The genetic diversity of Plasmodium malariae and Plasmodium brasilianum from human, simian and mosquito hosts in Brazil

Plasmodium malariae is a protozoan parasite that causes malaria in humans and is genetically indistinguishable from Plasmodium brasilianum, a parasite infecting New World monkeys in Central and South America. P. malariae has a wide and patchy global distribution in tropical and subtropical regions, being found in South America, Asia, and Africa. However, little is known regarding the genetics of these parasites and the similarity between them could be because until now there are only a very few genomic sequences available from simian Plasmodium species. This study presents the first molecular epidemiological data for P. malariae and P. brasilianum from Brazil obtained from different hosts and uses them to explore the genetic diversity in relation to geographical origin and hosts. By using microsatellite genotyping, we discovered that of the 14 human samples obtained from areas of the Atlantic forest, 5 different multilocus genotypes were recorded, while in a sample from an infected mosquito from the same region a different haplotype was found. We also analyzed the longitudinal change of circulating plasmodial genetic profile in two untreated non-symptomatic patients during a 12-months interval. The circulating genotypes in the two samples from the same patient presented nearly identical multilocus haplotypes (differing by a single locus). The more frequent haplotype persisted for almost 3 years in the human population. The allele Pm09-299 described previously as a genetic marker for South American P. malariae was not found in our samples. Of the 3 non-human primate samples from the Amazon Region, 3 different multilocus genotypes were recorded indicating a greater diversity among isolates of P. brasilianum compared to P. malariae and thus, P. malariae might in fact derive from P. brasilianum as has been proposed in recent studies. Taken together, our data show that based on the microsatellite data there is a relatively restricted polymorphism of P. malariae parasites as opposed to other geographic locations. (c) 2012 Elsevier B.V. All rights reserved.

Genetic aspects of adolescent idiopathic scoliosis in a family with multiple affected members: a research article

Abstract Background The etiology of idiopathic scoliosis remains unknown and different factors have been suggested as causal. Hereditary factors can also determine the etiology of the disease; however, the pattern of inheritance remains unknown. Autosomal dominant, X-linked and multifactorial patterns of inheritances have been reported. Other studies have suggested possible chromosome regions related to the etiology of idiopathic scoliosis. We report the genetic aspects of and investigate chromosome regions for adolescent idiopathic scoliosis in a Brazilian family. Methods Evaluation of 57 family members, distributed over 4 generations of a Brazilian family, with 9 carriers of adolescent idiopathic scoliosis. The proband presented a scoliotic curve of 75 degrees, as determined by the Cobb method. Genomic DNA from family members was genotyped. Results Locating a chromosome region linked to adolescent idiopathic scoliosis was not possible in the family studied. Conclusion While it was not possible to determine a chromosome region responsible for adolescent idiopathic scoliosis by investigation of genetic linkage using microsatellites markers during analysis of four generations of a Brazilian family with multiple affected members, analysis including other types of genomic variations, like single nucleotide polymorphisms (SNPs) could contribute to the continuity of this study.

Higher microsatellite diversity in Plasmodium vivax than in sympatric Plasmodium falciparum populations in Pursat, Western Cambodia

Previous microsatellite analyses of sympatric populations of Plasmodium vivax and Plasmodium falciparum in Brazil revealed higher diversity in the former species. However, it remains unclear whether regional species-specific differences in prevalence and transmission levels might account for these findings. Here, we examine sympatric populations of P. vivax (n = 87) and P. falciparum (n = 164) parasites from Pursat province, Western Cambodia, where both species are similarly prevalent. Using 10 genome-wide microsatellites for P. falciparum and 13 for P. vivax, we found that the P. vivax population was more diverse than the sympatric P. falciparum population (average virtual heterozygosity [HE], 0.87 vs. 0.66, P = 0.003), with more multiple-clone infections (89.6% vs. 47.6%) and larger mean number of alleles per marker (16.2 vs. 11.1, P = 0.07). Both populations showed significant multi-locus linkage disequilibrium suggestive of a predominantly clonal mode of parasite reproduction. The higher microsatellite diversity found in P. vivax isolates, compared to sympatric P. falciparum isolates, does not necessarily result from local differences in transmission level and may reflect differences in population history between species or increased mutation rates in P. vivax.

