DNA damage response pathways are a complicated network of proteins that function to remove and/or reverse DNA damage. Following genetic insult, a signal cascade is generated, which alerts the cell to the presence of damaged DNA. Once recognized, the damage is either removed or the damaged region is excised, and the original genetic sequence is restored. However, when these pathways are defective the cell is unable to effectively mediate the DNA damage response and the damage persists unrepaired. Thus, the proteins that maintain the DNA damage response pathway are critical in preserving genomic stability. One essential DNA repair protein is the Breast Cancer Associated gene, BRCA1. BRCA1 is essential for mediating the DNA damage response, facilitating DNA damage repair, and activating key cell cycle checkpoints. Moreover, mutations in BRCA1 lead to a higher incidence of breast and ovarian cancer, highlighting the importance of BRCA1 as a tumor suppressor. In an effort to better understand how BRCA1 carried out these functions, researchers sought to identify additional BRCA1 interacting proteins. This led to the identification of several proteins including the BRCA1 Associated C-terminal Helicase, BACH1. Due to the direct interaction of BACH1 with a region of BRCA1 essential for DNA repair and tumor suppression, it was speculated that BACH1 may help support these BRCA1 function(s). In fact, initial genetic screenings confirmed that mutations in BACH1 correlated not only with hereditary breast cancer, but also with defects in DNA damage repair processes. The initial correlation between BACH1 and cancer predisposition was further confirmed when mutations in BACH1 were identified in the cancer syndrome Fanconi anemia (FA) (complementation group FA-J), thus giving BACH1 its new name FANCJ. These findings supported a previously established link between the FA and BRCA pathways and between FA and DNA repair. In particular, we demonstrated that similar to other FA/BRCA proteins, suppression of FANCJ lead to a substantial decrease in homologous recombination and enhanced both the cellular sensitivity to DNA interstrand cross-linking agents and chromosomal instability. What remained unknown was specifically how FANCJ functioned and whether these functions were dependent on its interaction with BRCA1 or other associated partners. In fact, we identified that FANCJ interacted directly with the MMR protein MLH1. Moreover, we found that the FANCJ/BRCA1 interaction was not required to correct the cellular defects in FA-J cells, but rather that the FANCJ/MLH1 interaction was required. Although both the FA/BRCA and MMR pathways undoubtedly mediate the DNA damage response, there was no evidence to suggest that these pathways were linked, until recently. Our findings not only indicate a physical link between these pathways by protein-protein interaction, but also demonstrated a functional link.

Alors que la superficie des forêts de plantation continue d'augmenter dans le monde, leurcontribution à la conservation de la biodiversité reste controversée. L’objectif de cette thèse estd'identifier les facteurs clés, à la fois au niveau de l'habitat local et à celui du paysage, qui influent surla diversité des papillons de jour dans les paysages en mosaïque dominés par des plantations de pins.Les communautés de papillons ont été échantillonnées en lisière et à l’intérieur de plantations de pinmaritime, pare-feux, ripisylves et fragments de forêts de feuillus variant par la taille et le degréd’isolement spatial. Les traits biologiques et écologiques des papillons ont été liés auxcaractéristiques de l’habitat et aux variables paysagères.Les éléments les plus importants pour la conservation des papillons dans les paysages dominés parles plantations de pins sont les habitats semi-naturels: forêts de feuillus, pare-feux et lisières. Lesripisylves se révèlent être les plus riches en papillons forestiers, abritant des espèces spécialisées. Lespare-feux hébergent deux fois plus d'espèces que les autres types d'habitats et sont importants pourla conservation de plusieurs espèces menacées. Toutefois les plantations de pin ne sont pas vide depapillons. La qualité de l'habitat, notamment la présence de plantes hôtes, est le facteur le plusdéterminant de la composition des communautés de rhopalocères. La composition et laconfiguration du paysage ont également une influence importante sur la diversité des papillons. Denombreuses espèces de papillons ont été observées dans plusieurs types d'habitat suggérant que lacomplémentation et supplémentation des ressources soient des processus clés pour maintenir ladiversité des papillons dans les paysages forestiers hétérogènes. / While the area of plantation forests continues to increase worldwide, their contribution to theconservation of biodiversity is still controversial. The aim of this thesis is to identify key habitat andlandscape factors that drive butterfly diversity in mosaic landscapes dominated by pine plantations.Butterfly communities were sampled at edges and interiors of five successional stages of pine stands,in firebreaks, riparian forests and in deciduous woodlands varying in fragment size and isolation.Biological and ecological traits of butterflies were related to habitat patch attributes and tolandscape composition and configuration.The results highlighted the critical importance of semi-natural habitats for butterfly conservation inpine plantation mosaics, i.e. deciduous woodlands, firebreaks and edges. Riparian forests wereespecially rich in forest butterfly species, harboring specialized species with both narrow habitat andthermal ranges. Firebreaks had twice as many species as other habitat types and were ofconservation value for several threatened butterfly species. Our results also showed that pine standswere not ‘free of butterflies'. Habitat quality, particularly the presence of host plants, was the mostimportant driver of butterfly community composition. Landscape composition and configuration alsoinfluenced butterfly diversity. Many species used more than one distinct habitat type, suggestingthat resource complementation and supplementation are important mechanisms of butterflydiversity persistence in pine plantation mosaics.

