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Phylogeny and chloroplast evolution in Brassicaceae
Get PDFBrassicaceae is a large family of flowering plants, characterized by cruciform corolla, tetradynamous stamen and capsular fruit. In light of the important economic and scientific values of Brassicaceae, many phylogenetic and systematic studies were carried out. One recent and important phylogenetic analysis revealed three major lineages (I, II and III), however, classification at different taxonomic levels (tribe, genus, and species) remained problematic and evolutionary relationships among and within these lineages were still largely unclear. This is partly due to the fact that the past studies lacked information, as they mainly utilized the morphological data, nuclear DNA, partial chloroplast (cp) genes and so on. Nowadays, next generation sequencing (NGS) technology provides the possibility to make use of big data in phylogeny and evolutionary studies. Thus, we sequenced the chloroplast genomes of 80 representative species, using additional 15 reference chloroplast genomes from the NCBI database, and carried out both the phylogenetic reconstruction and the study of protein coding genes evolution in this novel dataset with different methods. Several novel results were obtained.
1 Successful application of NGS technology in chloroplast genome sequencing. During the final assembly, I could reconstruct full chloroplast genomes and the structure maps for 14 out of 80 sampled species, while the remaining were assembled nearly completely with only few gaps remaining.
2 Characterization of chloroplast genome structure. Gene number and order, single sequence repeat (SSR) as well as variety and distribution of large repeat sequence were characterized.
3 The difference of codon usage frequency was calculated between Cardamine resedifolia and Cardamine impatiens. Twelve genes with signatures of positive selection were identified at a family-wide level.
4 Three major lineages (I – III) were confirmed with high support values. Besides, the positions of various tribes were reclassified. Relationships among and within these lineages were highly resolved and supported in the final tree. Most of the tribes in the analyses were inferred to be monophyletic, only Thlaspideae was paraphyletic. Anastaticeae was for the first time classified into position of expanded lineage II, and position of tribe Lepidieae was delimited with relatively low support values in the final phylogenetic tree.
This study was a new and successful application of NGS in large-scale Brassicaceae phylogeny and evolution, which offered the chance to look in details of the structural and functional features of the chloroplast genome. These results provided a paradigm on how to proceed towards the full elucidation of the evolutionary relationships among various biological species in the tree of life
Investigation of the structural and molecular substrate of atrial fibrillation
Get PDFAtrial fibrillation (AF) is the most common sustained arrhythmia worldwide and a frequent cause of hospitalization. Moreover, it represents one of the most frequent complication following cardiac surgery with an incidence of around 30% and an important predictor of patient morbidity. The exact pathophysiological mechanisms responsible for the onset and perpetuation of AF are not completely understood. However, clinical and experimental insights on the factors causing AF have suggested that atrial fibrillation is a multi-factorial phenomenon. Atrial fibrillation is characterized by a highly complex and irregular electrical activation of the atrial tissue, which is the manifestation of diverse abnormalities (electrical, structural, metabolic, neurohormonal, and/or molecular alterations) in diverse pathological conditions. In particular, it has been shown that fibrosis, a phenomenon in which extracellular matrix (ECM) components, mainly fibrillar collagen, accumulate between cardiomyocytes, leads to the inhomogeneous atrial electrical conduction typical of fibrillation. Recent studies have suggested that the deregulation of gene expression may act as a molecular mechanism of arrhythmogenesis. In particular, miRNAs, a new class of non-coding RNAs have rapidly emerged as one of the key players in the gene expression regulatory network, so variations in their expression levels may constitute a pathway for the arrhythmia-induced atrial remodeling.