Análisis de la diversidad y genética de la caballa (Scomber colias, Gmelin, 1789) en Canarias y las zonas de influencia como metodología para contribuir en una gestión sostenible de las pesquerías

Diploma de Estudios Avanzados

Análisis de la diversidad genética en poblaciones naturales de especies vegetales amenzadas: Ilex Perado SSP. Lopezilloi (Aquifoliaceae), Silene Nocteolens (Caryophyllaceae) y Sorbus Aria (Rosaceae)

Se han elminado páginas en blanco

Biología de la conservación de endemismos vagetales de los parques nacionales canarios

[ES]El presente proyecto se centra en aplicar técnicas de biología molecular, demográficas y de biología reproductiva en cuatro endemismos canarios amenazados que se encuentran total o parcialmente localizados en los parques nacionales de Canarias: Silene nocteolens Webb & Berthel. (Parque Nacional del Teide, Tenerife); Ilex perado ssp. lopezlilloi (G. Kunkel) A. Hansen & Sunding (Parque Nacional Garajonay, La Gomera), Sorbus aria (L.) Crantz (Parque Nacional de la Caldera de Taburiente, La Palma) y Bencomia exstipulata Svent. (parques nacionales del Teide y Caldera de Taburiente). Se estableció un estudio genético a través de marcadores moleculares hipervariables, microsatélites, y se determinó para cada taxón la variación genética de sus poblaciones, para su posterior aplicación en la gestión en el ámbito de la Biología de la conservación de estos taxones.

Microsatellite dna reveals low ganetic differentiation among chub mackerel ("Scomber colias) sampled in Atlantic and Mediterranea

trabajo realizado por Medina Alcaraz, C., Castro, J.J., Sosa, P. A.

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.

Sviluppo di un sistema miniaturizzato per il controllo real-time di assetto di nano e microsatelliti

Microsatelliti e nanosatelliti, come ad esempio i Cubesat, sono carenti di sistemi integrati di controllo d’assetto e di manovra orbitale. Lo scopo di questa tesi è stato quello di realizzare un sistema compatibile con Cubesat di una unità, completo di attuatori magnetici e attuatori meccanici, comprendente tutti i sensori e l’elettronica necessaria per il suo funzionamento, creando un dispositivo totalmente indipendente dal veicolo su cui è installato, capace di funzionare sia autonomamente che ricevendo comandi da terra. Nella tesi sono descritte le campagne di simulazioni numeriche effettuate per validare le scelte tecnologiche effettuate, le fasi di sviluppo dell’elettronica e della meccanica, i test sui prototipi realizzati e il funzionamento del sistema finale. Una integrazione così estrema dei componenti può implicare delle interferenze tra un dispositivo e l’altro, come nel caso dei magnetotorquer e dei magnetometri. Sono stati quindi studiati e valutati gli effetti della loro interazione, verificandone l’entità e la validità del progetto. Poiché i componenti utilizzati sono tutti di basso costo e di derivazione terrestre, è stata effettuata una breve introduzione teorica agli effetti dell’ambiente spaziale sull’elettronica, per poi descrivere un sistema fault-tolerant basato su nuove teorie costruttive. Questo sistema è stato realizzato e testato, verificando così la possibilità di realizzare un controller affidabile e resistente all’ambiente spaziale per il sistema di controllo d’assetto. Sono state infine analizzate alcune possibili versioni avanzate del sistema, delineandone i principali aspetti progettuali, come ad esempio l’integrazione di GPS e l’implementazione di funzioni di determinazione d’assetto sfruttando i sensori presenti a bordo.

Study of variability and genetic structure of European populations of Myotis emarginatus and Myotis capaccinii (Chiroptera, Vespertilionidae)

The Geoffroy’s bat Myotis emarginatus is mainly present in southern, south-eastern and central Europe (Červerný, 1999) and is often recorded from northern Spain (Quetglas, 2002; Flaquer et al., 2004). It has demonstrated the species’ preference for forest. Myotis capaccinii, confined to the Mediterranean (Guille´n, 1999), is classified as ‘vulnerable’ on a global scale (Hutson, Mickleburgh & Racey, 2001). In general, the species preferred calm waters bordered by well-developed riparian vegetation and large (> 5 m) inter-bank distances (Biscardi et al. 2007). In this study we present the first results about population genetic structure of these two species of genus Myotis. We used two methods of sampling: invasive and non-invasive techniques. A total of 323 invasive samples and a total of 107 non-invasive samples were collected and analyzed. For Myotis emarginatus we have individuated for the first time a set of 7 microsatellites, which can work on this species, started from a set developed on Myotis myotis (Castella et al. 2000). We developed also a method for analysis of non-invasive samples, that given a good percentage of positive analyzed samples. The results have highlighted for the species Myotis emarginatus the presence on the European territory of two big groups, discovered by using the microsatellites tracers. On this species, 33 haplotypes of Dloop have been identified, some of them are presented only in some colonies. We identified respectively 33 haplotypes of Dloop and 10 of cytB for Myotis emarginatus and 25 of dloop and 15 of cytB for Myotis capaccinii. Myotis emarginatus’ results, both microsatellites and mtDNA, show that there is a strong genetic flow between different colonies across Europe. The results achieved on Myotis capaccinii are very interesting, in this case either for the microsatellites or the mitochondrial DNA sequences, and it has been highlighted a big difference between different colonies.

