A trophic study of the sympatric Amazonian freshwater turtles Podocnemis unifilis and Podocnemis expansa (Testudines, Podocnemidae) using carbon and nitrogen stable isotope analyses

The Yellow-spotted River Turtle (Podocnemis unifilis Troschel, 1848) and the South American River Turtle (Podocnemis expansa (Schweigger, 1812)) are two turtles species that are widely distributed and have ecological, economic, and cultural importance in the Amazon basin. Although sympatric regarding most of their distribution, few studies have addressed the coexistence of these two species. To examine this, we analyzed the trophic level and the primary carbon source from the diets of both species in Baixo Araguaia, Tocantins, Brazil, using stable isotope analyses of carbon (delta C-13) and nitrogen (delta N-15). We also verified possible intraspecific variations (related to sex and body mass) in the trophic levels and primary carbon sources of their diets. Podocnemis unifilis had higher values of delta N-15 than P. expansa, averaging 7.59 parts per thousand and 5.06 parts per thousand, respectively, a difference which may indicate a possible trophic change owing to exploiting different food resources. No differences were found between the two species in relation to delta C-13 (mean values of -26.2 parts per thousand and -26.1 parts per thousand, respectively). The similarity between delta C-13 values suggests that the sources of their basal feeding are the same, consisting mainly of C-3 plants. There was no intraspecific variation in the values of delta C-13 and delta N-15.

Respiratory syncytial virus (RSV) pneumonia in a southern muriqui (Brachyteles arachnoides)

Background An adult male Brachyteles arachanoides, kept in captivity since 1990, was found dead without apparent clinical evidence. Methods Necropsy report, histopathology, immunohistochemistry, and ultrastructural examination were conducted. Results Pulmonary syncytial cells were positive for respiratory syncytial virus (RSV), and ultrastructural examination revealed viral particles inside macrophages compatible with the Paramyxoviridae family. Conclusions Muriquis are susceptible to RSV pneumonia followed by respiratory distress syndrome and death.

Rickettsia bellii infecting Amblyomma sabanerae ticks in El Salvador

Four Amblyomma sabanerae ticks collected from a turtle (Kinosternon sp.) in San Miguel, El Salvador, were found by molecular analysis to be infected by Rickettsia bellii. We provide the first report of Rickettsia bellii in Central America, and the first report of a Rickettsia species in El Salvador.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (lncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. In the present work we investigated the relative abundance of a collection of lncRNAs in patients' pancreatic tissue samples aiming at identifying gene expression profiles correlated to pancreatic cancer and metastasis. Methods Custom 3,355-element spotted cDNA microarray interrogating protein-coding genes and putative lncRNA were used to obtain expression profiles from 38 clinical samples of tumor and non-tumor pancreatic tissues. Bioinformatics analyses were performed to characterize structure and conservation of lncRNAs expressed in pancreatic tissues, as well as to identify expression signatures correlated to tissue histology. Strand-specific reverse transcription followed by PCR and qRT-PCR were employed to determine strandedness of lncRNAs and to validate microarray results, respectively. Results We show that subsets of intronic/intergenic lncRNAs are expressed across tumor and non-tumor pancreatic tissue samples. Enrichment of promoter-associated chromatin marks and over-representation of conserved DNA elements and stable secondary structure predictions suggest that these transcripts are generated from independent transcriptional units and that at least a fraction is under evolutionary selection, and thus potentially functional. Statistically significant expression signatures comprising protein-coding mRNAs and lncRNAs that correlate to PDAC or to pancreatic cancer metastasis were identified. Interestingly, loci harboring intronic lncRNAs differentially expressed in PDAC metastases were enriched in genes associated to the MAPK pathway. Orientation-specific RT-PCR documented that intronic transcripts are expressed in sense, antisense or both orientations relative to protein-coding mRNAs. Differential expression of a subset of intronic lncRNAs (PPP3CB, MAP3K14 and DAPK1 loci) in metastatic samples was confirmed by Real-Time PCR. Conclusion Our findings reveal sets of intronic lncRNAs expressed in pancreatic tissues whose abundance is correlated to PDAC or metastasis, thus pointing to the potential relevance of this class of transcripts in biological processes related to malignant transformation and metastasis in pancreatic cancer.

