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Genetic evolution of the pathway controlling fruit carotenoid content in tomato (S. lycopersicum) and its wild relatives
Full text linkIl pomodoro (Solanum lycopersicum) e’ una specie ortiva molto importante sia dal punto di vista economico che nutritivo e costituisce la “pianta modello” per numerosi studi di tipo genetico grazie ad alcune sue proprieta’: ha un genoma di medie dimensioni (950 Mb), ha un ciclo vitale breve, per questa specie esiste un’ampia collezione di mutanti genici e inoltre possono essere applicate numerose tecniche di trasformazione e di manipolazione genetica. Alla fine del 2009 e’ stata resa disponibile la prima versione del genoma del pomodoro. La sequenza e’ stata generata grazie all’unione di due metodi il “whole menome shotgun” ed il “BAC-by-BAC”. Il genoma del pomodoro coltivato ha pero’ una variabilita’ genetica limitata, dovuta al processo di domesticazione e di breeding a cui e’ stato sottoposto dall’uomo. Le specie selvatiche del pomodoro sono originarie del Sud-America occidentale ed hanno la capacita’ di crescere e svilupparsi in habitat estremamente vari: esse infatti si trovano lungo le zone costiere del Peru’ fin sulle montagne a 3000 metri di altezza. Grazie alla loro storia evolutiva ed adattativa queste specie selvatiche hanno caratteri genetici che possono essere utilizzati per migliorare il genoma del pomodoro coltivato, come ad esempio la resistenza all’aridita’, alla salinita’ ed a molteplici patogeni; per questo motivo in questi ultimi anni l’interesse verso queste specie e’ andato via via crescendo. La storia dell’evoluzione del contenuto in carotenoidi della bacca del pomodoro e’ uno dei tratti di variabilita’ nei pomodori selvatici che ha generato maggiore interesse: il colore delle bacche nei pomodori selvatici varia dal verde all’arancio al rosso. Numerosi studi hanno dimostrato che il colore verde della bacca e’ il carattere piu’ ancestrale. Il motivo della transizione del colore durante l’evoluzione di queste specie non e’ ancora chiaro, probabilmente e’ correlato alla capacita’ delle bacche colorate di attrarre maggiormente gli animali per la dispersione del seme. L’accumulo di carotenoidi come metaboliti secondari nei frutti e nei fiori avviene grazie alla super regolazione a livello di espressione dei geni appartenenti alla via biosintetica dei carotenoidi. In questa tesi e’ stato utilizzato un approccio basato sullo studio di geni candidati, focalizzando l’attenzione su alcuni geni dei carotenoidi. Numerosi geni di questa via biosintetica sono stati sequenziati in specie selvatiche del pomodoro con diversa pigmentazione della bacca. Ecotipi selvatici di S. lycopersicum chiamati var. cerasiforme e 8 specie selvatiche (S. pimpinellifolium, S. cheesmaniae, S. neorickii, S. chmielewskii, S. chilense, S. habrochaites, S. pennellii e S. arcanum) sono state selezionate per rappresentare genotipi antichi e genotipi piu’ recenti. Grazie alla disponibilita’ della sequenza e dell’annotazione dei genomi del pomodoro, della patata e di Arabidopsis e’ stato condotto uno studio comparativo per valutare la presenza/assenza di microsintenia tra questi organismi nelle regioni genomiche fiancheggianti i geni codificanti la Fitoene sintasi. Grazie ai dati di annotazione del genoma del pomodoro sono stati individuati tre nuovi geni annotati rispettivamente come putativa Licopene beta-ciclasi (LCY-b), putativa Carotene isomerasi (CrtISO) e putativa Fitoene sintasi (PSY). Analisi preliminari effettuate sulle sequenze del trascrittoma del pomodoro, indicano che la putativa LCY-b e la putativa CrtISO sarebbero effettivamente espresse in diversi tessuti, incluse foglia e bacca, mentre la putativa PSY sembrerebbe essere uno speudo-gene. Il sequenziamento dei geni dei carotenoidi dalla Fitoene sintasi fino alla Licopene epsilon-ciclasi (LCY-e, alfa-branch) e fino alla Beta-carotene idrossilasi (CHY1 e 2, beta-branch) e’ stato completato per tutte le specie selvatiche studiate in questa tesi. L’analisi delle sequenze ha evidenziato numerose mutazioni: alcune mutazioni di tipo non sinonimo sono candidate ad essere alleli ipomorfi o ipermorfi delle proteine. Sono state condotte analisi preliminari di espressione in vitro delle proteine che presentano mutazioni non sinonime. Gli esperimenti sembrano confermare che una specie selvatica a bacca verde (S. arcanum) porta un allele di tipo ipermorfo della LCY-e. Per studiare meglio il profilo di maturazione delle bacche e’ stata misurata la produzione di etilene. Dalle analisi risulta che le specie selvatiche a bacca verde non differiscono significativamente da quelle a bacca colorata per quanto riguarda la produzione di etilene durante la maturazione, con l’eccezione di S. arcanum: questa specie ha il picco climaterico poco prima dell’abscissione. La variabilita’ della pigmentazione delle bacche non dipende quindi dalla diversa produzione di etilene. I profili di espressione genica dei carotenoidi nelle bacche di S. lycopersicum e della specie selvatica a bacca rossa (S. pimpinellifolium) sono molto simili e cio’ e’ in accordo con la loro vicinanza filogenetica. Al contrario di quanto atteso, la specie selvatica a bacca arancione (S. cheesmaniae) presenta, tra tutte le specie analizzate, il minor contenuto di carotenoidi. Le specie a bacca verde e quella a bacca arancione condividono sia un profilo trascrizionale che un contenuto di carotenoidi molto simili.Tomato (Solanum lycopersicum) is an economically and nutritionally valuable crop and constitutes a model plant for genetic research of the Solanaceae family thanks its compact genome (950 Mb), short generation time, the availability of a large set of mutants, routine transformation technology and availability of rich genetic and genomic resources.
