Molecular markers for the assessment of genetic variability in threatened plant species

La variabilità genetica è un importante strumento per lo studio e la conservazione della biodiversità in specie rare e minacciate di estinzione. Durante il mio dottorato mi sono quindi occupata di mettere a punto diverse metodologie molecolari al fine di valutare la diversità genetica in due specie rare della flora italiana che presentano problematiche diverse e specifiche. I marcatori arbitrari RAPD e i marcatori semi-arbitrari ISSR sono stati utilizzati per valutare la diversità genetica in Quercus crenata Lam. e per confermare l’ipotesi della sua origine ibridogena dalle due specie presunte parentali Quercus cerris L. e Quercus suber L., essendo Q. crenata presente in Italia settentrionale dove Q. suber è attualmente assente. I marcatori SSR o microsatelliti sono invece stati messi a punto su una specie a rischio di estinzione, endemica dell’Appennino Tosco-Emiliano, Primula apennina Widmer, applicando una metodologia specifica, basata sulla costruzione di una libreria genomica arricchita per l’isolamento di primer specifici. I marcatori RAPD e ISSR, utilizzati su un totale di 85 campioni, hanno mostrato alti livelli di diversità molecolare entro le specie studiate, eccetto per Q. suber le cui popolazioni rappresentano il margine orientale di distribuzione della specie, per questo più sottoposte ad impoverimento genetico. Oltre alla cluster analysis (UPGMA) e alla Analisi delle Componenti Principali effettuate per entrambi i marcatori, che confermano l’ipotesi dell’origine ibrida degli individui di Q. crenata diffusi in Italia Settentrionale, sono stati calcolati l’indice di ibridità basato sul maximum likelihood, che dimostra una introgressione asimmetrica di Q. crenata verso il parentale caratterizzato da superiorità demografica (Q. cerris) e il test di Mantel. Quest’ultimo ha permesso di confrontare i due marcatori RAPD e ISSR utilizzati ottenendo una bassa correlazione, a conferma del fatto che, amplificando tratti differenti del DNA nucleare, i dati non sono sovrapponibili, sebbene forniscano risultati analoghi. Per l’isolamento di loci microsatelliti ipervariabili ho utilizzato il protocolllo FIASCO (Fast isolation by AFLP of sequences containing repeats- Zane et al. 2002) che permette di costruire una libreria genomica arricchita partendo dal DNA estratto da P. apennina. Tale procedura ha previsto la digestione del DNA genomico per la produzione di una miscela di frammenti di DNA. Tramite ibridazione con opportune sonde sono stati isolati i frammenti contenenti i microsatelliti. Sequenziando i cloni ricombinanti, ho ottenuto sequenze contenenti repeats sulle cui regioni fiancheggianti sono stati costruiti 15 coppie di primer che potranno, in seguito, essere utilizzate per definire la quota di riproduzione clonale in P. apennina e per valutare la diversità genetica delle popolazioni che coprono l’areale di distribuzione della specie. Data la loro natura altamente variabile e la loro abbondanza nel DNA, gli SSR saranno, come i marcatori RAPD e gli ISSR, ugualmente validi per lo studio della variabilità genetica e per l’analisi di problematiche specifiche legate alle specie rare.

Molecular strategies for genetic diversity analysis and development of markers linked to resistance traits in apple

The goal of many plant scientists’ research is to explain natural phenotypic variation in term of simple changes in DNA sequence. DNA-based molecular markers are extensively used for the construction of genome-wide molecular maps and to perform genetic analysis for simple and complex traits. The PhD thesis was divided into two main research lines according to the different approaches adopted. The first research line is to analyze the genetic diversity in an Italian apple germplasm collection for the identification of markers tightly linked to targeted genes by an association genetic method. This made it possible to identify synomym and homonym accessions and triploids. The fruit red skin color trait has been used to test the reliability of the genetic approaches in this species. The second line is related to the development of molecular markers closely linked to the Rvi13 and Rvi5 scab resistance genes, previously mapped on apple’s chromosome 10 and 17 respectively by using the traditional linkage mapping method. Both region have been fine-mapped with various type of markers that could be used for marker-assisted selection in future breeding programs and to isolate the two resistance genes.