Distribution of Rickettsia rickettsii in ovary cells of Rhipicephalus sanguineus (Latreille1806) (Acari: Ixodidae)

Abstract Background Considering the fact that the dog tick, Rhipicephalus sanguineus, has a great potential to become the vector of Brazilian Spotted Fever (BSF) for humans, the present study aimed to describe the distribution of the bacterium Rickettsia rickettsii, the etiological agent of BSF, in different regions of the ovaries of R. sanguineus using histological techniques. The ovaries were obtained from positive females confirmed by the hemolymph test and fed in the nymph stage on guinea pigs inoculated with R. rickettsii. Results The results showed a general distribution of R. rickettsii in the ovary cells, being found in oocytes in all stages of development (I, II, III, IV and V) most commonly in the periphery of the oocyte and also in the cytoplasm of pedicel cells. Conclusions The histological analysis of the ovaries of R. sanguineus infected females confirmed the presence of the bacterium, indicating that the infection can interfere negatively in the process of reproduction of the ticks, once alterations were detected both in the shape and cell structure of the oocytes which contained bacteria.

Natural blood feeding and temperature shift modulate the global transcriptional profile of Rickettsia rickettsii infecting its tick vector

Rickettsia rickettsii is an obligate intracellular tick-borne bacterium that causes Rocky Mountain Spotted Fever (RMSF), the most lethal spotted fever rickettsiosis. When an infected starving tick begins blood feeding from a vertebrate host, R. rickettsii is exposed to a temperature elevation and to components in the blood meal. These two environmental stimuli have been previously associated with the reactivation of rickettsial virulence in ticks, but the factors responsible for this phenotype conversion have not been completely elucidated. Using customized oligonucleotide microarrays and high-throughput microfluidic qRT-PCR, we analyzed the effects of a 10 degrees C temperature elevation and of a blood meal on the transcriptional profile of R. rickettsii infecting the tick Amblyomma aureolatum. This is the first study of the transcriptome of a bacterium in the genus Rickettsia infecting a natural tick vector. Although both stimuli significantly increased bacterial load, blood feeding had a greater effect, modulating five-fold more genes than the temperature upshift. Certain components of the Type IV Secretion System (T4SS) were up-regulated by blood feeding. This suggests that this important bacterial transport system may be utilized to secrete effectors during the tick vector's blood meal. Blood feeding also up-regulated the expression of antioxidant enzymes, which might correspond to an attempt by R. rickettsii to protect itself against the deleterious effects of free radicals produced by fed ticks. The modulated genes identified in this study, including those encoding hypothetical proteins, require further functional analysis and may have potential as future targets for vaccine development.

Dynamics of cell and tissue genesis in the male reproductive system of ticks (Acari: Ixodidae) Amblyomma cajennense (Fabricius, 1787) and Amblyomma aureolatum (Pallas, 1772): a comparative analysis

Ticks are classified into three families: Argasidae, Ixodidae, and Nutalliellidae. The taxonomy and phylogeny within Ixodidae are still discussed by the specialists, thus requiring further studies. Amblyomma cajennese and Amblyomma aureolatum (Brazil) belong to two species complexes known as “cajennese” and “ovale”, respectively, and are directly related to the transmission of the Brazilian spotted fever. This confirms the medical and veterinary significance of these species, as well as the need for further morphological studies that will bring a better understanding of their taxonomy, phylogeny, and control. In this context, the present study aimed to characterize the morphology of the male reproductive system of A. cajennese and A. aureolatum when unfed and after 4 days of feeding, thereby seeking to: (a) distinguish the two species or “complexes”, and (b) study an internal system which has the potential to be targeted by acaricides. Therefore, males from both species (unfed and after 4 days of feeding) were cold-anesthetized, dissected, and had their reproductive systems removed for histological analysis. The results showed that the morphology of the male reproductive system is generally similar between both species, like in other Ixodidae ticks, exhibiting a multilobed accessory gland complex related to seminal fluid secretion, a pair of vasa deferentia and a pair of testes housing germ cells (spermatocytes) in different stages. The main differences were found in the development of the accessory gland complex cells and germ cells, showing that the maturation of the male reproductive system starts later in A. aureolatum, when compared to A. cajennese. However, during the blood meal, A. aureolatum development is increased, thus making germ cell maturation and gland complex activity higher than in A. cajennese. This study shows the differences in the development of the male reproductive systems of both species, while providing information that can assist in the establishment of new control methods.