The present study aims to investigate the structural and molecular features of atrial tissue, with particular attention to fibrosis, which may be involved in the formation of a pro-arrhythmic substrate. By using both histological and advanced microscopy techniques, intramural fibrotic content and 3D collagen network properties were determined in atrial samples, collected during cardiac surgery in patients who developed or not AF. The quantitative analysis indicated a general decrease of collagen content from the outer (the epicardium) to the inner (the endocardium) myocardial wall, in the overall patient population. However, AF patients presented higher fibrotic values compared to sinus rhythm (SR) patients in the deeper myocardial layers, thus supporting the hypothesis that an accumulation of fibrotic tissue within the myocardial wall may represent an important structural contributor in the pathophysiology of AF. In addition to a quantitative assessment, collagen properties such as fibers orientation (degree and anisotropy) and scale dimension, were determined by non-linear optical microscopy techniques. The analysis revealed that in SR patients collagen network showed a fine architecture characterized by thin fibrils with changing angles and directions compared to AF, where fibers tended to pack-up in larger bundles of defined directions. A quantitative analysis of the 3D collagen network features, throughout the atrial wall, revealed that fibers orientation and scale dimension changed along tissue depth in both SR and AF patients, with larger values of orientation and fiber changes in AF tissues. These results highlight the spatial rearrangement and thickening of the 3D collagen network in AF patients, suggesting its possible role in the maintenance of the arrhythmia.
Numerous evidence indicated that also an altered regulation of gene expression may play an important role in the mechanisms of atrial remodeling which underlie AF. In this perspective, the expression pattern of some miRNAs known to target different genes involved in diverse mechanisms that underlie AF was evaluated. A panel of miRNAs (miR-1, miR-133a/b, miR-30c, miR-29a/b, miR-208a/b, miR-328, miR-499, miR-590 and miR-21), principally involved in the formation of a pro-arrhythmic substrate, was selected after an accurate review of the literature and analyzed by RT-qPCR, in AF patients versus SR individuals. To accurately determine the levels of analyzed miRNAs, their expression data are usually normalized relatively to endogenous and/or exogenous reference genes. To date, no general agreement between different normalization strategies has been found, in particular in cardiac tissue, for the study of AF. For these reasons, a preliminary study aiming to establish the best endogenous reference genes for miRNAs data normalization was performed. Specifically, different well-established analysis tools such as NormFinder, GeNorm, BestKeeper and ∆Ct method, were applied on five commonly used endogenous reference transcripts such as 5S, U6, SNORD48, SNORD44 and miR-16. The suitable reference gene obtained, SNORD48, was applied for miRNAs data normalization. Our findings revealed that miRNAs expression levels were different in AF compared to SR patients. MiR-208a and miR-208b displayed statistically significant differences between the two populations. To investigate possible relationships between miRNAs expression levels and the fibrotic content a correlation measurement was also performed. Our analysis revealed that miR-21 and miR-208b were close to a significant correlation with fibrosis. In conclusion, this work introduced new techniques and implemented new methods of analysis for the study of the substrate of AF. In particular, the results obtained with this multiscale approach, from structural to molecular level, exacerbated the role of fibrosis as a critical contributor in the formation of a pro-arrhythmic substrate. Nonetheless, further studies are needed for a better understanding of the ways in which structural, molecular and also cellular remodeling may alter the impulse propagation in the myocardium
Rinascimento di pietra. Scultura nella Vicenza prepalladiana
Get PDFLa tesi, movendo da un riesame complessivo della scultura lapidea vicentina tra Quattro e Cinquecento, cerca di mettere meglio a fuoco alcune peculiarità e tendenze nello sviluppo dell’arte scultorea ai piedi dei Berici.
Procedendo con affondi mirati e inediti, si è definita in maniera più organica la situazione della scultura a Vicenza in quel torno di tempo e di comprendere meglio alcuni nessi altrimenti sfuggenti.
Una particolare attenzione è stata rivolta a indagare fatti artistici peculiari del territorio quali le pale d'altare che, scolpite nella tenera pietra delle cave vicentine, si sono imposte come un’autentica specificità locale, in ragione delle proporzioni assunte da questo interessante ‘fenomeno’. Ampiamente diffuse, specie nel contado, tali ancone sono evidentemente esemplate su modelli padovani di matrice donatelliana. Il periodo in esame, che va dalle ultime decadi del Quattrocento ai primi lustri del secolo seguente, è d’altronde caratterizzato da frequenti e fecondi scambi con Padova, avanguardia di modernità e ricca di capolavori del Rinascimento. Echi della lezione di Donatello si avvertono anche in una serie di altorilievi che rappresentano il Cristo passo, sorretto o meno da angeli, e sono ugualmente disseminati nella provincia vicentina.
