Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

West versus East Mediterranean Sea: origin and genetic differentiation of the sea cucumber Holothuria polii

We studied the genetic structure of the sea cucumber Holothuria (Roweothuria) polii (Delle Chiaje 1823) by analysing the mitochondrial DNA variation in two fragments of cytochrome oxidase I (COI) and 16S genes. Individuals were collected in seven locations along the Mediterranean Sea, which cover a wide range of the species distribution. We found high haplotype diversity for COI and moderate diversity for 16S, and low nucleotide diversity for both genes. Our results for the COI gene showed many recent and exclusive haplotypes with few mutational changes, suggesting recent or ongoing population expansion. The Western and Eastern Mediterranean populations exhibited slight but significant genetic differentiation (COI gene) with higher genetic diversity in the East. The most ancient haplotype was not present in the westernmost sampling location (SE Spain). The oldest expansion time was observed in Turkey, corresponding to mid-Pleistocene. Turkey had also the highest genetic diversity (number of total and exclusive haplotypes, polymorphisms, haplotype and nucleotide diversity). This suggests that this region could be the origin of the subsequent colonizations through the Mediterranean Sea, a hypothesis that should be assessed with nuclear markers in future research.

Forms of the Postmodern Historical Novel : Christoph Ransmayr, Daniel Kehlmann, Wolfgang Hildesheimer

L’émergence du postmodernisme aux Etats-unis, mouvement esthétique rejetant les dogmes modernistes, date des années 1960. En s’imposant, durant les dernières décennies du 20ème siècle, comme le paradigme esthétique de l’architecture, des arts et de la littérature, le postmodernisme a également créé les conditions propres à une renaissance du roman historique. Cependant, la fiction historique postmoderne constitue maintenant une nouvelle forme du genre basée sur la parodie, l’ironie et le scepticisme envers les discours dominants. Cette nouvelle forme ne se limite plus à la présentation des récits dans un cadre historique réaliste. Elle remet plutôt en question la validité et par conséquent la nature même du discours historique, problématisant et mettant ainsi à l’avant le processus d’interprétation et de reconstruction du passé. Dans cette optique, la fiction historique contemporaine reflète les débats actuels sur les formes de l’historiographie, débats lancés par Hayden White. Dans les années 1980, la fiction historique a de nouveau fleuri dans l'espace culturel allemand tout comme ailleurs. Le présent mémoire analyse des formes postmodernes de la fiction historique en se basant sur trois romans historiques de langue allemande parus entre 1981 et 2005: Die Schrecken des Eises und der Finsternis de Christoph Ransmayr, Die Vermessung der Welt de Daniel Kehlmann et Marbot : Eine Biographie de Wolfgang Hildesheimer. L’analyse s'appuie sur divers modèles de la fiction postmoderne, en particulier sur le schéma de catégorisation du roman historique élaboré par Ansgar Nünning. Le mémoire montre dans quelle mesure ces romans appliquent des moyens stylistiques typiques pour le postmodernisme et portent un regard critique ou comique sur l’histoire et la culture allemande et autrichienne.

Veteranness : Representations of Combat-related PTSD in U.S. Popular Visual Media

Posttraumatic stress and PTSD are becoming familiar terms to refer to what we often call the invisible wounds of war, yet these are recent additions to a popular discourse in which images of and ideas about combat-affected veterans have long circulated. A legacy of ideas about combat veterans and war trauma thus intersects with more recent clinical information about PTSD to become part of a discourse of visual media that has defined and continues to redefine veteran for popular audiences. In this dissertation I examine realist combat veteran representations in selected films and other visual media from three periods: during and after World Wars I and II (James Allen from I Am a Fugitive from a Chain Gang, Fred Derry and Al Stephenson from The Best Years of Our Lives); after the Vietnam War (Michael from The Deer Hunter, Eriksson from Casualties of War), and post 9/11 (Will James from The Hurt Locker, a collection of veterans from Wartorn: 1861-2010.) Employing a theoretical framework informed by visual media studies, Barthes’ concept of myth, and Foucault’s concept ofdiscursive unity, I analyze how these veteran representations are endowed with PTSD symptom-like behaviors and responses that seem reasonable and natural within the narrative arc. I contend that veteran myths appear through each veteran representation as the narrative develops and resolves. I argue that these veteran myths are many and varied but that they crystallize in a dominant veteran discourse, a discursive unity that I term veteranness. I further argue that veteranness entangles discrete categories such as veteran, combat veteran, and PTSD with veteran myths, often tying dominant discourse about combat-related PTSD to outdated or outmoded notions that significantly affect our attitudes about and treatment of veterans. A basic premise of my research is that unless and until we learn about the lasting effects of the trauma inherent to combat, we hinder our ability to fulfill our responsibilities to war veterans. A society that limits its understanding of posttraumatic stress, PTSD and post-war experiences of actual veterans affected by war trauma to veteranness or veteran myths risks normalizing or naturalizing an unexamined set of sociocultural expectations of all veterans, rendering them voice-less, invisible, and, ultimately disposable.

