Evaluation of cardiovascular disease markers in patients submitted to carotid artery stenting or endarterectomy

Introduction. Microembolization during the carotid artery revascularization procedure may cause cerebral lesions. Elevated C-Reactive Protein (hsCRP), Vascular endothelial growth factor (VEGF) and serum amyloid A protein (SAA) exert inflammatory activities thus promoting carotid plaque instability. Neuron specific enolase (NSE) is considered a marker of cerebral injury. Neoangiogenesis represents a crucial step in atherosclerosis, since neovessels density correlates with plaque destabilization. However their clinical significance on the outcome of revascularization is unknown. This study aims to establish the correlation between palque vulnerabilty, embolization and histological or serological markers of inflammation and neoangiogenesis. Methods. Serum hsCRP, SAA, VEGF, NSE mRNA, PAPP-A mRNA levels were evaluated in patients with symptomatic carotid stenosis who underwent filter-protected CAS or CEA procedure. Cerebral embolization, presence of neurologicals symptoms, plaque neovascularization were evaluated testing imaging, serological and histological methods. Results were compared by Fisher’s, Student T test and Mann-Whitney U test. Results. Patients with hsCRP<5 mg/l, SAA<10mg/L and VEGF<500pg/ml had a mean PO of 21.5% versus 35.3% (p<0.05). In either group, embolic material captured by the filter was identified as atherosclerotic plaque fragments. Cerebral lesions increased significantly in all patients with hsCRP>5mg/l and SAA>10mg/l (16.5 vs 2.8 mean number, 3564.6 vs 417.6 mm3 mean volume). Discussion. High hsCRP, SAA and VEGF levels are associated with significantly greater embolization during CAS and to the vulnerabiliy of the plaque. This data suggest CAS might not be indicated as a method of revascularization in this specific group of patients.

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.

Humane CD4 + CD25 + regulatorische T-Zellen: Charakterisierung von Subpopulationen und Identifizierung eines Markers

CD4+CD25+ regulatorische T-Zellen (CD4+CD25+ Tregs) sind essentiell an der Homöostase des Immunsystems beteiligt, indem sie eine antigenspezifische Toleranzinduktion in der Peripherie vermitteln und vor der Entstehung von Autoimmunerkrankungen schützen. Darüber hinaus sind diese Zellen wesentlich an der Kontrolle von Allergien, Infektionen und Tumoren beteiligt. Innerhalb dieser Arbeit konnten zwei bisher unbekannte Subpopulationen humaner CD4+CD25+ Tregs, isoliert aus dem peripheren Blut des Menschen, nachgewiesen werden. Diese Subpopulationen unterscheiden sich in ihrer Oberflächenexpression und exprimieren die Integrine a4b1 bzw. a4b7. Beide Treg-Subpopulationen supprimieren kokultivierte CD4+ T-Helferzellen Zellkontakt-abhängig und konvertieren gleichzeitig einen Teil dieser Zellen in sekundäre Suppressorzellen (iTregs). a4b1+ Tregs induzieren TGF-β-sezernierende iTregs, a4b7+ Tregs führen zur Bildung von IL-10-produzierenden iTregs. Differentielle Proteomanalysen humaner CD4+CD25+ Tregs, im Vergleich zu CD4+CD25- T-Helferzellen, führten zur Identifizierung von Galectin-10 als Markerprotein, das fast ausschließlich von CD4+CD25+ Tregs und nicht von CD4+ T-Helferzellen exprimiert wird. Galectin-10 ist ein intrazelluläres Protein, das essentiell für die funktionellen Eigenschaften humaner CD4+CD25+ Tregs ist. Die Blockade der Galectin-10-Bildung in den CD4+CD25+ Tregs durch RNA-Interferenz führte zu wesentlichen funktionellen Veränderungen der CD4+CD25+ Tregs. In Abwesenheit von Galectin-10 verlieren humane CD4+CD25+ Tregs ihre suppressiven Eigenschaften und ihren anergischen Phänotyp. Somit konnte mit Galectin-10 erstmals ein spezifischer Marker für humane CD4+CD25+ Tregs identifiziert werden, der wesentlich für den funktionellen Phänotyp dieser Regulatoren peripherer T-Zelltoleranz ist.

