle. The acquired data have been derived from the same samples already analyzed in the previous chapters, and will be integrated with data of diverse nature, such as the RNAseq.
Chapter 5 of the present thesis comes into the “system biology” area, initially among several technical difficulties, then partially solved, and gives an example of an alternative interpretation of the hormonal data put within a correlative network along with the RNAseq results achieved on the same samples
Profili trascrizionali dei geni coinvolti nella biosintesi e trasduzione del segnale etilenico durante l’abscissione dei frutticini in melo
No full textL’abscissione dei frutticini di melo è preceduta da una stimolazione della biosintesi dell’etilene e un aumento della sensibilità della zona di abscissione (AZ) agli stimoli promossi dall’ormone. Recentemente, è stato ipotizzato il ruolo dell’etilene come “carrier” del segnale abscissione che, generato nella cortex mediante l’instaurazione di un cross-talk con ABA, zuccheri e ROS, viene trasferito al seme nelle fasi che precedono l’attivazione dell’AZ. Rimangono tuttavia ancora molti aspetti da chiarire. A tal proposito, è stata condotta un’approfondita indagine a livello trascrizionale dei geni coinvolti nella biosintesi e trasduzione del segnale etilenico in cortex e seme di frutticini di melo trattati con benziladenina (BA). Sono stati identificati nella sequenza genomica 80 geni codificanti elementi della biosintesi (ACO e ACS), percezione (ETR, ERS, TPR e RTE) e trasduzione del segnale (CTR, EIN2 e EIN3/EIL), regolatori coinvolti nell’ubiquitinizzazione e degradazione mediante proteasoma (EBF e ETP) e altri elementi noti (EIN5 e RAN1). Inoltre, 13 geni codificanti chinasi (MAPK e MAPKK), coinvolte nella presunta via trasduttiva del segnale coordinata da CTR, sono stati presi in esame in questo lavoro. Un elevato livello di ridondanza è stato riscontrato per la maggior parte dei geni, probabilmente dovuto all’origine del genoma del melo e al recente evento di duplicazione a cui è andato incontro. In seguito, sono stati analizzati i profili trascrizionali dei geni identificati in cortex e seme di frutticini caratterizzati da diversi potenziali di abscissione. I risultati preliminari hanno evidenziato una notevole tessuto-specificità di espressione dei geni analizzati e differenze trascrizionali che potrebbero coordinare l’attivazione del segnale primario specifico dell’abscissione. Questo studio è finanziato dal Progetto AGER, grant n° 2010-2119
Identification of culturable bacterial endophyte community isolated from tissues of Vitis vinifera“Glera”
No full textEndophytes are micro-organisms that colonize the internal tissues of plants without inducing signs of negative effects and that can provide benefits to plant health and yield. In the present work, the culturable bacterial endophyte community, colonizing vegetative organs of grapevine, was isolated from surface-sterilized plant tissues and characterized by molecular methods. From roots, shoots and leaves of Vitis vinifera “Glera”, located in six different vineyards throughout the Conegliano-Valdobbiadene DOCG area (Veneto, Italy), 381 culturable strains were successfully isolated; amplified ribosomal DNA restriction analysis and nucleotide sequencing showed that approximately 30% of the endophyte community belonged to the genus Bacillus, which was the most represented; other genera such as Staphylococcus, Microbacterium, Paenibacillus,
Curtobacterium, Stenotrophomonas, Variovorax, Micrococcus and Agrococcus were identified. Endophyte community composition within each vine was different in respect to other endophyte populations living in grapevine plants coming from different vineyards; moreover, the bacterial composition changed depending on the season of sampling. The above data highlight the great diversity of culturable bacterial species inhabiting Glera grapevines and open the way for a characterization and selection of strains that could potentially be used to improve the vineyard management for plant growth and yield, plant responses to stresses, biocontrol and biofertilization
Thermographic imaging to identify abscising apple fruitlets after a thinning treatment
No full textMetamitron is a widely used active ingredient in pome fruit thinning. Its inhibitory action on photosynthesis determines a nutritional stress that in turn stimulates the weakest fruitlets to abscise. However, a successful thinning treatment with metamitron, commercially known as Brevis®, relies upon several interacting factors, both endogenous and exogenous, and its effects are difficult to predict under certain specific conditions. For this reason, new predictors are desirable to assist the growers in applying the treatment at optimal time and dosage. Moreover, the physiology of metamitron action is in part still unknown, especially at the fruitlet level. In the present research, a thermographic assessment was carried out to verify the hypothesis that high abscisic acid levels together with photosynthesis block in the fruitlet tissues cause the temperature to raise to higher levels in treated fruitlets than in the untreated ones. A specific trial was carried out in ‘Golden Delicious’, pointing out that both leaves and fruitlets of thinned trees show higher temperatures, which can be used to identify abscising fruitlets. A working model is also proposed that summarizes the way of action of Brevis® on both the considered organ
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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