Design and implementation of a novel multi-constellation FPGA-based dual frequency GNSS receiver for space applications

The PhD activity described in the document is part of the Microsatellite and Microsystem Laboratory of the II Faculty of Engineering, University of Bologna. The main objective is the design and development of a GNSS receiver for the orbit determination of microsatellites in low earth orbit. The development starts from the electronic design and goes up to the implementation of the navigation algorithms, covering all the aspects that are involved in this type of applications. The use of GPS receivers for orbit determination is a consolidated application used in many space missions, but the development of the new GNSS system within few years, such as the European Galileo, the Chinese COMPASS and the Russian modernized GLONASS, proposes new challenges and offers new opportunities to increase the orbit determination performances. The evaluation of improvements coming from the new systems together with the implementation of a receiver that is compatible with at least one of the new systems, are the main activities of the PhD. The activities can be divided in three section: receiver requirements definition and prototype implementation, design and analysis of the GNSS signal tracking algorithms, and design and analysis of the navigation algorithms. The receiver prototype is based on a Virtex FPGA by Xilinx, and includes a PowerPC processor. The architecture follows the software defined radio paradigm, so most of signal processing is performed in software while only what is strictly necessary is done in hardware. The tracking algorithms are implemented as a combination of Phase Locked Loop and Frequency Locked Loop for the carrier, and Delay Locked Loop with variable bandwidth for the code. The navigation algorithm is based on the extended Kalman filter and includes an accurate LEO orbit model.

Genomische Analyse von natürlichen Killerzell-Rezeptorgenen in nicht-humanen Primaten

Natürliche Killerzell-Rezeptoren, die MHC-Klasse-I-Moleküle binden, sind im Leukozyten Rezeptor Komplex (LRC) und im Natürlichen Killer Komplex (NKC) kodiert. Die Bindung klassischer MHC-Klasse-I-Moleküle erfolgt im Menschen durch die im LRC kodierten polymorphen Killerzell-Immunglobulin-ähnlichen Rezeptoren (KIR) und in Nagetieren durch die im NKC kodierten polymorphen C-Typ Lektin-ähnlichen Ly49-Rezeptoren. Die ebenfalls im NKC kodierten C-Typ Lektin-ähnlichen CD94/NKG2-Rezeptoren sowie der NKG2D-Rezeptor sind sowohl im Menschen als auch in Nagetieren konserviert und wenig polymorph. Im Rahmen dieser Arbeit wurde das CD94-Ly49L-Intervall der NKC-Region in einem Neuweltaffen, dem Weißbüschelaffen (Callithrix jacchus), sowie einem Feuchtnasenaffen, dem Grauen Mausmaki (Microcebus murinus), über Screening von BAC-Banken und Sequenzanalyse von BAC-Contigs untersucht. Das CD94-Ly49L-Intervall im Weißbüschelaffen hat eine Länge von 171 kb und weist orthologe Gene zu den humanen NKC-Genen auf. Eine Ausnahme bildet das Gen NKG2CE, welches äquidistant zu den humanen Genen NKG2C und NKG2E ist. NKG2F und Ly49L sind Pseudogene. Expressionsanalysen der NKC-Gene in neun Weißbüschelaffen-Individuen lieferten einen mäßigen Grad an allelischen Polymorphismen. Alternative Spleißprodukte wurden für CD94, NKG2D und NKG2A identifiziert. Für NKG2A wurden verschiedene Transkripte mit potentiell unterschiedlichen Translationsstartpunkten gefunden. Im Grauen Mausmaki beträgt die Länge des CD94-Ly49L-Intervalls 489 kb. CD94 und die NKG2-Gene sind vervielfacht und wesentlich polymorpher als im Menschen und im Weißbüschelaffen. Expressionsanalysen der NKC-Gene wurden im Grauen Mausmaki und einem weiteren madagassischen Lemuren, dem Schwarzweißen Vari (Varecia variegata), durchgeführt und zeigten, dass CD94 und die NKG2-Gene im Vari ebenfalls vervielfacht sind. Die NKG2-Moleküle der Lemuren weisen unterschiedliche Kombinationen an aktivierenden und inhibierenden Signalmotiven auf und üben somit möglicherweise diverse Funktionen aus. Ly49L stellt in den Lemuren einen potentiell funktionellen inhibierenden Rezeptor dar und NKG2D besitzt im Vergleich zum humanen NKG2D-Protein eine verkürzte Zytoplasmaregion. Alternative Spleißprodukte der NKC-Gene existieren auch in den Lemuren. Darüber hinaus wurden mehrere CD94-Gene in einem weiteren Feuchtnasenaffen, dem Potto (Perodicticus potto) und einem Trockennasenaffen, dem Philippinen-Koboldmaki (Tarsius syrichta), nachgewiesen. Ein Alu-Element, welches ausschließlich in Intron 4 der CD94-Sequenzen des Philippinen-Koboldmakis auftritt, deutet darauf hin, dass sich CD94 in der Linie der Koboldmakis und in der Linie der Feuchtnasenaffen unabhängig voneinander vervielfacht hat. Die vervielfachten, polymorphen CD94/NKG2-Rezeptoren der niederen Primaten stellen möglicherweise das funktionelle Äquivalent zu den polymorphen KIR der höheren Primaten und den polymorphen Ly49-Rezeptoren der Nagetiere dar.

