Mechanisms of Transposable Element Repression by Piwi Proteins in the piRNA Pathway of Drosophila Germ Cells

The ability to reproduce is a defining characteristic of all living organisms. During reproduction, the integrity of genetic material transferred from one generation to the next is of utmost importance. Organisms have diverse strategies to ensure the fidelity of genomic information inherited between generations of individuals. In sexually reproducing animals, the piRNA pathway is an RNA-interference (RNAi) mechanism that protects the genomes of germ cells from the replication of ‘selfish’ genetic sequences called transposable elements (TE). When left unabated, the replication of TE sequences can cause gene disruption, double-stranded DNA breaks, and germ cell death that results in sterility of the organism. In Drosophila, the piRNA pathway is divided into a cytoplasmic and nuclear branch that involves the functions of three Piwi-clade Argonaute proteins—Piwi, Aubergine (Aub) and Argonaute-3 (Ago3)—which bind piwi-interacting RNA (piRNA) to form the effector complexes that represses deleterious TE sequences.

The work presented in this thesis examines the function and regulation of Piwi proteins in Drosophila germ cells. Chapter 1 presents an introduction to piRNA biogenesis and to the essential roles occupied by each Piwi protein in the repression of TE. We discuss the architecture and function of germ granules as the cellular compartments where much of the piRNA pathway operates. In Chapter 2, we present how Piwi in the nucleus co-transcriptionally targets genomic loci expressing TE sequences to direct the deposition of repressive chromatin marks. Chapter 3 examines the cytoplasmic function of the piRNA pathway, where we find that the protein Krimper coordinates Aub and Ago3 in the piRNA ping-pong pathway to adaptively target and destroy TE transcripts. Chapter 4 explores how interactions of Piwis with associated proteins are modulated by arginine methylation modifications. Lastly, in Chapter 5 I present evidence that the cytoplasmic branch of the piRNA pathway can potentially ‘cross-talk’ with the nuclear branch to transfer sequence information to better target and co-transcriptionally silence the genomic loci coding active TE sequences. Overall, the work presented in this thesis constitutes a part of the first steps in understanding the molecular mechanisms that protect germ cells from invasion by TE sequences.

O Protocolo de Kyoto e o mercado de crédito de carbono: estudo de caso das emissões de gases de efeito estufa da fábrica de combustível nuclear pertencente às Indústrias Nucleares do Brasil no ano de 2008

A presente dissertação discute as questões relacionadas à intensificação das mudanças climáticas por causas antrópicas conforme a evolução no uso dos recursos naturais, inovações nos processos produtivos, transformações econômicas, sociais, culturais, políticas e, especialmente ambientais. Aborda a comercialização dos créditos de carbono através de projetos de Mecanismo de Desenvolvimento Limpo (MDL), um dos mecanismos de flexibilização criados pelo Protocolo de Kyoto. No contexto de mudanças climáticas, uma matriz energética que utilize fontes de energia que não emitam gases causadores do efeito estufa (GEE) se mostra uma importante estratégia de desenvolvimento sustentável. Sob essa perspectiva, a energia nucleoelétrica é apresentada como uma alternativa viável aos combustíveis fósseis, considerando que esta é uma energia limpa e compatível com a perspectiva de desenvolvimento sustentável. A Fábrica de Combustível Nuclear (FCN), localizada em Resende (Rio de Janeiro), pertencente às Indústrias Nucleares do Brasil (INB), é um conjunto de sofisticadas fábricas nas quais se processam etapas importantes do ciclo do combustível nuclear. Na FCN, o Centro Zoobotânico realiza a gestão das atividades voltadas para a conservação da natureza tais como o Programa de Recuperação de Mata Ciliar, Reflorestamento e Fauna. O Relatório de inventário das emissões diretas e indiretas de GEE da FCN, elaborado pela INB para o ano de 2008, permite a auto-avaliação da empresa, retratando a preocupação corporativa com as questões relativas às mudanças climáticas. Segundo este Relatório, o total de emissões de GEE quantificado corresponde a 12,14% da capacidade total de sequestro de dióxido de carbono, no período de Janeiro a Dezembro de 2008. A proteção de florestas e a plantação de árvores são componentes essenciais de qualquer estratégia global para mitigação da mudança climática, e a participação da INB no mercado de crédito de carbono pode proporcionar externalidades positivas, tais como ganhos de imagem, adequação a padrões ambientais e melhoria do relacionamento com a sociedade.

