Fluid-rock interactions and their implications on carbonate reservoir characterization

The objective of my research has been to define the interactions between fluid and rock properties at different environmental conditions and observation scale to reduce the uncertainty in the carbonate reservoir characterization. Here, I integrate field observations, subsurface data, petrophysical and frictional laboratory measurements focusing on carbonate-bearing rocks to better constrain factors controlling fluid-rock interactions with applications to active petroleum systems. In particular, I focus on the Burano-Bolognano carbonate petroleum system that extends from the northern sector of the Majella mountain to the Cigno/Vallecupa oil fields, in Abruzzo Region (Central Italy). This area is of particular interest because of the following reasons: It has received great attention by oil companies in the past for its structural, stratigraphic, and geodynamic evolution, which led it to be an important target for hydrocarbon exploration during the past century. For this reason, it is characterized by a public dense dataset of wells, reports, maps, etc. It allows to study all petroleum system elements (with the exception of the source rock), such as: reservoir, seal, traps, and migration pathways at field scale. It allows to understand the influence of subsurface fluids on the petrophysical properties of carbonate reservoir rocks since the outcropping portions of reservoir interval are both clean and hydrocarbon-saturated. This allows measuring and comparing the variations of petrophysical properties between hydrocarbon-bearing and hydrocarbon-free samples. It is regarded as an analogue of a faulted and fractured reservoir for other carbonate petroleum systems worldwide and in particular in the Adriatic area. The results of my research quantify the influence of fluid properties in changing of the petrophysical and frictional properties of the bearing-carbonate rocks. The presence of viscous fluids, such as heavy hydrocarbons, at ambient temperature defines an increase of the wave velocities respect to those of the unsaturated samples and determines a possible strengthening and stiffening of the reservoir rock. With increasing temperature, distinct downward trends are recorded, especially for the P-wave velocities. Moreover, the presence of fluids along faults promotes a slow slip behaviour, which was more marked with the presence of clay minerals along fault surface. Finally, starting from these results, I simulate the evolution of the Burano-Bolognano petroleum system and the related fluids movements, inferring that within this petroleum system the vertically hydrocarbon migration is driven by fractures/faults and the subsequently lateral migration determinates a gradual oil biodegradation with an increase of its density

The evaluation of grey literature using bibliometric indicators: A methodological proposal

pp. 57-6

An intersectional approach to analyse gender productivity and open access: a bibliometric analysis of the Italian National Research Council

AbstractGender equality and Open Access (OA) are priorities within the European Research Area and cross-cutting issues in European research program H2020. Gender and openness are also key elements of responsible research and innovation. However, despite the common underlying targets of fostering an inclusive, transparent and sustainable research environment, both issues are analysed as independent topics. This paper represents a first exploration of the inter-linkages between gender and OA analysing the scientific production of researchers of the Italian National Research Council under a gender perspective integrated with the different OA publications modes. A bibliometric analysis was carried out for articles published in the period 2016–2018 and retrieved from the Web of Science. Results are presented constantly analysing CNR scientific production in relation to gender, disciplinary fields and OA publication modes. These variables are also used when analysing articles that receive financial support. Our results indicate that gender disparities in scientific production still persist particularly in STEM disciplines, while the gender gap is the closest to parity in medical and agricultural sciences. A positive dynamic toward OA publishing and women's scientific production is shown when disciplines with well-established open practices are related to articles supported by funds. A slightly higher women's propensity toward OA is shown when considering Gold OA, or authorships with women in the first and last article by-line position. The prevalence of Italian funded articles with women's contributions published in Gold OA journals seems to confirm this tendency, especially if considering the weak enforcement of the Italian OA policies

Phenotypic and molecular selection of a superior Solanum pennellii introgression sub-line suitable for improving quality traits of cultivated tomatoes

The Solanum pennellii Introgression Line (IL) population can be exploited to identify favorable alleles that can improve yield and fruit quality traits in commercial tomato varieties. Over the past few years, we have selected ILs that exhibit increased content of antioxidant compounds in the fruit compared to the cultivar M82, which represents the genetic background in which the different wild regions of the S. pennellii ILs were included. Recently, we have identified seven sub-lines of the IL7-3 accumulating different amounts of antioxidants in the ripe fruit. Since the wild region carried on chromosome 7 induces a low fruit production in IL7-3, the first aim of the present work was to evaluate yield performances of the selected sub-lines in three experimental fields located in the South of Italy. Another aim was to confirm in the same lines the high levels of antioxidants and evaluate other fruit quality traits. On red ripe fruit, the levels of soluble solids content, firmness, and ascorbic acid (AsA) were highly variable among the sub-lines grown in three environmental conditions, evidencing a significant genotype by environment interaction for soluble solids and AsA content. Only one sub-line (coded R182) exhibited a significantly higher firmness, even though no differences were observed for this trait between the parental lines M82 and IL7-3. The same sub-line showed significantly higher AsA content compared to M82, thus resembling IL7-3. Even though IL7-3 always exhibited a significantly lower yield, all the sub-lines showed yield variability over the three trials. Interestingly, the sub-line R182, selected for its better performances in terms of fruit quality, in all the trials showed a production comparable to that of the control line M82. A group of species-specific molecular markers was tested on R182 and on the parental genotypes in order to better define the wild genomic regions carried by the elite line R182. In these regions three candidate genes that could increase the level of AsA in the fruit were identified. In the future, the line R182 could be used as pre-breeding material in order to obtain new varieties improved for nutritional traits.info:eu-repo/semantics/publishedVersio