Study of Candidate Genes for production and carcass traits in Italian Heavy Pigs: identification of a new DNA Markers, Expression Studies and Association Analysis using Different Experimental Design

Heavy pig breeding in Italy is mainly oriented for the production of high quality processed products. Of particular importance is the dry cured ham production, which is strictly regulated and requires specific carcass characteristics correlated with green leg characteristics. Furthermore, as pigs are slaughtered at about 160 kg live weight, the Italian pig breeding sector faces severe problems of production efficiency that are related to all biological aspects linked to growth, feed conversion, fat deposition and so on. It is well known that production and carcass traits are in part genetically determined. Therefore, as a first step to understand genetic basis of traits that could have a direct or indirect impact on dry cured ham production, a candidate gene approach can be used to identify DNA markers associated with parameters of economic importance. In this thesis, we investigated three candidate genes for carcass and production traits (TRIB3, PCSK1, MUC4) in pig breeds used for dry cured ham production, using different experimental approaches in order to find molecular markers associated with these parameters.

Genomic and transcriptional analysis of allergen genes in apple (Malus x domestica)

Apple consumption is highly recomended for a healthy diet and is the most important fruit produced in temperate climate regions. Unfortunately, it is also one of the fruit that most ofthen provoks allergy in atopic patients and the only treatment available up to date for these apple allergic patients is the avoidance. Apple allergy is due to the presence of four major classes of allergens: Mal d 1 (PR-10/Bet v 1-like proteins), Mal d 2 (Thaumatine-like proteins), Mal d 3 (Lipid transfer protein) and Mal d 4 (profilin). In this work new advances in the characterization of apple allergen gene families have been reached using a multidisciplinary approach. First of all, a genomic approach was used for the characterization of the allergen gene families of Mal d 1 (task of Chapter 1), Mal d 2 and Mal d 4 (task of Chapter 5). In particular, in Chapter 1 the study of two large contiguos blocks of DNA sequences containing the Mal d 1 gene cluster on LG16 allowed to acquire many new findings on number and orientation of genes in the cluster, their physical distances, their regulatory sequences and the presence of other genes or pseudogenes in this genomic region. Three new members were discovered co-localizing with the other Mal d 1 genes of LG16 suggesting that the complexity of the genetic base of allergenicity will increase with new advances. Many retrotranspon elements were also retrieved in this cluster. Due to the developement of molecular markers on the two sequences, the anchoring of the physical and the genetic map of the region has been successfully achieved. Moreover, in Chapter 5 the existence of other loci for the Thaumatine-like protein family in apple (Mal d 2.03 on LG4 and Mal d 2.02 on LG17) respect the one reported up to now was demonstred for the first time. Also one new locus for profilins (Mal d 4.04) was mapped on LG2, close to the Mal d 4.02 locus, suggesting a cluster organization for this gene family, as is well reported for Mal d 1 family. Secondly, a methodological approach was used to set up an highly specific tool to discriminate and quantify the expression of each Mal d 1 allergen gene (task of Chapter 2). In aprticular, a set of 20 Mal d 1 gene specific primer pairs for the quantitative Real time PCR technique was validated and optimized. As a first application, this tool was used on leaves and fruit tissues of the cultivar Florina in order to identify the Mal d 1 allergen genes that are expressed in different tissues. The differential expression retrieved in this study revealed a tissue-specificity for some Mal d 1 genes: 10/20 Mal d 1 genes were expressed in fruits and, indeed, probably more involved in the allergic reactions; while 17/20 Mal d 1 genes were expressed in leaves challenged with the fungus Venturia inaequalis and therefore probably interesting in the study of the plant defense mechanism. In Chapter 3 the specific expression levels of the 10 Mal d 1 isoallergen genes, found to be expressed in fruits, were studied for the first time in skin and flesh of apples of different genotypes. A complex gene expression profile was obtained due to the high gene-, tissue- and genotype-variability. Despite this, Mal d 1.06A and Mal d 1.07 expression patterns resulted particularly associated with the degree of allergenicity of the different cultivars. They were not the most expressed Mal d 1 genes in apple but here it was hypotized a relevant importance in the determination of allergenicity for both qualitative and quantitative aspects of the Mal d 1 gene expression levels. In Chapter 4 a clear modulation for all the 17 PR-10 genes tested in young leaves of Florina after challenging with the fungus V. inaequalis have been reported but with a peculiar expression profile for each gene. Interestingly, all the Mal d 1 genes resulted up-regulated except Mal d 1.10 that was down-regulated after the challenging with the fungus. The differences in direction, timing and magnitude of induction seem to confirm the hypothesis of a subfunctionalization inside the gene family despite an high sequencce and structure similarity. Moreover, a modulation of PR-10 genes was showed both in compatible (Gala-V. inaequalis) and incompatible (Florina-V. inaequalis) interactions contribute to validate the hypothesis of an indirect role for at least some of these proteins in the induced defense responses. Finally, a certain modulation of PR-10 transcripts retrieved also in leaves treated with water confirm their abilty to respond also to abiotic stress. To conclude, the genomic approach used here allowed to create a comprehensive inventory of all the genes of allergen families, especially in the case of extended gene families like Mal d 1. This knowledge can be considered a basal prerequisite for many further studies. On the other hand, the specific transcriptional approach make it possible to evaluate the Mal d 1 genes behavior on different samples and conditions and therefore, to speculate on their involvement on apple allergenicity process. Considering the double nature of Mal d 1 proteins, as apple allergens and as PR-10 proteins, the gene expression analysis upon the attack of the fungus created the base for unravel the Mal d 1 biological functions. In particular, the knowledge acquired in this work about the PR-10 genes putatively more involved in the specific Malus-V. inaequalis interaction will be helpful, in the future, to drive the apple breeding for hypo-allergenicity genotype without compromise the mechanism of response of the plants to stress conditions. For the future, the survey of the differences in allergenicity among cultivars has to be be thorough including other genotypes and allergic patients in the tests. After this, the allelic diversity analysis with the high and low allergenic cultivars on all the allergen genes, in particular on the ones with transcription levels correlated to allergencity, will provide the genetic background of the low ones. This step from genes to alleles will allow the develop of molecular markers for them that might be used to effectively addressed the apple breeding for hypo-allergenicity. Another important step forward for the study of apple allergens will be the use of a specific proteomic approach since apple allergy is a multifactor-determined disease and only an interdisciplinary and integrated approach can be effective for its prevention and treatment.