Kinetics and mechanisms of adsorption of Escherichia coli bacteriophage T_4 to activated carbon

A study was conducted on the adsorption of Escherichia coli bacteriophage T₄ to activated carbon. Preliminary adsorption experiments were also made with poliovirus Type III. The effectiveness of such adsorbents as diatomaceous earth, Ottawa sand, and coconut charcoal was also tested for virus adsorption.

The kinetics of adsorption were studied in an agitated solution containing virus and carbon. The mechanism of attachment and site characteristics were investigated by varying pH and ionic strength and using site-blocking reagents.

Plaque assay procedures were developed for bacteriophage T₄ on Escherichia coli cells and poliovirus Type III on monkey kidney cells. Factors influencing the efficiency of plaque formation were investigated.

The kinetics of bacteriophage T₄ adsorption to activated carbon can be described by a reversible second-order equation. The reaction order was first order with respect to both virus and carbon concentration. This kinetic representation, however, is probably incorrect at optimum adsorption conditions, which occurred at a pH of 7.0 and ionic strength of 0.08. At optimum conditions the adsorption rate was satisfactorily described by a diffusion-limited process. Interpretation of adsorption data by a development of the diffusion equation for Langmuir adsorption yielded a diffusion coefficient of 12 X 10^-8 cm²/sec for bacteriophage T₄. This diffusion coefficient is in excellent agreement with the accepted value of 8 X 10^-8 cm²/sec. A diffusion-limited theory may also represent adsorption at conditions other than the maximal. A clear conclusion on the limiting process cannot be made.

Adsorption of bacteriophage T₄ to activated carbon obeys the Langmuir isotherm and is thermodynamically reversible. Thus virus is not inactivated by adsorption. Adsorption is unimolecular with very inefficient use of the available carbon surface area. The virus is probably completely excluded from pores due to its size.

Adsorption is of a physical nature and independent of temperature. Attraction is due to electrostatic forces between the virus and carbon. Effects of pH and ionic strength indicated that carboxyl groups, amino groups, and the virus's tail fibers are involved in the attachment of virus to carbon. The active sites on activated carbon for adsorption of bacteriophage T₄ are carboxyl groups. Adsorption can be completely blocked by esterifying these groups.

Simulations and mechanisms of subtropical low-cloud response to climate change

This thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change.

First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach. However, the cumulus response to climate warming subject to energetic constraints differs significantly from the conventional approach with fixed SST. Under the energetic constraint, the subtropics warm less than the tropics, since longwave (LW) cooling is more efficient with the drier subtropical free troposphere. The surface latent heat flux (LHF) also increases only weakly subject to the surface energetic constraint. Both factors contribute to an increased estimated inversion strength (EIS), and decreased inversion height. The decreased Cu-depth contributes to a decrease of liquid water path (LWP) and weak positive cloud feedback. The conventional fixed-SST approach instead simulates a strong increase in LHF and deepening of the Cu layer, leading to a weakly negative cloud feedback. This illustrates the importance of energetic constraints to the simulation and understanding of the sign and magnitude of low-cloud feedback.

Second, an extended eddy-diffusivity mass-flux (EDMF) closure for the unified representation of sub-grid scale (SGS) turbulence and convection processes in general circulation models (GCM) is presented. The inclusion of prognostic terms and the elimination of the infinitesimal updraft fraction assumption makes it more flexible for implementation in models across different scales. This framework can be consistently extended to formulate multiple updrafts and downdrafts, as well as variances and covariances. It has been verified with LES in different boundary layer regimes in the current climate, and further development and implementation of this closure may help to improve our simulation skills and understanding of low-cloud feedback through GCMs.

Observation and interpretation of tectonic strain release mechanisms

In four chapters various aspects of earthquake source are studied.