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.

The vulnerable carotid plaque. Identification of endothelial markers predictive of plaque weakness, rupture predisposition and neoangiogenesis

Background. Neoangiogenesis is crucial in plaque progression and instability. Previous data from our group demonstrated that intra-plaque neovessels show both a Nestin+/WT+ and a Nestin+/WT1- phenotype, the latter being correlated with complications and plaque instability. Aims. The aims of the present thesis are: (i) to confirm our previous results on Nestin/WT1 phenotype in a larger series of carotid atheromatous plaques, (ii) to evaluate the relationship between the Nestin+/WT1- neoangiogenesis phenotype and plaque morphology, (iii) to evaluate the relationship between the immunohistochemical and histopathological characteristics and the clinical instability of the plaques. Materials and Methods. Seventy-three patients (53 males, 20 females, mean age 71 years) were consecutively enrolled. Symptoms, brain CT scan, 14 histological variables, including intraplaque hemorrhage and diffuse calcifications, were collected. Immunohistochemistry for CD34, Nestin and WT1 was performed. RT-PCR was performed to evaluate Nestin and WT1 mRNA (including 5 healthy arteries as controls). Results. Diffusely calcified plaques (13 out of 73) were found predominantly in females (P=0.017), with a significantly lower incidence of symptoms (TIA/stroke) and brain focal lesions (P=0.019 and P=0.013 respectively) than not-calcified plaques, but with the same incidence of intraplaque complications (P=0.156). Accordingly, both calcified and not calcified plaques showed similar mean densities of positivity for CD34, Nestin and WT1. The density of Nestin and WT1 correlated with the occurrence of intra-plaque hemorrhage in all cases, while the density of CD34 correlated only in not-calcified plaques. Conclusions. We confirmed that the Nestin+/WT1- phenotype characterizes the neovessels of instable plaques, regardless the real amount of CD34-positive neoangiogenesis. The calcified plaques show the same incidence of histological complications, albeit they do not influence symptomatology and plaque vulnerability. Female patients show a much higher incidence of not-complicated or calcified plaques, receiving de facto a sort of protection compared to male patients.

Identification and characterization of novel tumor-associated proteins as potential tumor markers for diagnosis and therapy

This study deals with the discovery and characterization of EXN6 and EXN11 as novel tumor-associated proteins. EXN6 is mainly present in breast and ovary cancers (40 and 35%) while EXN11 is mainly detected in primary and metastatic colon cancer (40%). A characterization of the two proteins confirmed that they could be novel targets for cancer therapy.

The genetic history of Italians: new-insights from uniparentally-inherited markers

Genetic differences among human groups can be ascribed both to the broad-scale extents of pre-historical and historical migrations and to the fine-scale impacts of socio-cultural and geographic heterogeneity. In this thesis, the genetic information provided by uniparental markers were exploited to address different aspects of the Italian population history, by combining macro- and micro-geographic investigations at different spatial and temporal scales. To firstly assess the overall Italian variability, Y-chromosome and mtDNA markers were deeply typed in ~900 individuals from continental Italy, Sicily and Sardinia. Sex-biased patterns and contrasting demographic histories were observed for males and females. Differential European and Mediterranean contributions were invoked to explain the paternal genetic sub-structure observed in peninsular Italy, compared to the homogeneous maternal genetic landscape. If Neolithic showed to be one principal determinant of the detected paternal structure, local insights into specific Italian regional contexts highlighted the importance of Post-Neolithic contributions. Among them, migrations from the Balkans (particularly Greece) during late Metal Ages, played a relevant role in the cultural and genetic transitions occurred in Sicily and Southern Italy. On a finer geographic and temporal perspective, the more recent layers of Italian genetic history and some aspects of the gene-culture interaction were assessed by exploring the genetic variability within two “marginal populations”: Arbereshe of Southern Italy and Partecipanza in Northern Italy. The Arbereshe are Albanian-speaking communities settled in Sicily and Calabria since the end of Middle Ages. Despite sharing common genetic and cultural backgrounds, these groups revealed diverging micro-evolutionary histories, implying different founding events and different patterns of cultural isolation and local admixture. Partecipanza is an idiosyncratic institution of Medieval origin aimed at sharing and devolving collective lands. This case-study exemplified that socio-economic stratification within the same population may induce sex-biased genetic structuring and the maintenance of otherwise hidden historical genetic traces.