Controllo molecolare del differenziamento osteoblestico per applicazioni nel campo della rigenerazione del tessuto osseo

The aim of the study was to identify expression signatures unique for specific stages of osteoblast differentiation in order to improve our knowledge of the molecular mechanisms underlying bone repair and regeneration. We performed a microarray analysis on the whole transcriptome of human mesenchymal stem cells (hMSCs) obtained from the femoral canal of patients undergoing hip replacement. By defining different time-points within the differentiation and mineralization phases of hMSCs, temporal gene expression changes were visualised. Importantly, the gene expression of adherent bone marrow mononuclear cells, being the undifferentiated progenitors of bone cells, was used as reference. In addition, only the cultures able to form mineral nodules at the final time-point were considered for the gene expression analyses. To obtain the genes of our interest, we only focused on genes: i) whose expression was significantly upregulated; ii) which are involved in pathways or biological processes relevant to proliferation, differentiation and functions of bone cells; iii) which changed considerably during the different steps of differentiation and/or mineralization. Among the 213 genes identified as differentially expressed by microarray analysis, we selected 65 molecular markers related to specific steps of osteogenic differentiation. These markers are grouped into various gene clusters according to their involvement in processes which play a key role in bone cell biology such as angiogenesis, ossification, cell communication, development and in pathways like TGF beta and Wnt signaling pathways. Taken together, these results allow us to monitor hMSC cultures and to distinguish between different stages of differentiation and mineralization. The signatures represent a useful tool to analyse a broad spectrum of functions of hMSCs cultured on scaffolds, especially when the constructs are conceived for releasing growth factors or other signals to promote bone regeneration. Morover, this work will enhance our understanding of bone development and will enable us to recognize molecular defects that compromise normal bone function as occurs in pathological conditions.