A corredo del terzo capitolo della tesi, incentrato proprio su tale importante fenomeno artistico, si è allestito un repertorio completo dei singoli manufatti (pale plastiche e Cristi passi), di cui s'è trattato in ampie schede dove si sono ripercorse anche le vicende storico-architettoniche dei diversi contesti spaziali di pertinenza, non sempre rimasti immutati nei secoli
Sentential Representations in Distributional Semantics
No full textThis thesis is about the problem of representing sentential meaning in distributional semantics. Distributional semantics obtains the meanings of words through their usage, based on the hypothesis that words occurring in similar contexts will have similar meanings. In this framework, words are modeled as distributions over contexts and are represented as vectors in high dimensional space. Compositional distributional semantics attempts to extend this approach to higher linguistics structures. Some basic composition models proposed in literature to obtain the meaning of phrases or possibly sentences show promising results in modeling simple phrases. The goal of the thesis is to further extend these composition models to obtain sentence meaning representations. The thesis puts more focus on unsupervised methods which make use of the context of phrases and sentences to optimize the parameters of a model. Three different methods are presented. The first model is the PLF model, a practical composition and linguistically mo tivated model which is based on the lexical function model introduced by Baroni and Zamparelli (2010) and Coecke et al. (2010). The second model is the Chunk-based Smoothed Tree Kernels (CSTKs) model, extending Smoothed Tree Kernels (Mehdad et al., 2010)by utilizing vector representations of chunks. The final model is the C-PHRASE model, a neural network-based approach, which jointly optimizes the vector representations of words and phrases using a context predicting objective. The thesis makes three principal contributions to the field of compositional distributional semantics. The first is to propose a general framework to estimate the parameters and evaluate the basic composition models. This provides a fair way to comparing the models using a set of phrasal datasets. The second is to extend these basic models to the sentence level, using syntactic information to build up the sentence vectors. The third con tribution is to evaluate all the proposed models, showing that they perform on par with or outperform competing models presented in the literature
Investigating multisensory integration in human early visual and auditory areas with intracranial electrophysiological recordings: insights and perspectives
No full textCross-modal processing and multisensory integration (MSI) can be observed at early stages of sensory processing in the cortex. However, the neurophysiological mechanisms underlying these processes and how they vary across sensory systems remain elusive. The aim of this study was to investigate how cross-modal processing and MSI are reflected in power and phase of oscillatory neuronal activity at different temporal scales in different sensory cortices. To this goal, we recorded stereo-electroencephalographic (SEEG) responses from early visual (calcarine and pericalcarine) and auditory (Heschl’s gyrus and planum temporale) regions in patients with drug-resistant epilepsy while performing an audio-visual oddball task. To Investigate crossmodal processing and MSI in the power domain of oscillatory activity, we explored a wide range of frequency bands (theta/alpha band: 5-13Hz; beta band: 13-30 Hz; gamma band: 30-80 Hz; high-gamma band: 80-200 Hz) during the first 150 ms post-stimulus onset. Differently, to investigate crossmodal processing and MSI in the phase domain of oscillatory activity, we explored a narrow range of frequency bands (theta/alpha band: 5-13Hz; beta band: 13-30 Hz; gamma band: 30-80 Hz) during the first 300 ms post-stimulus onset. In the power domain, we showed that cross-modal processing occurs mainly in the high-gamma band (80-200Hz) in both cortices. However, we evidenced that the way MSI is expressed across modalities differs considerably: in the visual cortex, MSI relies mainly on the beta band, however it is also evident, to a lesser extent, in the gamma and high-gamma band, while the auditory cortex reveals widespread MSI in the high-gamma band and, to a lesser extent, across the gamma band and the other investigated frequency bands. In the phase domain, we showed that cross-modal processing is differently expressed across modalities: in the auditory cortex it induces an increased phase concentration index (PCI) in ongoing oscillatory activity across all the investigated frequency bands, while, in the visual cortex, it induces an increased PCI particularly evident in the theta/alpha band with few or no effect respectively in the gamma and beta band. Importantly in both cortices, the most part of the COIs showing increased PCI, were not accompanied by a concomitant increase in power. These results indicate that in both auditory and visual cortex, cross-modal processing induces a pure phase resetting of the oscillatory activity. During MSI processing we observed, in both cortices, a stronger increase in PCI, in comparison to the intramodal processing, in the theta/alpha band and in the gamma band.