A study of the impact of persuasive argumentation in political debates

Persuasive communication is the process of shaping, reinforcing and changing others' responses. In political debates, speakers express their views towards the debated topics by choosing both the content of their discourse and the argumentation process. In this work we study the use of semantic frames for modelling argumentation in speakers' discourse. We investigate the impact of a speaker's argumentation style and their effect in influencing an audience in supporting their candidature. We model the influence index of each candidate based on their relative standings in the polls released prior to the debate and present a system which ranks speakers in terms of their relative influence using a combination of content and persuasive argumentation features. Our results show that although content alone is predictive of a speaker's influence rank, persuasive argumentation also affects such indices.

Forms of the Postmodern Historical Novel : Christoph Ransmayr, Daniel Kehlmann, Wolfgang Hildesheimer

L’émergence du postmodernisme aux Etats-unis, mouvement esthétique rejetant les dogmes modernistes, date des années 1960. En s’imposant, durant les dernières décennies du 20ème siècle, comme le paradigme esthétique de l’architecture, des arts et de la littérature, le postmodernisme a également créé les conditions propres à une renaissance du roman historique. Cependant, la fiction historique postmoderne constitue maintenant une nouvelle forme du genre basée sur la parodie, l’ironie et le scepticisme envers les discours dominants. Cette nouvelle forme ne se limite plus à la présentation des récits dans un cadre historique réaliste. Elle remet plutôt en question la validité et par conséquent la nature même du discours historique, problématisant et mettant ainsi à l’avant le processus d’interprétation et de reconstruction du passé. Dans cette optique, la fiction historique contemporaine reflète les débats actuels sur les formes de l’historiographie, débats lancés par Hayden White. Dans les années 1980, la fiction historique a de nouveau fleuri dans l'espace culturel allemand tout comme ailleurs. Le présent mémoire analyse des formes postmodernes de la fiction historique en se basant sur trois romans historiques de langue allemande parus entre 1981 et 2005: Die Schrecken des Eises und der Finsternis de Christoph Ransmayr, Die Vermessung der Welt de Daniel Kehlmann et Marbot : Eine Biographie de Wolfgang Hildesheimer. L’analyse s'appuie sur divers modèles de la fiction postmoderne, en particulier sur le schéma de catégorisation du roman historique élaboré par Ansgar Nünning. Le mémoire montre dans quelle mesure ces romans appliquent des moyens stylistiques typiques pour le postmodernisme et portent un regard critique ou comique sur l’histoire et la culture allemande et autrichienne.

The influence of queer theory on marriage and civil partnership in Scotland

This thesis will explore the whether queer theory has had any real influence on the law on marriage and civil partnership in Scotland. It will do so by examining the work of Michael Foucault and Judith Butler, reviewing both The History of Sexuality Volume One, and Gender Trouble to establish what queer theory has to say on gender and sexuality. Both works expose the artificiality of gender and sexuality, and in doing so, show that marriage and civil partnership are institutions created to support these artificial structures. Marriage and civil partnership are not isolated from the continuing influence of queer discourse on both gender and sexuality; however, as I will show, the influence has been contained largely to opening up privilege, both legally and socially, to those who wish to conform to structures that remain heteronormative and prescriptive.

Occurrence of plastic debris in the stomach of the invasive crab Eriocheir sinensis

The Chinese mitten crab is known as a pest causing damage to fishing gears and fish. On the other hand, this highly invasive species is considered a delicacy by Asian migrants and therefore commercially fished and sold in many countries. The ingestion of plastic by the Chinese mitten crab Eriocheir sinensis from the Baltic coastal waters (Poland) and the Tagus Estuary (Portugal) was studied based on stomach content analysis. As many as 13% of the 302 analysed males and females (38.07–89.07 mm carapace width) from both regions, contained microplastic in the form of strands and balls. Most of them were transparent. Ingested plastic particles were identified as fragments of fishing gears. Contamination with plastic may have a negative impact on this species as well as on higher trophic levels feeding on crabs.