The pre-release of the tomato genome sequence, produced combining a whole genome shotgun and a BAC-by-BAC approach, has been announced at the end of 2009 and a first genome annotation is available and is continuously updated. The genome of cultivated tomato, however, has a limited sequence variation due to bottlenecks during domestication and breeding.
The wild tomatoes are native to Western South America and grow in a variety of habitats, from near sea level along the arid Pacific coast to high mountains up to 3300 m. Thanks to their evolutionary and adaptive history, the wild tomato species contain useful traits that can be introgressed into cultivated tomato, such as tolerance to drought and salinity and resistance to multiple pathogens. In recent years there has been an increasing interest in analyzing various biological properties of natural genetic diversity and wild species provide a wealth of useful genetic traits to improve cultivated tomatoes.
The evolution of carotenoid pigments affecting berry colour is one of the variable characters within tomato and its wild relatives that have obtained much attention: the fruit colour of wild tomatoes varies from green to orange and red. Numerous studies have demonstrated that green fruit is the ancestral character. The reason behind a transition to coloured fruits during the evolution of the group is still not clear, but probably is related to attraction of animals for seed dispersal. Accumulation of carotenoids as secondary metabolites in fruits and flowers occurs through up-regulation of the pathway at the gene expression level.
A candidate gene approach has been used, focusing our attention on the carotenoid biosynthetic pathway. Several genes of this pathway have been sequenced in the wild tomato species with different berry colour. Accessions of the S. lycopersicum var. cerasiforme as well as wild tomato species (S. pimpinellifolium, S. cheesmaniae, S. neorickii, S. chmielewskii, S. chilense, S. habrochaites, S. pennellii, S. arcanum) were selected to represent ancestral and closely related progenitor genotypes.
Thanks to the availability of the genome sequences and annotation data of tomato, potato and A. thaliana, a comparison was undertaken to investigate the presence/absence of microsynteny around the Phytoene Synthase genes among these organisms. Moreover, we have obtained structural information on the organization of the carotenoid genes object of this thesis. The analysis has highlighted the presence of three new genes, annotated respectively as putative LCY-b, putative CrtISO and putative LCY-b: from preliminary transcriptome data the genes codifying for these proteins seem to be expressed.
The sequencing of carotenoid genes from PSY down to LCY-e (-branch) and CHY1-2 (-branch) has been completed for all the wild species studied in this thesis. The sequence analysis has highlighted the presence of numerous mutations. Some non-synonymous substitutions are candidate to be hypo- or hypermorphic alleles. Preliminary analysis on in vitro protein expression seems to confirm that one of the green-fruited species analysed carries a hypermorphic allele of LCY-e.
Green-fruited species did not differ systematically from coloured-fruited ones in climacteric ethylene production or fruit softening, with the exception of S. arcanum, which shows an ethylene peak just before fruit abscission.
Carotenoid and gene expression profiles of the red-fruited species, S. lycopersicum and S. pimpinellifolium, are very similar, in agreement with their phylogenetic closeness. In contrast to expectations, orange-fruited S. cheesmaniae has the lowest carotenoid content among all species and has carotenoid and transcriptional profiles similar to the green-fruited species
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Full text linkWe 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
A new application of capacitive sensors for the nucleic acids revelation
No full textIn this paper, a new methodological approach for nucleic acid (DNA, RNA and PNA) detection and analysis is introduced. It is based on
nucleic acids dielectric capacitance measurement performed by capacitive sensors.Asensor system exploiting the properties of miniaturized
arrays of capacitive sensors is illustrated. The sensor array signal is processed by a proper software that converts the signals into an image.
The extraction of information about the properties of nucleic acids is then obtained with classical algorithms for image analysis.
Results show that the sensor can discriminate among different kinds of DNA and can provide an estimate of DNA concentrations
Bimatoprost 0.01% solution compositions for the treatment of ocular hypertension
No full textThe invention relates to topical ophthalmic preparations in eye drops containing bimatoprost as an active ingredient at the concentration of 0.1 mg/ml, wherein the presence of benzalkonium chloride is limited to the indispensable minimum commonly required for its activity as an antimicrobial preservative, i.e. from 50 at 80 ppm, and the bioavailability of the product is ensured by the addition of specific non-ionic surfactants, i.e., poloxamers
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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