Our results confirm the presence of cross-modal information representations at neuronal populations level and conform to a model where the cross-modal input induces phase-locked modulation of the ongoing oscillations. Importantly, our data showed that the way MSI is expressed in power modulations differs between the investigated sensory cortices suggesting the presence of different types of neurophysiological interactions during this process. These results are discussed in the framework of the current literature
Study of Visual Clutter in Geographic Node-Link Diagrams
No full textAn increasing amount of geographic data is now freely available on the Internet, and this number is expected to increase as monitoring systems and sensors are becoming a ubiquitous part of our environment.
A substantial subset is structured as networks (or graphs). Notable examples are import/export of goods, networks of climate stations, flight connections, migration flows and Internet traffic. To fully comprehend such networks, it is needed to know both their geographic and relational information. For this purpose, the most common visual representation is the node-link diagram, where vertices are depicted as points and the edges connecting them are drawn as lines. This Thesis focuses on an instance of node-link diagrams, where nodes are over-imposed on a map and fixed according to their geographical information.
The major issue of this visualization is the visual clutter of nodes or edges, defined in literature as ``the state in which excess items, or their representation or organization, lead to a degradation of performance at some task''. In particular, nodes and links may cause occlusion and ambiguity in the graph representation. Such problems characterize a cluttered diagram because they reduce the potential usefulness of the visualization.
The goal of this thesis is to advance the state of the art in Graph Visualization with respect to visual clutter.
On the theoretical perspective, our goal is to acquire a deep understanding of existing approaches for visualizing geographic networks and for reducing visual clutter. Initially, we provide a classification of geographic node-link diagrams and a survey on techniques to reduce the visual clutter on such visualizations. Afterwards, we present a schematization of techniques that helps the reader to decide, given a task and a geographical node-link diagram, which are the candidate solutions that help to reduce the visual clutter. On the practical perspective, our goal is the development of visualization and interaction techniques to overcome various issues of the state-of-the-art approaches. On the one hand, we present an interactive lens that faces the issues of links organization over a map. On the other hand, we describe a deformation-based technique that reveals nodes and links otherwise hidden behind the globe surface. Finally, we introduce a method that automatically generates flow map layouts starting from multivariate geographical datasets
Minor Powers Confronting Major Powers: A Comparative Examination of the Conditions Facilitating Decisions to go to War
No full textThe political landscape of the world is constituted by states of varying degrees of influence and capability. Major powers have immense resources at their disposal, while minor powers are often constrained in terms of structure and material. Thus, for minor powers, engaging in conventional wars against much larger and more powerful states is potentially ruinous to their economies and endangers their political survival. While researchers have explored interstate asymmetric conflicts involving major and middle powers, this project specifically analyzes asymmetric conflicts between minor and major powers, focusing on the former, and the post Cold-war period. This research aims to analyze conditions, highlighted by theories on war, under which minor powers go to war challenging major powers. This research employs multiple theories, thereby establishing an innovative, pluri-theoretical framework. This theoretical framework works well with a mixed-methods approach, a medium-N research design (crisp set methodology in Qualitative Comparative Analysis), and three comparative case studies: Iraq (1990), Moldova (1992) and Serbia (1999).