Metamorfismo ercinico di bassa-pressione: evoluzione tettonico-metamorfica del complesso di mandatoriccio (massiccio della Sila - Calabria)

Low-pressure/high-temperature (LP/HT) metamorphic belts are characterised by rocks that experienced abnormal heat flow in shallow crustal levels (T > 600 °C; P < 4 kbar) resulting in anomalous geothermal gradients (60-150 °C/km). The abnormal amount of heat has been related to crustal underplating of mantle-derived basic magmas or to thermal perturbation linked to intrusion of large volumes of granitoids in the intermediate crust. In particular, in this latter context, magmatic or aqueous fluids are able to transport relevant amounts of heat by advection, thus favouring regional LP/HT metamorphism. However, the thermal perturbation consequent to heat released by cooling magmas is responsible also for contact metamorphic effects. A first problem is that time and space relationships between regional LP/HT metamorphism and contact metamorphism are usually unclear. A second problem is related to the high temperature conditions reached at different crustal levels. These, in some cases, can completely erase the previous metamorphic history. Notwithstanding this problem is very marked in lower crustal levels, petrologic and geochronologic studies usually concentrate in these attractive portions of the crust. However, only in the intermediate/upper-crustal levels of a LP/HT metamorphic belt the tectono-metamorphic events preceding the temperature peak, usually not preserved in the lower crustal portions, can be readily unravelled. The Hercynian Orogen of Western Europe is a well-documented example of a continental collision zone with widespread LP/HT metamorphism, intense crustal anatexis and granite magmatism. Owing to the exposure of a nearly continuous cross-section of the Hercynian continental crust, the Sila massif (northern Calabria) represents a favourable area to understand large-scale relationships between granitoids and LP/HT metamorphic rocks, and to discriminate regional LP/HT metamorphic events from contact metamorphic effects. Granulite-facies rocks of the lower crust and greenschist- to amphibolite-facies rocks of the intermediate-upper crust are separated by granitoids emplaced into the intermediate level during the late stages of the Hercynian orogeny. Up to now, advanced petrologic studies have been focused mostly in understanding P-T evolution of deeper crustal levels and magmatic bodies, whereas the metamorphic history of the shallower crustal levels is poorly constrained. The Hercynian upper crust exposed in Sila has been subdivided in two different metamorphic complexes by previous authors: the low- to very low-grade Bocchigliero complex and the greenschist- to amphibolite-facies Mandatoriccio complex. The latter contains favourable mineral assemblages in order to unravel the tectono-metamorphic evolution of the Hercynian upper crust. The Mandatoriccio complex consists mainly of metapelites, meta-arenites, acid metavolcanites and metabasites with rare intercalations of marbles and orthogneisses. Siliciclastic metasediments show a static porphyroblastic growth mainly of biotite, garnet, andalusite, staurolite and muscovite, whereas cordierite and fibrolite are less common. U-Pb ages and internal features of zircons suggest that the protoliths of the Mandatoriccio complex formed in a sedimentary basin filled by Cambrian to Silurian magmatic products as well as by siliciclastic sediments derived from older igneous and metamorphic rocks. In some localities, metamorphic rocks are injected by numerous aplite/pegmatite veins. Small granite bodies are also present and are always associated to spotted schists with large porphyroblasts. They occur along a NW-SE trending transcurrent cataclastic fault zone, which represents the tectonic contact between the Bocchigliero and the Mandatoriccio complexes. This cataclastic fault zone shows evidence of activity at least from middle-Miocene to Recent, indicating that brittle deformation post-dated the Hercynian orogeny. P-T pseudosections show that micaschists and paragneisses of the Mandatoriccio complex followed a clockwise P-T path characterised by four main prograde phases: thickening, peak-pressure condition, decompression and peak-temperature condition. During the thickening phase, garnet blastesis started up with spessartine-rich syntectonic core developed within micaschists and paragneisses. Coevally (340 ± 9.6 Ma), mafic sills and dykes injected the upper crustal volcaniclastic sedimentary sequence of the Mandatoriccio complex. After reaching the peak-pressure condition (≈4 kbar), the upper crust experienced a period of deformation quiescence marked by the static overgrowths of S2 by Almandine-rich-garnet rims and by porphyroblasts of biotite and staurolite. Probably, this metamorphic phase is related to isotherms relaxation after the thickening episode recorder by the Rb/Sr isotopic system (326 ± 6 Ma isochron age). The post-collisional period was mainly characterised by decompression with increasing temperature. This stage is documented by the andalusite+biotite coronas overgrown on staurolite porphyroblasts and represents a critical point of the metamorphic history, since metamorphic rocks begin to record a significant thermal perturbation. Peak-temperature conditions (≈620 °C) were reached at the end of this stage. They are well constrained by some reaction textures and mineral assemblages observed almost exclusively within paragneisses. The later appearance of fibrolitic sillimanite documents a small excursion of the P-T path across the And-Sil boundary due to the heating. Stephanian U-Pb ages of monazite crystals from the paragneiss, can be related to this heating phase. Similar monazite U-Pb ages from the micaschist combined with the lack of fibrolitic sillimanite suggest that, during the same thermal perturbation, micaschists recorded temperatures slightly lower than those reached by paragneisses. The metamorphic history ended with the crystallisation of cordierite mainly at the expense of andalusite. Consequently, the Ms+Bt+St+And+Sill+Crd mineral assemblage observed in the paragneisses is the result of a polyphasic evolution and is characterised by the metastable persistence of the staurolite in the stability fields of the cordierite. Geologic, geochronologic and petrographic data suggest that the thermal peak recorded by the intermediate/upper crust could be strictly connected with the emplacement of large amounts of granitoid magmas in the middle crust. Probably, the lithospheric extension in the relatively heated crust favoured ascent and emplacement of granitoids and further exhumation of metamorphic rocks. After a comparison among the tectono-metamorphic evolutions of the different Hercynian crustal levels exposed in Sila, it is concluded that the intermediate/upper crustal level offers the possibility to reconstruct a more detailed tectono-metamorphic history. The P-T paths proposed for the lower crustal levels probably underestimate the amount of the decompression. Apart from these considerations, the comparative analysis indicates that P-T paths at various crustal levels in the Sila cross section are well compatible with a unique geologic scenario, characterized by post-collisional extensional tectonics and magmas ascent.