“Losanga” decorated imitations of italic late republican black gloss tableware from South-Western Iberia: A multi-analytical/microchemical characterization

The micro-chemical/mineralogical composition of samples of grey-paste imitations of Italic Late Republican black gloss tableware displaying a particular kind of lozenge-shaped decoration (“Losanga pottery”) from Portuguese and Spanish archaeological sites in SW Iberia has been analysed by BSEM + EDS, μXRD, Powder XRD, Portable XRF and μRaman spectroscopy. “Losanga” decorated ceramics have been found throughout the Western Mediterranean. Most of the sherds display a green-brown to greyish-black engobe at the surface resembling the gloss found in Attic pottery from Classical Greece. The overall chemical, mineralogical and fossiliferous homogeneities of the ceramic paste show common features (low K-feldspar/plagioclase ratio, high Ca content, abundance of well-preserved fragments of foraminifera microfossils) that indicate low firing conditions in the kiln ranging from 650 to 900 °C. With respect to the ceramic body, analytical results confirm an enrichment in the surface gloss layer of iron, potassium and aluminium and a depletion in silicon and calcium; the very fine grain size of the surface coating suggests elutriation of iron oxide-rich clays as confirmed by the presence of magnetite, maghemite and goethite in μ-XRD scan. Chemical and mineralogical data also suggest that the firing process was performed in a 600–850 °C temperature range, adopting the well-known technique of alternating oxidizing and reducing firing conditions largely employed at the time. The analytical results, while compatible with the archaeological hypothesis of a common provenance of the raw materials for pottery production from the Guadalquivir valley workshops cannot be considered conclusive due to the similarity in the geological substrate in the two SW Iberian regions under study.

Identification and effects of mixed infection of Potyvirus isolates with Cucumber mosaic virus in cucurbits.

Mixed infections in cucurbits are frequently observed in natural conditions between viruses from the Potyvirus genus and Cucumber mosaic virus (CMV), which significantly decreases productivity. The objectives of the present study was to compare the host range of PRSV-W, WMV, and ZYMV isolates and evaluate the effects of mixed infections with CMV in zucchini plants (Cucurbita pepo L.). Host range studies comprising 23 plant species confirmed some similarities and biological differences among the isolates of PRSV-W, ZYMV, and WMV. RT-PCR confirmed the amplification of DNA fragments of the PRSV-W, WMV, and ZYMV coat protein gene (cp) and cytoplasm inclusion gene (ci). The virus interaction studies in zucchini Caserta plants indicated synergistic interactions, particularly among species from the Potyvirus genus, and some CMV interference with some virus combinations.

Electrochemistry of polycyclic aromatic molecules for advanced carbon nanostructures: luminescence and transistor applications

Polycyclic aromatic hydrocarbons (PAHs) are a large class of π-conjugated organic molecules with fused aromatic rings, which can be considered as fragments of 2D-graphene and have been extensively studied for their unique optical and electronic properties. The aim of this study is to understand the complex electrochemical behaviour of planar, curved, and heteroatom doped polycyclic aromatic molecules, particularly focusing on the oxidative coupling of their radical cations and the electrochemically induced cyclodehydrogenation reactions. In the first part of this thesis, the class of PAHs and aromatic nanostructures are introduced, and the reactivity of electrogenerated species is discussed, focusing on the electrochemical approach for the synthesis of extended π-conjugated structures. Subsequently, the electrochemical properties and reactivity of electrogenerated radical ions of planar and curved polyaromatics are correlated to their structures. In the third chapter, electrochemical cyclodehydrogenation of hexaphenylbenzene is used to prepare self-assembled hexabenzocoronene, directly deposited on an interdigitated electrode, which was characterised as organic electrochemical transistor. In the fourth chapter, the electrochemical behaviour of a family of azapyrene derivatives has been carefully investigated together with the electrogenerated chemiluminescence (ECL), both by ion-annihilation and co-reactant methods. Two structural azapyrene isomers with different nitrogen positions are thoroughly discussed in terms of redox and ECL properties. Interestingly, the ECL of only one of them showed a double emission with excimer formation. A detailed mechanism is discussed for the ECL by co-reactant benzoyl peroxide, to rationalise the different ECL behaviours of the two isomers on the basis of their topologically modulated electronic properties. In conclusion, the different electrochemical behaviours of PAHs were shown, focussing on the chemical reactivity of the electrogenerated species and taking advantage of it for important processes spanning from unconventional synthesis methods for carbon nanostructures to the exploitation of self-assembled nanostructured systems in organic electronics, to novel organic emitters in ECL.