This dissertation finds that by looking through the lenses of multiple theories, one can observe a more nuanced relationship between conditions faced by minor powers in militarized disputes and their decisions to go to war against a major power. First, different combinations of conditions can result in conflict. Second, domestic crisis, not external threat, tends to be of primary concern to minor powers. Third, minor powers enter a war to win based on very modest expectations. Fourth, minor powers of autocratic regime type can also misperceive the situation through anomalous beliefs. The importance of the study stems from the observation that minor powers still fight conventional asymmetric wars, despite growing military capabilities of major powers. Understanding the risks, minor powers gamble, hoping to keep their political benefits. This study enhances our understanding of conditions shaping the occurrence of asymmetric conflict
Autoria e complicità nel reato collettivo. Studio storico e comparato su un'integrazione tra modelli di concorso
No full textL'istituto del concorso di persone, nella sua funzione estensiva della punibilità, costituisce uno snodo fondamentale tra il principio di legalità – inteso nell'accezione più strettamente relativa a tassatività e determinatezza – e quello di necessaria personalità della responsabilità penale. La questione emerge con particolare evidenza nelle ipotesi di reati commessi nell'ambito di formazioni collettive connotate da strutture organizzative e gerarchiche, in cui appare particolarmente arduo stabilire i meccanismi di ascrizione della responsabilità in capo ai singoli in base alle regole classiche della compartecipazione. La presente indagine parte da questa constatazione, e si propone di affrontare il tema attraverso l'utilizzo della comparazione giurisprudenziale tra due ordinamenti che hanno optato per due modelli antitetici di disciplina: l'opzione unitaria del codice Rocco, e il Beteiligungssystem tedesco. Inoltre, ci si propone di approfondire l'indagine comparata attraverso un riferimento all'evoluzione storica delle categorie di autoria e complicità, e altresì mediante un accenno allo sviluppo della materia in relazione a processi di grande rilevanza storico-politica, in particolare avendo riguardo alla notevole influenza che la teoria roxiniana dell'Organisationsherrschaft ha esercitato sulla giurisprudenza sudamericana e sulla Corte penale internazionale. Proprio il dibattito scaturito dall'applicazione della disposizione dell'art. 25 dello Statuto di Roma, in tema di responsabilità individuale, sembra costituire un buono spunto per una discussione sull'auspicabilità di un concetto di partecipazione nel reato a livello europeo, in una prospettiva di armonizzazione. Nell'esporre una riflessione personale su tale questione, si cerca di prendere le mosse dagli esiti della comparazione diacronica, sincronica e dell'indagine sul piano sovranazionale, in modo da presentare una soluzione che possa essere al tempo stesso agile sul piano applicativo, espressiva degli elementi di convergenza tra i vari modelli esaminati, e rispettosa dei principii fondamentali che regolano l'imputazione penale
Identification and functional characterization of microRNA regulatory elements in Brassicaceae
Get PDFAs a class of short non-coding RNAs, microRNAs can regulate gene expression by a post-transcriptional pathway through repressing or degrading mRNA. In the evolutionary history, many plant microRNAs are highly conserved from green alge to land plants. In recent years, dramatic studies demonstrate that microRNAs play a crucial in plant growth and development, in response to environmental stresses. Some microRNAs can response to plant hormones, while some others are tissue or cell specific. The understanding of how these microRNAs are regulated at the transcriptional level is just initiated. With the aim to understand the regulatory mechanism of plant microRNA in evolutionary tem, and identify the most relevant cisregulatory elements in some microRNAs for improving the agriculture in the future, this study was carried out. microRNA390 is one of the many conserved microRNAs, it can indirectly regulate the ARFs expression level by targeting TAS3, and consequently regulate lateral organ and later root development in plants. In order to understand the regulatory mechanism of microRNAs in an evolutionary term, microRNA390a and microRNA390b in Arabidopsis were chosen and studied. In 16 phylogenetically related species within Brassicaceae, we analyzed the microRNA promoter sequences and identified overall conserved cREs in microRNA390 promoter regions, and accompanied with functional characterization, we obtained a good view of microRNA390 regulatory network. Based on 454 sequencing technique, took the microRNA sequences of sequenced Arabidopsis as reference, by assembling and aligning the microRNA promoter sequences, calculated the PWM and predicted the putative motifs with both MEME program and PlantCARE database, subsequently compared the motif similarities by TOMTOM program, we eventually obtained the putative ones met the required E-value. In the meantime, we reconstructed the phylogenetic trees of both paralogs by MEGA7 program. We identified 6 and 5 overall conserved cREs. Subsequently, we experimentally validated the putative cREs by Arabidopsis transformation and site-specific mutagenesis.