Ontologie per il Web Semantico: un'analisi comparativa

Il lavoro svolto in questa tesi è stato quello di analizzare il Web Semantico e i suoi linguaggi di rappresentazione delle informazioni. Inoltre sono state introdotte le ontologie evidenziando il loro ruolo all’interno del Web Semantico. Infine è stato fatto uno studio riguardo le ontologie attualmente sviluppate, allo scopo di portare a termine un’analisi comparativa delle stesse.

Interfaccia web per un sistema di condivisione semantica dell'informazione: studio e implementazione

Questa tesi progettuale nasce per integrare gli sforzi attuali sullo sviluppo del web semantico. La piattaforma di riferimento sulla quale è stato svolto il presente lavoro è SMART-M3. Questa piattaforma mette a disposizione uno spazio condiviso di informazioni, rappresentate e accessibili secondo le tecnologie del web semantico. In questo scenario, nasce la necessità di disporre di un'interfaccia web capace di interagire con la piattaforma - in grado di risolvere la complessità intrinseca dei dati semantici - allo scopo di averne un completo controllo; ricerche precedenti a questo proposito hanno dato come frutto una libreria PHP che mi è stata consegnata come strumento per lo sviluppo dell'interfaccia. La tesi si è articolata in 3 fasi principali: una fase iniziale di documentazione sull'argomento, eseguita principalmente sul libro “A developer's guide to the semantic web” di Liyang Yu e sulla tesi “Ontologie per il web semantico: un'analisi comparativa.” di Indrit Beqiri; una seconda fase, quella principale, di sviluppo del progetto informatico; una terza fase, infine, di sviluppo di questo elaborato di tesi, da considerarsi come la trattazione di tutto il percorso soprascritto, dall'inizio alla fine, secondo l'ordine cronologico in cui si svolto l'intero processo della tesi.