Impiego di cellule staminali in terapia veterinaria

Over the past few years, in veterinary medicine there has been an increased interest in understanding the biology of mesenchymal stem cells (MSCs). This interest comes from their potential clinical use especially in wound repair, tissue engineering and application in therapeutics fields, including regenerative surgery. MSCs can be isolated directly from bone marrow aspirates, adipose tissue, umbilical cord and various foetal tissues. In this study, mesenchymal stem cells were isolated from equine bone marrow, adipose tissue, cord blood, Wharton’s Jelly and, for the first time, amniotic fluid. All these cell lines underwent in vitro differentiation in chondrocytes, osteocytes and adipocytes. After molecular characterization, cells resulted positive for mesenchymal markers such as CD90, CD105, CD44 and negative for CD45, CD14, CD34 and CD73. Adipose tissue and bone marrow mesenchymal stem cells were successfully applied in the treatment of tendinitis in race horses. Furthermore, for the first time in the horse, skin wounds of septicemic foal, were treated applying amniotic stem cells. Finally, results never reported have been obtained in the present study, isolating mesenchymal stem cells from domestic cat foetal fluid and membranes. All cell lines underwent in vitro differentiation and expressed mesenchymal molecular markers.

Phylogeny and population dynamics in European Reticulitermes and Kalotermes genera (Insecta, Isoptera)

The aim of this thesis is to detect the phylogeny and the population dynamics of the European termites of the genera Reticulitermes and Kalotermes, by the use of different mitochondrial (16S, COI/tRNA/COII, CR) and nuclear (microsatellites and Inter-SINE) molecular markers. In the phylogenetic analyses, the obtained results have well defined the cladogenetic events that generated the nowadays species biodiversity of the genus Reticulitermes, while the analysis of the Kalotermes flavicollis taxon showed the presence of at least four genetic clades, defined on the basis of the geographical distance. The second part of the thesis is centred on the population dynamics of two species: Reticulitermes urbis and Kalotermes flavicollis. The first species, native of the Balkans, is known to be present in some cities of Italy and France. I’ve analyzed the colony genetic structure of the introduced population of Bagnacavallo (RA, Italy), using nine microsatellite loci. The obtained results are in accordance with those obtained from another population in France: this species in fact confirms its invasive and infestation capacities. The analysis of the natural population of K. flavicollis, performed with a combination of mitochondrial (control region) and nuclear (microsatellites and I-SINE) markers, clearly evidenced the presence of two genetic lineages that coexist in the same area. Moreover, results clearly indicate that the cross-breeding is allowed. Finally, the whole results are discussed in a comparative view to better understand the differences in ecology, evolutionary dynamics and colony social structure between these two genera.

Phylogeny and genetic diversity of Italian species of hares (genus Lepus)

In this study we have analysed the genetic variability in ca. 700 samples belonging to six species of genus Lepus using maternal and biparental molecular markers (mitochondrial DNA, microsatellites, Single Nucleotide Polimorphisms). We aimed to reconstruct the phylogenetic relationships of species of hares living in Europe, and assess the occurrence of hybridization between the European hare Lepus europaeus and the Italian hare Lepus corsicanus. Results showed a deep genetic differentiation and absence of hybridization between L. corsicanus and L. europaeus, confirming that they are distinct and distantly related biological species. In contrast, we showed small genetic distances and a close phylogenetic relationship between the Italian hare and Cantabrian hare L. castroviejoi, which suggest a deeper evaluation of their taxonomic status. Populations of L. corsicanus are geographically differentiated. In particular, the peninsular and Sicilian populations of Italian hares are sharply genetically distinct, which calls for avoiding any translocation between Italy and Sicily. Information on genetic variability and population structure is being used to implement the Italian Action Plan for L. corsicanus.

Identificazione e dosaggio di marcatori molecolari dell'endometriosi nel sangue periferico

Purpose: to quantify the mRNA levels of MMP-3, MMP-9, VEGF and Survivin in peripheral blood and the serum levels of CA-125, Ca19-9 in women with and without endometriosis and to investigate the performance of these markers to differentiate between deep and ovarian endometriosis. Methods: a case controls study enrolled a series of 60 patients. Twenty controls have been matched with 20 cases of ovarian and 20 cases of deep endometriosis. Univariable and multivariable performance of serum CA125 and CA19-9, mRNA for Survivin, MMP9, MMP3 and VEGF genes have been evaluated by means of ROC curves and logistic regression respectively. Results: No difference in markers concentration were detected between ovarian and deep endometriosis. In comparison with controls serum CA19 and CA125 yielded the better sensitivity followed by mRNA for Survivin gene (81.5%, 51.9% and 7.5% at 10% false positive rate respectively). Multivariable estimated odds of endometriosis yielded a sensitivity of 87% at the same false positive rate. Conclusions: A combination of serum and molecular markers could allow a better diagnosis of endometriosis.