The results we have obtained were as follows:
(1) There were totally 29 microRNA loci in 9 families identified to be highly conserved, and totally 104 putative motifs were predicted in their promoter regions.
(2) The reconstructed phylogenetic trees based on miRNA390a and miRNA390b promoter sequences respectively were compared with the the phylogenetic relationships (species trees) in known Brassicaceae phylogeny. The data derived from both promoter sequences were inconsistent with Brassicaceae phylogeny. This implied that there might be multiple copies of specific cREs in some specific species, hence the promoter sequences evolution of microRNA is not reflective of species phylogeny.
(3) Took Arabidopsis thaliana as model plant, we successfully constructed GUS-fused promoters of miRNA390a and miRNA390b. The GUS histochemical assay indicated that the two paralogs expressed in different tissues in transgenic Arabidopsis. miRNA390a expressed in lateral root primordia, true leaves, cotyledons, as well as in the floral organs, yet it was absent from lateral root tip and shoot apical meristem; whereas miRNA390b specifically expressed on lateral root tips, and a more restricted expression pattern was detected on aerial part of true leaves and floral organ. These differences indicated possible sub-functionalization with respect to their ancestral miR390 during the evolutionary process.
(4) Based on the six putative cREs identified in miRNA390a and the reliable WT constructs, we also constructed six GUS-fused promoters that undergone site-specific mutagenesis. The GUS assay demonstrated that the activity of putative cis-elements varied with distance to TSS. Mutations of proximal sites (m2 and m3) enhanced expression thereby M2 and M3 were likely to be silencers; while mutations of distal elements (m5 and m6) tended to decrease the promoter expression, hence M5 and M6 probably work as enhancers. These evidences suggest there was a specific modular cooperativity of miR390a cREs in regulating gene expression and mediating plant development.
Furthermore, we treated the 7d-old transgenic seedlings with iron-deficiency, both the GUS assay and qRT-PCR data conferred the iron responsiveness of putative iron-deficiency related E-box M3 and the iron-deficiency responsive cis-element 1 M6
Discovery and characterization of novel Nef-like infectivity factor
No full textThe SERINC family is a highly conserved group of genes which in the human genome comprises 5 members, encoding five homologous multipass transmembrane proteins. SERINC5, and to a lesser extent SERINC3, are powerful inhibitors of Human immunodeficiency virus 1 (HIV-1). SERINC5, expressed in virus-producing cells, is incorporated into the envelope of newly formed retroviral particles and inhibits an early stage of the virus infection process of the target cell, by preventing the delivery of the retroviral core into the target cell cytoplasm. Nef, an accessory protein of HIV-1, counteracts the antiretroviral activity of SERINC5 by promoting its endocytosis, which results in its removal from the cell surface, preventing its incorporation into retroviral particles. SERINC5 inhibits not only HIV-1, but also other divergent retroviruses, such as Murine leukemia virus (MLV). During my Ph.D. studies I demonstrated that the S2 auxiliary protein from Equine infectious anemia virus (EIAV) functionally resembles Nef and MLV glycoGag and counteracts SERINC5 with a similar mechanism.
While the inhibitory effect of SERINC5 has been established on retroviruses, nothing is yet known about its effect on other viruses. Here I describe evidence which indicates the possible inhibitory activity of the SERINC gene family against other RNA viruses