Identificazione di markers morfologici e sierologici di vulnerabilità della placca carotidea

Introduzione: L’indicazione alla rivascolarizzazione carotidea è comunemente posta in base alla percentuale di stenosi, alla presenza di sintomi neurologici ed alle condizioni cliniche del paziente. Una placca ad elevato potenziale embolico viene definita “vulnerabile”; la sua caratterizzazione, tuttavia, non è universalmente accettata ai fini della rivascolarizzazione. Lo scopo dello studio è indagare il ruolo del mezzo di contrasto ecografico (CEUS) nell’identificazione della placca carotidea vulnerabile. Materiali e Metodi: I pazienti sottoposti a endoarterectomia carotidea, sono stati valutati mediante TC cerebrale preoperatoria e CEUS. Le microbolle di contrasto rilevate nella placca, indicative di neovascolarizzazione, sono state quantificate in dB-E ed istologicamente valutate per cinque caratteristiche: (densità dei microvasi, spessore del cappuccio fibroso, estensione delle calcificazioni, infiltrato infiammatorio e core lipidico) il valore da 1 a 5, ottenuto in cieco, indica in grado di vulnerabilità della placca. L'ANOVA test, il test di Fisher e t Student sono stati usati per correlare le caratteristiche dei pazienti ed istologiche col valore di dB-E. Risultati: Di 22 pazienti (range 2-7.8, media 4.85 ±1.9 SD) vi era un numero più alto di sintomatici (7.40 ± 0.5) rispetto agli asintomatici (3.5 ± 1.4) (p = 0.002). Un più alto valore di dB-E si associava con la presenza di un sottile cappuccino fibroso (<200 µm, 5.96±1.5 vs. 3 ± 1,p = 0.01) ed un maggiore infiltrato infiammatorio (3.2 ± 0.9 vs. 6.4 ± 1.2, p = 0.03). Placche con vulnerabilità 5 si associavano ad un valore più alto di dB-E rispetto alle placche con vulnerabilità 1 (7.6 ± 0.2 vs. 2.5 ± 0.6, rispettivamente, p=0.001). Preoperatoriamente, le lesioni emboliche ipsilaterali alla TC, correlavano con un più alto valore di dB-E (5.96±1.5 vs. 3.0±1.0, p=0.01). Conclusioni: Il valore di dB-E alla CEUS indica l’estensione della neovascolarizzazione della placca carotidea e può essere utilizzato come marker di vulnerabilità della placca.

Identification of stock units of Mullus barbatus (Linnaeus, 1758) in the Italian seas: development of genomic 2b-RAD markers and biological variation analysis.

This thesis is settled within the STOCKMAPPING project, which represents one of the studies that were developed in the framework of RITMARE Flagship project. The main goals of STOCKMAPPING were the creation of a genomic mapping for stocks of demersal target species and the assembling of a database of population genomic, in order to identify stocks and stocks boundaries. The thesis focuses on three main objectives representing the core for the initial assessment of the methodologies and structure that would be applied to the entire STOCKMAPPING project: individuation of an analytical design to identify and locate stocks and stocks boundaries of Mullus barbatus, application of a multidisciplinary approach to validate biological methods and an initial assessment and improvement for the genotyping by sequencing technique utilized (2b-RAD). The first step is the individuation of an analytical design that has to take in to account the biological characteristics of red mullet and being representative for STOCKMAPPING commitments. In this framework a reduction and selection steps was needed due to budget reduction. Sampling areas were ranked according the individuation of four priorities. To guarantee a multidisciplinary approach the biological data associated to the collected samples were used to investigate differences between sampling areas and GSAs. Genomic techniques were applied to red mullet for the first time so an initial assessment of molecular protocols for DNA extraction and 2b-RAD processing were needed. At the end 192 good quality DNAs have been extracted and eight samples have been processed with 2b-RAD. Utilizing the software Stacks for sequences analyses a great number of SNPs markers among the eight samples have been identified. Several tests have been performed changing the main parameter of the Stacks pipeline in order to identify the most explicative and functional sets of parameters.