Mappaggio fine di un QTL principale per la resa in granella sul cromosoma 3B di frumento duro

In durum wheat, two major QTL for grain yield (Qyld.idw-2B and Qyld.idw-3B) and related traits were identified in a recombinant population derived from Kofa and Svevo (Maccaferri et al. 2008). To further investigate the genetic and physiological basis of allelic variation for this important trait, the fine mapping of Qyld.idw-2B e Qyld.idw-3B was done during the PhD. In this regard, new molecular markers were added to increase the map resolution in the target interval. For Qyld.idw-2B region COS markers derived from the synteny between wheat and rice/ sorghum /brachypodiu genomes were screened. While for Qyld.idw-3B region SSR, ISBP and COS markers obtained from BAC end-sequences and BAC sequences generated during the construction of the 3B physical map (Paux et al., 2008) were screened. In the RIL population a final map resolution of 2,8 markers/cM for Qyld.idw-2B and 0,6 markers/cM for Qyld.idw-3B were obtained. Eighteen pairs of near-isogenic lines (NILs) for Qyld.idw-3B were obtained from F4:5 heterogeneous inbred families. In order to confirm the phenotypic effect of the QTL all pairs were evaluated in field trials (2010 and 2011) for all traits. Three pairs of NILs, with contrasted haplotypes at the target region, were crossed to produce a large F2 population (ca. 7,500 plants in total) that was screened for the identification of recombinants. A total of 233 homozygous F4:5 segmental isolines were obtained and the phenotypic and genotypic characterization of these materials were done. A fine mapping for Qyld.idw-3B was obtained and the QTL peak was identified in a interval of 0,4 cM. All markers were anchored to the Chinese Spring physical map of chr. 3B, which allowed us to identify the BAC Contigs spanning the QTL region and to assign the QTL peak to Contig 954. Sequencing of this contig has revealed the presence of 42 genes.

Ricerca di marcatori molecolari nella prevenzione dei tumori di testa e collo

Oral cavity cancers (OSCC) are among the most malignances worldwide. OSCC tipically affects men in their IV or V dedade of life, and the most relevant risk factors are tobacco and alcohol consumption. OSCCs generally exhibit poor prognosis, and late stage identification correlates with higher mortality rates. Basic prognostic factors, are tumor size and presence of lymph node and/or distance metastases (T classification, N, M). However, tumors with the same TNM grade and similar morphology may have completely different evolution, because of their intrinsic biological characteristics. For these reasons, the identification of new molecular markers with a predictive value, could represent useful tools in OSCC prevention, prognosis and treatment. In the first part of my PhD project I evaluated the loss of heterozygosity as a possible cause of deregulation of well-known tumor suppressors genes. Obtained data put on light the importance of this rearrangement and genes PDCD4, CTNB1, CASP4 and HSP23, in the onset and progression of OSCC. Subsequently, the analysis of the expression profile of miRNAs, led to the identification of some miRNAs that seems to be involved in cancer development and metastatic progression. In both cases, we need further investigations to understand whether these molecules may be used ideal markers in OSCC diagnosis and treatment.

Individuazione e caratterizzazione dei prodotti di degradazione ossidativa dei secoiridoidi nell'olio vergine di oliva mediante tecniche analitiche innovative

Lo scopo di questo lavoro di tesi è la caratterizzazione dei prodotti di ossidazione di diversi fenoli idrofili contenuti nell’olio vergine d’oliva come idrossitirosolo, tirosolo e la forma dialdeidica dell’acido decarbossimetil elenolico legato all’idrossitirosolo, e la loro identificazione nel prodotto durante la conservazione. L’obiettivo della ricerca è trovare degli indici analitici che possono essere usati sia come marker di “freschezza” dell’olio vergine di oliva sia nella valutazione della “shelf life” del prodotto stesso. Due sistemi di ossidazione sono stati usati per ossidare le molecole sopracitate: ossidazione enzimatica e ossidazione di Fenton. I prodotti di ossidazione sono stati identificati come chinoni, dimeri e acidi.