Exploiting Genetic and Genomic Resources to Enhance Heat-Tolerance in Tomatoes

High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the phenotypic and genomic variations of a tomato landrace collection grown at high temperatures. Fifteen genotypes were selected as the best performing in two experimental fields. The selection was based on six yield-related traits, including flower earliness, number of flowers per inflorescence, fruit set, number of fruit per plant, fruit weight and yield per plant. In order to identify markers targeting traits that could be highly influenced by adverse climate conditions, such as flowering and fruit setting, an association mapping approach was undertaken exploiting a tomato high-throughput genomic array. The phenotypic variability observed allowed us to identify a total of 15 common markers associated with the studied traits. In particular, the most relevant associations co-localized with genes involved in the floral structure development, such as the style2.1 gene, or with genes directly involved in the response to abiotic stresses. These promising candidate genes will be functionally validated and transferred to a cultivated tomato to improve its performance under high temperatures

Dissecting a QTL into Candidate Genes Highlighted the Key Role of Pectinesterases in Regulating the Ascorbic Acid Content in Tomato Fruit

Tomato (Solanum lycopersicum) is a crucial component of the human diet because of its high nutritional value and the antioxidant content of its fruit. As a member of the Solanaceae family, it is considered a model species for genomic studies in this family, especially since its genome has been completely sequenced. Among genomic resources available, Solanum pennellii introgression lines represent a valuable tool to mine the genetic diversity present in wild species. One introgression line, IL12-4, was previously selected for high ascorbic acid (AsA) content, and a transcriptomic analysis indicated the involvement of genes controlling pectin degradation in AsA accumulation. In this study the integration of data from different "omics" platforms has been exploited to identify candidate genes that increase AsA belonging to the wild region 12-4. Thirty-two genes potentially involved in pathways controlling AsA levels were analyzed with bioinformatic tools. Two hundred-fifty nonsynonymous polymorphisms were detected in their coding regions, and 11.6% revealed deleterious effects on predicted protein function. To reduce the number of genes that had to be functionally validated, introgression sublines of the region 12–4 were selected using species-specific polymor phic markers between the two Solanum species. Four sublines were obtained and we demonstrated that a subregion of around 1 Mbp includes 12 candidate genes potentially involved in AsA accumulation. Among these, only five exhibited structural delete rious variants, and one of the 12 was differentially expressed between the two Solanum species. We have highlighted the role of three polymorphic pectinesterases and inhibitors of pectinesterases that merit further investigation

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes

Verso una open peer review dei dati: uno studio pilota nelle scienze sociali

L’open peer review (OPR) può essere applicata a tutte le tipologie di risultati della ricerca, dagli articoli scientifici, alle proposte di progetto fino ai dataset. Tuttavia, a partire dalla sua definizione, vanno ancora analizzati i criteri e modalità per assicurare una valutazione trasparente ed efficace per il progresso della ricerca scientifica. Ciò si inquadra nell’ambito dell’Open Science che coglie l’esigenza di analizzare le trasformazioni strutturali e tecnologiche nel sistema della comunicazione scientifica odierna. E’ proprio in tale contesto che i principi di Merton – in particolare quelli di communality e organized skepticism – diventano importanti punti di riferimento. Questo studio ha lo scopo di analizzare l’applicabilità della revisione paritaria aperta dei dati della ricerca prodotti nelle discipline afferenti alle scienze sociali. Lo studio inserisce nel progetto europeo OpenUP (OPENing UP new methods, indicators and tools for peer review, dissemination of research results, and impact measurement), che intende analizzare le trasformazioni nell’attuale scenario della ricerca scientifica allo scopo di 1) identificare meccanismi, processi e strumenti innovativi per la peer review applicata a tutti i risultati della ricerca (pubblicazioni, software e dati), 2) esplorare i meccanismi della disseminazione innovativa efficaci per le imprese, l’industria, il settore educativo e la società nel suo insieme e 3) analizzare un insieme di nuovi indicatori (altmetric) che valutano l’impatto dei risultati della ricerca collegandoli ai canali per la disseminazione. OpenUp utilizza una metodologia centrata sull’utente. Questo approccio metodologico non solo coinvolge tutti gli stakeholder (ricercatori, case editrici, enti che finanziano la ricerca, istituzioni, industria e il pubblico in generale) in una serie di workshops, conferenze e corsi di formazione, ma vuole testare i risultati acquisiti in un set di studi pilota. Questi ultimi sono collegati ai tre pilastri del progetto (revisione paritaria, disseminazione innovativa dei risultati e altmetric) e sono applicati ad alcune comunità e settori della ricerca specifici: scienze umane, scienze sociali, energia e scienze della vita. Nello specifico il lavoro presentato intende descrivere la metodologia usata per sviluppare lo studio pilota sull’OPR dei dati nelle scienze sociali. In particolare si concentra sulla prima fase che intende ricostruire il contesto generale della diffusione e condivisione dei dati. Sulla base di questa analisi, saranno identificati i criteri di selezione della comunità da coinvolgere nello studio pilota, insieme alle caratteristiche e alle problematiche specifiche che verranno successivamente indagate durante il suo svolgimento. L’analisi prende in considerazione sia la prospettiva di coloro che forniscono i dati sia quella degli utenti che li utilizzano. Essa si pone nella prospettiva di considerare i principi Mertoniani ed in particolare le problematiche legate alla loro applicabilità nella condivisione e valutazione dei dati della ricerca