Orientador: Sonia Maria Lazzarini Cyrino / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Estudos da Linguagem / Made available in DSpace on 2018-08-22T08:47:05Z (GMT). No. of bitstreams: 1 Meira_Vivian_D.pdf: 1178142 bytes, checksum: e326a7771cea8102eee5851541fef4ea (MD5) Previous issue date: 2013 / Resumo: Esta tese investiga padrões de referencialidade em complementação sentencial no português, italiano e grego moderno, especialmente, o fenômeno conhecido como obviação ou referência disjunta. Esta é uma restrição atestada nas línguas e se caracteriza pelo fato de o sujeito da oração subordinada ser obrigatoriamente disjunto em referência ao sujeito da oração matriz. Tradicionalmente, assume-se que a obviação é uma propriedade de complementação subjuntiva ou um fenômeno resultante, juntamente com o controle, da competição entre formas finitas/não-finitas. No entanto, os dados não condizem com essas hipóteses, já que a obviação é exibida tanto em complementação indicativa quanto nos contextos de infinitivo flexionado. Além disso, nem todo contexto volitivo exibe obviação. Assumindo a teoria de seleção semântica e a versão minimalista de subcategorização (cf. Adger, 2004), propomos que a obviação, exibida em complementação sentencial, é uma restrição semântica exigida por três tipos de predicados, os causativos, os volitivos e os perceptivos físicos, que serão tomados como predicados modais no sentido de serem capazes de impor restrições semânticas aos seus complementos. Estes predicados foram denominados de predicados de obviação, por compartilharem entre si algumas propriedades, como denotar leitura eventiva/não-epistêmica, exigir sujeito pronominal na encaixada independente referencialmente do sujeito matriz e subcategorizar complemento TP. Argumentamos ainda que esses predicados, devido ao seu caráter modal, selecionam semanticamente um traço [obviativo], que é transmitido ao sujeito da encaixada. Predicados de obviação se distinguem de outro grupo de predicado modal, os predicados de controle, por estes não permitirem que o argumento da encaixada seja disjunto do sujeito matriz. Esses dois grupos se distinguem de outro grupo de verbos que permitem referência livre, constituído especialmente por predicados epistêmicos, declarativos, dentre outros, que denotam leitura epistêmica/proposicional e subcategorizam complemento CP. Sintaticamente este grupo de predicados se distingue dos predicados de obviação por subcategorizarem estruturas distintas, pois, enquanto estes têm complemento TP, aqueles selecionam complemento CP. Para explicar por que obviação e controle são exibidos pelo predicado volitivo, propomos que há dois tipos de acepções no volitivo nas línguas: o volitivo padrão, que seleciona controle e o volitivo causativo, que exige obviação. Defendemos que o complemento infinitivo flexionado selecionado por causativo e perceptivo é uma estrutura TP, o que o diferencia da estrutura de infinitivo flexionado selecionada por factivos/epistêmicos/declarativos, que é tomado como um CP. Estes permitem referência livre e aqueles exigem obviação. Nossa proposta é mostrar que a obviação, exibida em complementação sentencial, não é um fenômeno restrito às línguas românicas ou às línguas que exibem a distinção finito/não-finito, mas são uma restrição semântica imposta por predicados de obviação os seus complementos e, devido a isso, essa restrição semântica será exibida por línguas que dispõem desses contextos em complementação sentencial / Abstract: This thesis investigates patterns of referentiality in sentential complementation in Portuguese, Italian and Modern Greek, especially the phenomenon known as obviation or disjoint reference. This is a constraint attested in languages, and it is characterized by the fact that the subject of the subordinate clause must be disjoint in reference to the subject of the matrix sentence. Traditionally, obviation has been assumed to be a property of subjunctive complementation, or a phenomenon arising along with the control from the competition between finite/non-finite forms. However, the data are not consistent with these hypotheses, since obviation appears in indicative complementation and inflected infinitive contexts. Moreover, obviation is not displayed in every volitional context. Based on the theory of semantic selection and a minimalist version of subcategorization (cf. Adger, 2004), this thesis proposes that obviation, in sentential complementation, is a semantic constraint required by three types of predicates, the causative, volitional and physical perceptive predicates, which will be taken as predicates able to impose semantic constraints on their complements. These