Stock boundaries of Parapenaeus longirostris (Lucas, 1846) populations in the Italian seas: Development of genomic 2b-RAD markers and biological variation analysis.

This thesis is developed in the contest of Ritmare project WP1, which main objective is the development of a sustainable fishery through the identification of populations boundaries in commercially important species in Italian Seas. Three main objectives are discussed in order to help reach the main purpose of identification of stock boundaries in Parapenaeus longirostris: 1 -Development of a representative sampling design for Italian seas; 2 -Evaluation of 2b-RAD protocol; 3 -Investigation of populations through biological data analysis. First of all we defined and accomplished a sampling design which properly represents all Italian seas. Then we used information and data about nursery areas distribution, abundance of populations and importance of P. longirostris in local fishery, to develop an experimental design that prioritize the most important areas to maximize the results with actual project funds. We introduced for the first time the use of 2b-RAD on this species, a genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Thanks to this method we were able to move from genetics to the more complex genomics. In order to proceed with 2b-RAD we performed several tests to identify the best DNA extraction kit and protocol and finally we were able to extract 192 high quality DNA extracts ready to be processed. We tested 2b-RAD with five samples and after high-throughput sequencing of libraries we used the software “Stacks” to analyze the sequences. We obtained positive results identifying a great number of SNP markers among the five samples. To guarantee a multidisciplinary approach we used the biological data associated to the collected samples to investigate differences between geographical samples. Such approach assures continuity with other project, for instance STOCKMED, which utilize a combination of molecular and biological analysis as well.

Sleep motor activity in parkinsonian syndromes at onset: a prospective study to determine potential diagnostic and prognostic markers

Aim of this study is to describe the possible diagnostic value of sleep disturbances in the differential diagnosis of neurodegenerative diseases characterized by parkinsonism at onset. 42 consecutive patients with parkinsonian features and disease duration up to 3 years were included in the BO-ProPark study. Each patient was evaluated twice, at baseline (T0) and 16 months later (T1). Patients were diagnosed as Parkinson disease (PD, 27 patients), PD plus (PD with cognitive impairment/dementia or dysautonomia, 4 patients) and parkinsonian syndrome (PS, 11 patients). All patients underwent a full night video-polysomnography scored by a neurologist blinded to the clinical diagnosis. Sleep efficiency and total sleep time were reduced in all patients; wake after sleep onset was higher in patients with atypical parkinsonisms than in PD patients. No significant differences between groups of patients were detected in other sleep parameters. The mean percentage of epochs with enhanced tonic muscle EMG activity during REM sleep was higher in PD plus and PS than in PD. No difference in phasic muscle EMG activity during REM sleep was seen between the two groups. REM behaviour disorder was more frequent in PD plus and PS than in PD patients. Our data suggest that REM sleep motor control is more frequently impaired at disease onset in patients with PS and PD plus compared to PD patients. The presence of RBD or an enhanced tonic muscle EMG activity in a patient with recent onset parkinsonian features should suggest a diagnosis of atypical parkinsonism, rather than PD. More data are needed to establish the diagnostic value of these features in the differential diagnosis of parkinsonisms. The evaluation of sleep disorders may be a useful tool in the differential diagnosis of parkinsonism at onset.

Reproduction and artificial restocking of Acipenser naccarii (Bonaparte, 1836). Genetic and physiological characterization through microsatellite markers and radioimmunoassay of sexual steroids