Modelli per l'aggregazione di dati federati: il caso degli orari di apertura degli esercizi commerciali e enti pubblici

Questa tesi tratta di scambio di dati aperti (open data exchange). In particolare, tratta di intervalli temporali con annesse informazioni di vario tipo. Le attività commerciali, come aziende, bar, ristoranti, cinema, teatri, e via dicendo, hanno bisogno di un modo comune per poter condividere i dati inerenti ai propri orari (timetable). Lo scopo di questa tesi è quello di mostrare un modello efficiente, compatto e completo per poter condividere tali informazioni con l'ausilio di formati standard (XML). Oggi giorno esistono diverse soluzioni atte a far fronte a questa necessità ma si tratta di soluzioni incomplete e che gestiscono tali informazioni separatamente. Il problema sorto è quello di avere un'unica struttura che posso unificare informazioni di diverso carattere con gli orari di un'attività: un cinema ha la necessità di fornire orari di diverse proiezioni svolte in sale diverse, una tournée dovrà poter specificare le coordinate geografiche del prossimo evento e così discorrendo.

Conversione per il Semantic Web di dati Turistico-Culturali: il progetto QRPlaces - Semantic Events

Il progetto QRPlaces - Semantic Events, oggetto di questo lavoro, focalizza l’attenzione sull’analisi, la progettazione e l’implementazione di un sistema che sia in grado di modellare i dati, relativi a diversi eventi facenti parte del patrimonio turistico - culturale della Regione Emilia Romagna 1, rendendo evidenti i vantaggi associati ad una rappresentazione formale incentrata sulla Semantica. I dati turistico - culturali sono intesi in questo ambito sia come una rappresentazione di “qualcosa che accade in un certo punto ad un certo momento” (come ad esempio un concerto, una sagra, una raccolta fondi, una rappresentazione teatrale e quant’altro) sia come tradizioni e costumi che costituiscono il patrimonio turistico-culturale e a cui si fa spesso riferimento con il nome di “Cultural Heritage”. Essi hanno la caratteristica intrinseca di richiedere una conoscenza completa di diverse informa- zioni correlata, come informazioni di geo localizzazione relative al luogo fisico che ospita l’evento, dati biografici riferiti all’autore o al soggetto che è presente nell’evento piuttosto che riferirsi ad informazioni che descrivono nel dettaglio tutti gli oggetti, come teatri, cinema, compagnie teatrali che caratterizzano l’evento stesso. Una corretta rappresentazione della conoscenza ad essi legata richiede, pertanto, una modellazione in cui i dati possano essere interconnessi, rivelando un valore informativo che altrimenti resterebbe nascosto. Il lavoro svolto ha avuto lo scopo di realizzare un dataset rispondente alle caratteristiche tipiche del Semantic Web grazie al quale è stato possibile potenziare il circuito di comunicazione e informazione turistica QRPlaces 2. Nello specifico, attraverso la conversione ontologica di dati di vario genere relativi ad eventi dislocati nel territorio, e sfruttando i principi e le tecnologie del Linked Data, si è cercato di ottenere un modello informativo quanto più possibile correlato e arricchito da dati esterni. L’obiettivo finale è stato quello di ottenere una sorgente informativa di dati interconnessi non solo tra loro ma anche con quelli presenti in sorgenti esterne, dando vita ad un percorso di collegamenti in grado di evidenziare una ricchezza informativa utilizzabile per la creazione di valore aggiunto che altrimenti non sarebbe possibile ottenere. Questo aspetto è stato realizzato attraverso un’in- terfaccia di MashUp che utilizza come sorgente il dataset creato e tutti i collegamenti con la rete del Linked Data, in grado di reperire informazioni aggiuntive multi dominio.