predicates are called obviation predicates, which share some common properties, as denoting eventive/non-epistemic reading, they require referentially independent subject pronouns in an embedded clause, and select a TP complement. We argue that these predicates, because of their modal character, select semantically a trace [obviative], which is transmitted to the subject in the embedded clause. Obviation predicates are distinguished from another group of modal predicates, control predicates, which do not allow, in an embedded clause, an argument referentially independent from the matrix subject. These two groups are distinguished from yet another group of verbs that allow free reference, specially constituted by epistemic, declarative predicates, among others, which denote an epistemic/propositional reading and select CP complements. Syntactically, this group can be distinguished from obviation predicates by selecting distinct structures, because while these have a TP complement, the former select CP complements. To explain why both obviation and control are displayed by volitional predicates, we propose that there are two types of volitional meanings in the languages: the default volitional that selects control, and the causative volitional, that requires obviation. Furthermore, we argue that the inflected infinitive complement selected by causative and perceptive verbs is a TP structure, and they require obviation, which differ from the inflected infinitive selected by factives/epistemic/declarative verb, which take CP complements and allows free reference. The purpose of this thesis is to show that obviation, in sentential complementation, is not a phenomenon restricted to the Romance languages, or languages that exhibit a distinction between finite and non-finite forms, but that it is a semantic constraint imposed by obviation predicates on their complements and, consequently, this constraint will appear in languages which have these contexts in sentential complementation / Doutorado / Linguistica / Doutora em Linguística

In the search for the mitochondrion of oxymonads, DNA of Monocercomonoides exilis - an oxymonad isolated from the gut of Chinchilla, was isolated and its genome was sequenced. Sequencing resulted in a fairly complete genome which was extensively searched or genes for mitochondrion related proteins, but no reliable candidate for such gene was identified. Even genes for the ISC pathway, which is responsible for Fe-S cluster assembly and considered to be the only essential function of reduced mitochondrion-like organelles (MROs), were absent. Instead, we were able to detect the presence of a SUF pathway which functionally replaced the ISC pathway. Closer examination of the SUF pathway based on heterologous localisation revealed that this pathway localised in the cytosol. In silico analysis showed that SUF genes are highly conserved at the level of secondary and tertiary structure and most catalytic residues and motifs are present in their sequences. The functionality of these proteins was further indirectly confirmed by complementation experiments in Escherichia coli where SUF proteins of M. exilis were able to restore at least partially Fe-S cluster assembly of strains deficient in the SUF and ISC pathways. We also proved by bacterial adenylate cyclase two-hybrid system that SufB and SufC can form...

The objective of the thesis is to describe and compare the modifying uses of two adjectives which can appear both as premodifiers as well as bare postmodifiers, namely available and responsible. Both modifying positions are examined with respect to the textual environment, the complexity of noun phrases and adjective phrases in which the adjectives function, reference and other features in order to outline the patterns in which these two adjectives appear. The data for the analytical part have been extracted from the British National Corpus using the basic query and limiting the search to the written part of the corpus. After manual assessment of the initial samples of 500 concordance lines, 154 concordance lines containing the adjective available and 147 containing the adjective responsible proved to be suitable for the analysis. The final samples of the data are further categorized and analysed concerning the complexity of the noun phrase, premodification, postmodification and complementation of the adjectives, semantic preference of the head nouns, and the motivation for the pre- or postnominal placement of the modifiers. Key words: adjective, adjective phrase, premodification, postmodification, complementation, attributive function, predicative function, postpositive function, bare adjective,...