Exploiting genomics resources to identify candidate genes underlying antioxidants content in tomato fruit

The tomato is a model species for fleshy fruit development and ripening, as well as for genomics studies of others Solanaceae. Many genetic and genomics resources, including databases for sequencing, transcriptomics and metabolomics data, have been developed and are today available. The purpose of the present work was to uncover new genes and/or alleles that determine ascorbic acid and carotenoids accumulation, by exploiting one Solanum pennellii introgression lines (IL7-3) harboring quantitative trait loci (QTL) that increase the content of these metabolites in the fruit. The higher ascorbic acid and carotenoids content in IL7-3 was confirmed at three fruit developmental stages. The tomato genome reference sequence and the recently released S. pennellii genome sequence were investigated to identify candidate genes (CGs) that might control ascorbic acid and carotenoids accumulation. First of all, a refinement of the wild region borders in the IL7-3 was achieved by analyzing CAPS markers designed in our laboratory. Afterward, six CGs associated to ascorbic acid and one with carotenoids metabolism were identified exploring the annotation and the Gene Ontology terms of genes included in the region. Variants between the sequence of the wild and the cultivated alleles of these genes were investigated for their functional relevance and their potential effects on the protein sequences were predicted. Transcriptional levels of CGs in the introgression region were extracted from RNA-Seq data available for the entire S. pennellii introgression lines collection and verified by Real-Time qPCR. Finally, seven IL7-3 sub-lines were genotyped using 28 species-specific markers and then were evaluated for metabolites content. These analyses evidenced a significant decrease in transcript abundance for one 9-cis-epoxycarotenoid dioxygenase and one L-ascorbate oxidase homolog, whose role in the accumulation of carotenoids and ascorbic acid is discussed. Comprehensively, the reported results demonstrated that combining genetic and genomic resources in tomato, including bioinformatics tools, was a successful strategy to dissect one QTL for the increase of ascorbic acid and carotenoids in tomato fruit

Metabolic and molecular changes of the phenylpropanoid pathway in tomato (Solanum lycopersicum) lines carrying different Solanum pennellii wild Chromosomal regions

Solanum lycopersicum represents an important dietary source of bioactive compounds including the antioxidants flavonoids and phenolic acids. We previously identified two genotypes (IL7-3 and IL12-4) carrying loci from the wild species Solanum pennellii, which increased antioxidants in the fruit. Successively, these lines were crossed and two genotypes carrying both introgressions at the homozygous condition (DHO88 and DHO88-SL) were selected. The amount of total antioxidant compounds was increased in DHOs compared to both ILs and the control genotype M82. In order to understand the genetic mechanisms underlying the positive interaction between the two wild regions pyramided in DHO genotypes, detailed analyses of the metabolites accumulated in the fruit were carried out by colorimetric methods and LC/MS/MS. These analyses evidenced a lower content of flavonoids in DHOs and in ILs, compared to M82. By contrast, in the DHOs the relative content of phenolic acids increased, particularly the fraction of hexoses, thus evidencing a redirection of the phenylpropanoid flux towards the biosynthesis of phenolic acid glycosides in these genotypes. In addition, the line DHO88 exhibited a lower content of free phenolic acids compared to M82. Interestingly, the two DHOs analyzed differ in the size of the wild region on chromosome 12. Genes mapping in the introgression regions were further investigated. Several genes of the phenylpropanoid biosynthetic pathway were identified, such as one 4-coumarate:CoA ligase and two UDP-glycosyltransferases in the region 12-4 and one chalcone isomerase and one UDP-glycosyltransferase in the region 7-3. Transcriptomic analyses demonstrated a different expression of the detected genes in the ILs and in the DHOs compared to M82.These analyses, combined with biochemical analyses, suggested a central role of the 4-coumarate:CoA ligase in redirecting the phenylpropanoid pathways towards the biosynthesis of phenolic acids in the pyramided lines. Moreover, analyses here carried out suggest the presence in the introgression regions of novel regulatory proteins, such as one Myb4 detected on chromosome 7 and one bHLH detected in chromosome 12. Overall our data indicates that structural and regulatory genes identified in this study might have a key role for the manipulation of the phenylpropanoid metabolic pathway in tomato fruit