Diretrizes curriculares nacionais para o ensino médio: avaliação de documento

This text offers some contributions to the debate on the changes proposed to the National Curricular Directives to reform secondary education in Brazil. In the first part, the political and economic scene is evaluated as the context which generated the last stage of reforms in the educational field in the 90s. It questions the option for a model of structural reform (in the Brazilian case more restricted to the Program for Reform of Professional Education - PROEP) and of the curriculum, whose themes find their justification in the contemporary economic, social cultural and political context. It discusses the use of a model that bases itself on experiences developed in other countries and takes the international orientation of the multilateral organizations as its theoretical methodological reference, leaving out the peculiarities and injunctions of the Brazilian political administrative system. Such a policy measure can increase the tension and distance normally existing between government programs and the possibility of their real implementation in the school network. In the second part, it discusses the Resolution of the National Education Council, the Congress on Basic Education, no.3, of 16.698 that instituted the National Curricular Directives for secondary education, as well as the Legal Bases - Part I - of the National Curricular Parameters for secondary education. The analysis of official discourse takes Bardin's (1977, p. 209) proposals as its methodological reference for the models of structural analysis, seeking to make the implicit values and the connotations of the legal texts explicit

Flora arbustivo-arbórea do fragmento de floresta estacional semidecidual do Ribeirão Cachoeira, município de Campinas, SP

An inventory of the woody flora (trees and shrubs), was carried out in the Ribeirão Cachoeria forest (233.7ha, 650m high, 46°55'58''W, 22°50'13''S), the second largest and best conserved fragment of semideciduous tropical forest in the municipality of Campinas, São Paulo state, Southeastern Brazil. The soil is a red-yellow podsol and the climate is of Köppen's Cwag type. Collections were made from August/1996 to September/1997. Only fertile individuals with a perimeter at breast height of 9cm or greater were included in the survey. One hyndred and seventhy five species were identified, belonging to 119 genera and 49 families. The most important families were Myrtaceae (14 species), Rutaceae and Fabaceae (13), Caesalpiniaceae (11), Solanaceae (9), and Rubiaceae (8). Some species were found for the first time in the region: Tachigali multijuga Benth. and Schoepfia brasiliensis A.DC. The flowering peak for most species was from August to October. Maximum fruit production was from August to November. Most species are zoochoric (58%), but 23% were anemochoric and 19% autochoric. The floristic composition of this forest and another 20 forests from São Paulo state were compared. The results obtained indicate the existence of distinct groups of forests. The most homogeneus group contains forests from the municipality of Campinas with similarity of 40%. This suggests that these forests are possibly fragments of a original continuous forest in the Campinas region.

Lianas da estação ecológica do Noroeste Paulista, São José do Rio Preto/Mirassol, SP, Brasil

Lianas are characteristic, abundant and ecologically important members of tropical forest but they have been neglected in floristics and phytossociological studies. This work presents a floristic survey of the lianas species at Estação Ecológica do Noroeste Paulista (EENP), and a comparison of the list of species recorded in this work with those reported for other fragments of São Paulo state. The EENP (20º48'36'' S and 49º22'50'' W) is at 468 m of altitude and comprises an area of 168,43 ha, divided into three fragments of vegetation. Samples of lianas were collected in the interior and along the edges of the forest fragments. It was identified 105 species: 99 Magnoliopsida (60 genera and 22 families); six Liliopsida (three genera and three families). The richest families in species comprised 59% of the total of lianas sampled. The dendrogram of similarity showed a low similarity between the forest situated in the littoral (Atlantic Forest) and those located in the interior of the state of São Paulo. Some other authors, also analysing the similarity of forest of the interior and Atlantic Forest of São Paulo state, but considering only the trees reported similar result.

FORMAÇÕES DISCURSIVAS E PROCESSOS IDENTIFICATÓRIOS NA AQUISIÇÃO DE LÍNGUAS

This paper discusses theoretical results of the research project Linguistic Identity and Identification: A Study of Functions of Second Language in Enunciating Subject Constitution. Non-cognitive factors that have a crucial incidence in the degree of success and ways of accomplishment of second language acquisition process are focused. A transdisciplinary perspective is adopted, mobilising categories from Discourse Analysis and Psychoanalysis. The most relevant ones are: discursive formation, intradiscourse, interdiscourse, forgetting n° 1, forgetting n° 2 (Pêcheux, 1982), identity, identification (Freud, 1966; Lacan, 1977; Nasio, 1995). Revuz s views (1991) are discussed. Her main claim is that during the process of learning a foreign language, the foundations of psychical structure, and consequently first language, are required. After examining how nomination and predication processes work in first and second languages, components of identity and identification processes are focused on, in an attempt to show how second language acquisition strategies depend on them. It is stated that methodological affairs of language teaching, learner s explicit motivation and the like are subordinated to the comprehension of deeper non-cognitive factors that determine the accomplishment of the second language acquisition process. It is also pointed out that those factors are to be approached, questioning the bipolar biological-social conception of subjectivity in the study of language acquisition and use and including in the analysis symbolic and significant dimensions of the discourse constitution process.