The DNA damage response (DDR) pathway is a complicated network of interacting proteins that function to sense and remove DNA damage. Upon exposure to DNA damage, a signaling cascade is generated. The damage is either removed, restoring the original genetic sequence, or apoptosis is activated. In the absence of DDR, cells are unable to effectively process DNA damage. Unprocessed DNA damage can lead to chromosomal changes, gene mutations, and malignant transformation. Thus, the proteins involved in DDR are critical for maintaining genomic stability. One essential DDR protein is the BRCA1 Associated C-terminal Helicase, BACH1. BACH1 was initially identified through its direct association with the BRCT domain of the Breast Cancer Associated Gene, BRCA1. Similar to BRCA1, germline mutations in BACH1were identified in patients with early onset breast cancer. Interestingly, the disease-associated mutations in BACH1 were shown to have altered helicase activity in vitro, providing a direct link between BACH1 helicase activity and disease development. The correlation between BACH1 and cancer predisposition was further confirmed by the identification of BACH1 as the cancer syndrome Fanconi anemia (FA) gene product, FANCJ. Similar to other FA proteins, suppression of FANCJ leads to decreased homologous recombination, enhanced sensitivity to DNA interstrand crosslinking (ICL) agents, and chromosomal instability. In an effort to further understand the function of FANCJ in DDR, FANCJ was shown to directly associate with the mismatch repair (MMR) protein MLH1. This interaction is facilitated by lysines 141 and 142 within the helicase domain of FANCJ. Importantly, the FANCJ/MLH1 interaction is critical for ICL repair. Furthermore, in an attempt to dissect the binding site of FANCJ on MLH1, we discovered an HNPCC associated MLH1 mutation (L607H) that has intact mismatch repair, but lacks FANCJ interaction. In contrast to the MLH1 interaction, the FANCJ/BRCA1 interaction was not required for correcting the cellular defects in FANCJ null cells. Thus, in an effort to understand the functional significance of the FANCJ/BRCA1 interaction, we discovered that FANCJ promotes Pol η dependent translesion synthesis (TLS) bypass when uncoupled from BRCA1. In this thesis, we provide evidence suggesting that FANCJ and MLH1 are functionally linked and that the interaction of these proteins is critical for repair choice.

No description available.

RNA interference (RNAi) is a conserved mechanism in a wide range of eukaryotes. Introduction of synthetic dsRNA could specifically target suppression of a gene or could result in off-target silencing of another gene due to sequence similarity. To verify if the observed phenotype in an RNAi transgenic line is due to silencing of a specific gene or if it is due to another nontarget gene, a synthetic gene complementation approach could be used. Synthetic gene complementation described in this method uses the technology of synthesizing a variant of a native gene (used in RNAi silencing) to maximize the difference in DNA sequences while coding for the exact same amino acids as the original native gene. This is achieved through the use of alternate codons. The new variant gene is expressed in the original RNAi transgenic lines and analyzed for complementation of the RNAi phenotype. Complementation of the RNAi-induced phenotype will indicate gene-specific silencing and not off-target silencing.