Conservation genetics of European wildcat (Felis silvestris silvestris): a wide and integrating analysis protocol for admixture inferences and population structure

Introgression of domestic cat genes into European wildcat (Felis silvestris silvestris) populations and reduction of wildcats’ range in Europe, leaded by habitat loss and fragmentation, are considered two of the main conservation problems for this endangered feline. This thesis addressed the questions related with the artificial hybridization and populations’ fragmentation, using a conservation genetics perspective. We combined the use of highly polymorphic loci, Bayesian statistical inferences and landscape analyses tools to investigate the origin of the geographic-genetic substructure of European wildcats (Felis silvestris silvestris) in Italy and Europe. The genetic variability of microsatellites evidenced that European wildcat populations currently distributed in Italy differentiated in, and expanded from two distinct glacial refuges during the Last Glacial Maximum. The genetic and geographic substructure detected between the eastern and western sides of the Apennine ridge, resulted by adaptation to specific ecological conditions of the Mediterranean habitats. European wildcat populations in Europe are strongly structured into 5 geographic-genetic macro clusters corresponding to: the Italian peninsular & Sicily; Balkans & north-eastern Italy; Germany eastern; central Europe; and Iberian Peninsula. Central European population might have differentiated in the extra-Mediterranean Würm ice age refuge areas (Northern Alps, Carpathians, and the Bulgarian mountain systems), while the divergence among and within the southern European populations might have resulted by the Pleistocene bio geographical framework of Europe, with three southern refugia localized in the Balkans, Italian Peninsula and Iberia Peninsula. We further combined the use of most informative autosomal SNPs with uniparental markers (mtDNA and Y-linked) for accurately detecting parental genotypes and levels of introgressive hybridization between European wild and domestic cats. A total of 11 hybrids were identified. The presence of domestic mitochondrial haplotypes shared with some wild individuals led us to hypnotize the possibility that ancient introgressive events might have occurred and that further investigation should be recommended.

Structural verification of the ESEO spacecraft: from launch loads analysis to composite panels verification

The present thesis work was performed in the frame of ESEO (European Student Earth Orbiter) project. The activities that are described in this document were carried out in the Microsatellites and Space Micro systems Lab led by Professor Paolo Tortora and in ALMASpace company facilities. The thesis deals with ESEO structural analysis, at system and unit level, and verification: after determining the design limit loads to be applied to the spacecraft as an envelope of different launchers load profiles, a finite element structural analysis was performed on the model of the satellite in order to ensure the capability to withstand the loads encountered during the launch; all the analyses were performed according to ESA standards and using the software MSC NASTRAN SIMXPERT. Amplification factors were derived and used to determine loads to be considered at unit level. In particular structural analyses were carried out on the GPS unit, the payload developed for ESEO by students of University of Bologna and results were used in the preparation of GPS payload design definition file. As for the verification phase a study on the panels and inserts to be used in the spacecraft was performed: different designs were created exploiting methods to optimize weight and mechanical behavior. The configurations have been analyzed and results compared to select the final design.