Identificazione di un profilo molecolare di rischio nei pazienti pediatrici affetti da Linfoma di Hodgkin

Obiettivi: nonostante i miglioramenti nel trattamento, circa il 30% dei pazienti pediatrici affetti da Linfoma di Hodgkin (LH) in stadio avanzato recidiva o muore per progressione di malattia e i correnti metodi predittivi biologico-clinici non consentono di individuare tali pazienti. L’obiettivo dello studio è stato quello di definire un profilo molecolare di rischio che correli con l’outcome in questi pazienti. Materiali e metodi: studio retrospettico condotto su pazienti pediatrici affetti da LH omogeneamente trattati dal 2004 in poi. Su tali pazienti è stato intrapreso uno studio di validazione di marcatori molecolari già identificati in studi esplorativi precedenti. 27 geni sono stati analizzati in RT PCR su campioni di tessuto istologico prelevato alla diagnosi fissato in formalina e processato in paraffina relativi a una coorte di 37 pazienti, 12 ad outcome sfavorevole e 25 ad outcome favorevole. Risultati: dall’analisi univariata è emerso che solo l’espressione di CASP3 e CYCS, appartenenti al pathway apoptotico, è in grado di influenzare l’EFS in modo significativo nella nostra coorte di pazienti. Lo studio delle possibili combinazioni di questi geni ha mostrato l’esistenza di 3 gruppi di rischio che correlano con l’EFS: alto rischio (down regolazione di entrambi i geni), rischio intermedio (down regolazione di uno solo dei 2 geni), basso rischio (up regolazione di entrambi i geni). Dall’analisi multivariata è emerso che CASP3 è l’unica variabile che mantiene la sua indipendenza nell’influenzare la prognosi con un rischio di eventi di oltre il doppio di chi ha un’espressione bassa di questo gene. Conclusioni: i risultati ottenuti sulla nostra coorte di pazienti pediatrici affetti da LH confermano l’impatto sulla prognosi di due marcatori molecolari CASP3 e CYCS coinvolti nel patwhay apoptotico. La valutazione del profilo di espressione di tali geni, potrebbe pertanto essere utilizzata in corso di stadiazione, come criterio di predittività.

A SMO inhibitor drug reduces the progenitor cell's maintenance in the Drosophila hematopoietic organ: a novel model to study Chronic Myelogenous Leukemia relapse

The chronic myeloid leukemia complexity and the difficulties of disease eradication have recently led to the development of drugs which, together with the inhibitors of TK, could eliminate leukemia stem cells preventing the occurrence of relapses in patients undergoing transplantation. The Hedgehog (Hh) signaling pathway positively regulates the self-renewal and the maintenance of leukemic stem cells and not, and this function is evolutionarily conserved. Using Drosophila as a model, we studied the efficacy of the SMO inhibitor drug that inhibit the human protein Smoothened (SMO). SMO is a crucial component in the signal transduction of Hh and its blockade in mammals leads to a reduction in the disease induction. Here we show that administration of the SMO inhibitor to animals has a specific effect directed against the Drosophila ortholog protein, causing loss of quiescence and hematopoietic precursors mobilization. The SMO inhibitor induces in L3 larvae the appearance of melanotic nodules generated as response by Drosophila immune system to the increase of its hemocytes. The same phenotype is induced even by the dsRNA:SMO specific expression in hematopoietic precursors of the lymph gland. The drug action is also confirmed at cellular level. The study of molecular markers has allowed us to demonstrate that SMO inhibitor leads to a reduction of the quiescent precursors and to an increase of the differentiated cells. Moreover administering the inhibitor to heterozygous for a null allele of Smo, we observe a significant increase in the phenotype penetrance compared to administration to wild type animals. This helps to confirm the specific effect of the drug itself. These data taken together indicate that the study of inhibitors of Smo in Drosophila can represent a useful way to dissect their action mechanism at the molecular-genetic level in order to collect information applicable to the studies of the disease in humans.