Les récepteurs couplés aux protéines G (RCPGs) constituent la plus grande classe de récepteurs membranaires impliqués dans la transmission des signaux extracellulaires. Traditionnellement, la transmission de la signalisation par les RCPGs implique l’activation d’une protéine G hétéro-trimérique qui pourra à son tour moduler l’activité de divers effecteurs intracellulaires. Ce schéma classique de signalisation s’est complexifié au fils des années et l’on sait maintenant qu’en plus d’interagir avec les protéines G, les RCPGs s’associent avec une panoplie d’autres protéines afin de transmettre adéquatement les signaux extracellulaires. En particulier, la découverte d’une famille de protéines transmembranaires modulant la fonction des RCPGs, baptisées protéines modifiant l’activité des récepteurs (« receptor activity-modifying proteins » ; RAMPs), a changé la façon de concevoir la signalisation par certains RCPGs. Dans le cas du récepteur similaire au récepteur de la calcitonine (« calcitonin-like receptor » ; CLR), l’association avec les RAMPs permet l’acheminement à la surface cellulaire du récepteur tout en modulant ses propriétés pharmacologiques. Lorsqu’il est associé avec RAMP1, le CLR fonctionne comme un récepteur du peptide relié au gène de la calcitonine (« calcitonin gene-related peptide » ; CGRP), alors qu’il devient un récepteur de l’adrénomedulline lorsqu’il interagit avec RAMP2 ou RAMP3. D’autre part, en plus d’interagir avec des protéines accessoires transmembranaires telles les RAMPs, les RCPGs peuvent aussi s’associer entre eux pour former des oligomères de récepteurs. Dans cette thèse, nous nous sommes penchés sur les interactions entre les RCPGs et les RAMPs, et plus particulièrement sur l’interrelation entre ce type d’association RCPG/RAMP et l’assemblage en oligomères de récepteurs, en utilisant le récepteur du CGRP comme modèle d’étude. Une première étude nous a tout d’abord permis de confirmer l’interaction entre le récepteur CLR et RAMP1, dans un contexte de cellules vivantes. Nous avons démontré que ce complexe CLR/RAMP1 active la protéine G et recrute la protéine de signalisation -arrestine suite à une stimulation par le CGRP. Ensuite, nous avons déterminé que même s’il doit obligatoirement former un hétéro-oligomère avec les RAMPs pour être actif, le CLR conserve malgré tout sa capacité à interagir avec d’autres RCPGs. En plus d’observer la présence d’homo-oligomère de CLR, nous avons constaté que tout comme les RCPGs, les RAMPs peuvent eux-aussi s’associer entre eux pour former des complexes oligomériques pouvant comprendre différents sous-types (RAMP1/RAMP2 et RAMP1/RAMP3). Cette observation de la présence d’homo-oligomères de CLR et de RAMP1, nous a amené à nous questionner sur la stœchiométrie d’interaction du complexe CLR/RAMP1. Dans une deuxième étude ayant pour but d’établir la composition moléculaire du récepteur CGRP1 in vivo, nous avons développé une nouvelle approche permettant l’étude de l’interaction entre trois protéines dans un contexte de cellules vivantes. Cette technique baptisée BRET/BiFC, est basée sur le transfert d’énergie de résonance de bioluminescence entre un donneur luminescent, la Renilla luciférase, et un accepteur fluorescent, la protéine fluorescente jaune (YFP), reconstituée suite au ré-assemblage de ces deux fragments. En utilisant cette approche, nous avons pu déterminer que le récepteur CGRP1 est constitué d’un homo-oligomère de CLR interagissant avec un monomère de RAMP1. En démontrant un assemblage oligomérique asymétrique pour le récepteur CGRP1 à partir d’une nouvelle approche biophysique, nous croyons que les travaux présentés dans cette thèse ont contribué à élargir nos connaissances sur le fonctionnement de la grande famille des RCPGs, et seront utile à la poursuite des recherches sur les complexes protéiques impliqués dans la signalisation. / G protein coupled receptors (GPCRs) constitute the largest family of membrane receptors involved in signal transduction. Traditionally, signal transduction by GPCRs involves the activation of a hetero-trimeric G protein which will then modulate the activity of several intracellular effectors. We can now appreciate the fact that in addition to their interaction with G proteins, GPCRs also associate with several other proteins, in order to allow proper signal transduction. In particular, the discovery of a family of proteins called receptor activity-modifying proteins (RAMPs) has challenged the traditional views of signal transduction by some GPCRs. In the case of the calcitonin-like receptor (CLR), the association with RAMPs allows the proper cell surface targeting of the receptor in addition to modulate it’s pharmacological properties. Co-expression of CLR with RAMP1 leads to a calcitonin gene-related peptide (CGRP) receptor, whereas CLR association with RAMP2 or RAMP3 promotes the formation of an adrenomedullin receptor. In addition to their interaction with transmembrane accessory proteins such as RAMPs, GPCRs can also interact with other receptors to form receptors oligomers. In this thesis, we were interested in the interactions between GPCRs and RAMPs, and particularly, in the link