The Adriatic sturgeon, Acipenser naccarii (Bonaparte, 1836), is a highly threatened species due to human activities, particularly overfishing and habitat destruction. Its peculiar ecology and biology (restricted areal and anadromy) makes this species particularly vulnerable. In March 2010 the IUCN has identified the Adriatic sturgeon as a critically endangered species according to the Red List of Threatened Species. Due to its rapid decline, starting from the 80s, at present there is no evidence of natural reproduction in wild environment, which makes the Adriatic sturgeon dependenton captive breeding programs that need to be improved in order to be effective for the survival of the species. For this purpose this study aims to characterize artificial restocking population of Adriatic sturgeon, with both genetic and physiological analysis in order to establish an efficient restocking program for future reproductions. The research is structured on two levels: First genetically, by analyzing 9 microsatellite loci. This gives information relatively about parent allocation and kinship between individuals that were sampled for this study. Hence to predict which reproduction events are the most optimal in terms of incrementing genetic diversity, by the estimation of multilocus pairwise band sharing coefficients. Second step, physiological analysis: testosterone (T) concentration levels in each individual were measured for sexing, without sacrificing the lives of the animals with the use of an invasive examination of the gonads. The combination of interdisciplinary analysis is important to obtain an overall picture in order to indicate the main broodstock participating in reproduction events and future optimal potential participants, in order to ensure a valid management for restocking program and their monitoring.

Inference of Raja miraletus population structure using mitochondrial and nuclear DNA: comparing the resolution power of molecular markers in exploring species and population boundaries

This study focused on the role of oceanographic discontinuities and the presence of transitional areas in shaping the population structure and the phylogeography of the Raja miraletus species complex, coupled with the test of the effective occurrence of past speciation events. The comparisons between the Atlantic African and the North-Eastern Atlantic-Mediterranean geographic populations were unravelled using both Cytochrome Oxidase I and eight microsatellite loci. This approach guaranteed a robust dataset for the identification of a speciation event between the Atlantic African clade, corresponding to the ex Raja ocellifera nominal species, and the NE Atlantic-Mediterranean R. miraletus clade. As a matter of fact, the origin of the Atlantic Africa and the NE Atlantic-Mediterranean deep split dated about 11.74MYA and was likely due to the synergic influence currents and two upwelling areas crossing the Western African Waters. Within the Mediterranean Sea, particular attention was also paid to the transitional area represented by Adventura and Maltese Bank, that might have contributed in sustaining the connectivity of the Western and the Eastern Mediterranean geographical populations. Furthermore, the geology of the easternmost part of Sicily and the geo-morphological depression of the Calabrian Arc could have driven the differentiation of the Eastern Mediterranean Sea. Although bathymetric and oceanographic discontinuity could represent barriers to dispersal and migration between Eastern and Western Mediterranean samples, a clear and complete genetic separation among them was not detected. Results produced by this work identified a speciation event defining Raja ocellifera and R. miraletus as two different species, and describing the R. miraletus species complex as the most ancient cryptic speciation event in the family Rajidae, representing another example of how strictly connected the environment, the behavioural habits and the evolutionary and ecologic drivers are.

Meta-analyses qualify metzincins and related genes as acute rejection markers in renal transplant patients

Definition of acute renal allograft rejection (AR) markers remains clinically relevant. Features of T-cell-mediated AR are tubulointerstitial and vascular inflammation associated with excessive extracellular matrix (ECM) remodeling, regulated by metzincins, including matrix metalloproteases (MMP). Our study focused on expression of metzincins (METS), and metzincins and related genes (MARGS) in renal allograft biopsies using four independent microarray data sets. Our own cases included normal histology (N, n = 20), borderline changes (BL, n = 4), AR (n = 10) and AR + IF/TA (n = 7). MARGS enriched in all data sets were further examined on mRNA and/or protein level in additional patients. METS and MARGS differentiated AR from BL, AR + IF/TA and N in a principal component analysis. Their expression changes correlated to Banff t- and i-scores. Two AR classifiers, based on METS (including MMP7, TIMP1), or on MARGS were established in our own and validated in the three additional data sets. Thirteen MARGS were significantly enriched in AR patients of all data sets comprising MMP7, -9, TIMP1, -2, thrombospondin2 (THBS2) and fibrillin1. RT-PCR using microdissected glomeruli/tubuli confirmed MMP7, -9 and THBS2 microarray results; immunohistochemistry showed augmentation of MMP2, -9 and TIMP1 in AR. TIMP1 and THBS2 were enriched in AR patient serum. Therefore, differentially expressed METS and MARGS especially TIMP1, MMP7/-9 represent potential molecular AR markers.