between these GPCR/RAMP interactions and the assembly of receptor oligomers, using CGRP1 receptor as a model. We first confirmed the interaction between CLR and RAMP1 in living cells. We showed that this CLR/RAMP1 complex activates G proteins and recruits the signalling protein -arrestin upon CGRP stimulation. Next, we demonstrated that even if the CLR requires hetero-oligomeric assembly with RAMPs in order to be active, this receptor can still interact with other GPCRs. In addition to CLR homo-oligomers, we observed that RAMPs can also self-associate to form oligomeric complexes which can involve different subtypes (RAMP1/RAMP2 and RAMP1/RAMP3). This observation of the presence of CLR and RAMP1 homo-oligomers raised the question of the stoiechiometry of interaction of the CLR/RAMP1 complex. In order to establish the molecular composition of the CGRP1 receptor in vivo, we developed a novel approach allowing the detection of the interaction between three proteins in living cells. This method called BRET/BiFC is based on the bioluminescence resonance energy transfer between a luminescent energy donor, Renilla luciferase, and a fluorescent energy acceptor, the yellow fluorescent protein (YFP), reconstituted after the re-association of its two fragments. Using this approach, we showed that the CGRP1 receptor consist of a homo-oligomer of CLR interacting with a monomer of RAMP1. By demonstrating the asymmetrical organization of the CGRP1 receptor complex using a novel biophysical approach, we believe that the results presented herein have contributed to increase our knowledge of the mechanisms of function of the large family of GPCRs and will be useful for the pursuit of research on protein complexes involved in signalling pathways.

Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / Desde a redemocratização do país em 1985 o MRE já vinha se posicionando à favor do diálogo com os mais diversos grupos e entidades sociais. Neste sentido, observou-se ao longo dos últimos anos um aprofundamento da interação com parlamentares, governos estaduais e municipais, empresários, sindicalistas, ONGs e imprensa. A construção de vínculos entre as organizações da sociedade civil críticas das negociações comerciais ao longo da década de 1990 permite falar na criação de um novo campo de ação coletiva transnacional, definido como um espaço de ação política formado por indivíduos e organizações da sociedade civil que participam do processo de elaboração de um conjunto comum de práticas, objetivos e crenças. O que se pode concluir é que diante de um contexto mais competitivo e globalizado, após processo de abertura comercial e intensificação da participação brasileira nas negociações internacionais, a representação dos interesses da classe empresarial teve que se adaptar criando uma nova forma de organização. Desse modo, o presente trabalho visa analisar a crescente interferência de grupos de interesse no processo de tomada de decisão, no que tange aos assuntos de política externa comercial brasileira, tais como as negociações comerciais internacionais por se tratar de um ambiente cujos interesses da classe empresarial mais podem ser afetados. As negociações comerciais internacionais é o ambiente em que a atuação empresarial mais pode ser percebida. As negociações do Mercosul e da ALCA possibilitam observar a participação ativa destes novos atores. Sendo assim, o trabalho apresenta a nova dinâmica de relacionamento entre Estado e grupos da sociedade civil (classe empresarial) para temas ligados a comércio exterior. / Since the democratization of the country in 1985 the Ministry of Foreign Affairs was already positioning itself to promote a dialogue with the various groups and charities. In this sense, it was observed over the past year a further interaction with lawmakers, state and local governments, businessmen, trade unionists, NGOs and media. The building of links between civil society organizations critical of trade negotiations throughout the 1990s allows us to speak on creating a new field of transnational collective action, defined as a space for political action made up of individuals and civil society organizations that participate the process of developing a common set of practices, beliefs and goals. What can be concluded is that before a more competitive and globalized, after opening up of trade and intensification of the Brazilian participation in international negotiations, representing the interests of the business class had to adapt by creating a new form of organization. Thus, this study aims to examine the growing interference of interest groups in decision-making process, with respect to matters of Brazilian foreign trade policy, such as international trade negotiations because it is an environment whose interests the business class more may be affected. International trade negotiations are the environment in which business activity can be more noticeable. Negotiations of the Mercosur and the FTAA allow you to observe the active participation of new actors. Thus, the paper presents a new dynamic relationship between state and civil society groups (business class) for issues related to foreign trade.