Chapter I

Surface displacements that followed the Parkfield, 1966, earthquakes were measured for two years with six small-scale geodetic networks straddling the fault trace. The logarithmic rate and the periodic nature of the creep displacement recorded on a strain meter made it possible to predict creep episodes on the San Andreas fault. Some individual earthquakes were related directly to surface displacement, while in general, slow creep and aftershock activity were found to occur independently. The Parkfield earthquake is interpreted as a buried dislocation.

Chapter II

The source parameters of earthquakes between magnitude 1 and 6 were studied using field observations, fault plane solutions, and surface wave and S-wave spectral analysis. The seismic moment, M_O, was found to be related to local magnitude, M_L, by log M_O = 1.7 M_L + 15.1. The source length vs magnitude relation for the San Andreas system found to be: M_L = 1.9 log L - 6.7. The surface wave envelope parameter AR gives the moment according to log M_O = log AR₃₀₀ + 30.1, and the stress drop, τ, was found to be related to the magnitude by τ = 0.54 M - 2.58. The relation between surface wave magnitude M_S and M_L is proposed to be M_S = 1.7 M_L - 4.1. It is proposed to estimate the relative stress level (and possibly the strength) of a source-region by the amplitude ratio of high-frequency to low-frequency waves. An apparent stress map for Southern California is presented.

Chapter III

Seismic triggering and seismic shaking are proposed as two closely related mechanisms of strain release which explain observations of the character of the P wave generated by the Alaskan earthquake of 1964, and distant fault slippage observed after the Borrego Mountain, California earthquake of 1968. The Alaska, 1964, earthquake is shown to be adequately described as a series of individual rupture events. The first of these events had a body wave magnitude of 6.6 and is considered to have initiated or triggered the whole sequence. The propagation velocity of the disturbance is estimated to be 3.5 km/sec. On the basis of circumstantial evidence it is proposed that the Borrego Mountain, 1968, earthquake caused release of tectonic strain along three active faults at distances of 45 to 75 km from the epicenter. It is suggested that this mechanism of strain release is best described as "seismic shaking."

Chapter IV

The changes of apparent stress with depth are studied in the South American deep seismic zone. For shallow earthquakes the apparent stress is 20 bars on the average, the same as for earthquakes in the Aleutians and on Oceanic Ridges. At depths between 50 and 150 km the apparent stresses are relatively high, approximately 380 bars, and around 600 km depth they are again near 20 bars. The seismic efficiency is estimated to be 0.1. This suggests that the true stress is obtained by multiplying the apparent stress by ten. The variation of apparent stress with depth is explained in terms of the hypothesis of ocean floor consumption.

On the economics of the "meeting competition defense" under the Robinson-Patman Act

Documento de trabajo

Mechanisms of E2F2-mediated transcriptional repression

In this work we wanted to study the mechanism of E2F2-mediated repression. Our hypothesis is that E2F2 activates the expression of one or more E2F members of the “repressor” subset of the family through the E2F motifs present in their promoters, and those repressor E2F(s) would subsequently repress the target promoters. To address this hypothesis, we focused on E2F7. E2F7 is a repressor that lacks the Rb binding domain, and associates with DNA through E2F binding sites (de Bruin et al., 2003). Furthermore, E2F7 itself is also regulated by E2F motifs on its own promoter, and it has been shown to repress DNA metabolism and replication genes in late S-phase (de Bruin et al., 2003; Westendorp et al., 2012). E2F7, together with E2F8 has been found to form heterodimers, being critical on cell proliferation and development, and both seem to have similar functions (Li et al., 2008). Preliminary results from Zubiaga’s group have indicated that E2F2 activates E2F7 transcription in U2OS cells, suggesting that E2F2’s repressor function could be mediated by E2F7. For this purpose, we focused on studying E2F7’s role on the target genes previously known to be repressed by E2F2: Chk1 and Mcm5. The specific aims for this work were the following: - Confirm that E2F2 induces E2F7 in HEK-293T cells - Assess whether E2F7 acts as a transcriptional repressor on E2F sites - Evaluate the role of E2F7 on E2F2-mediated transcriptional repression of Chk1 and Mcm5.

Part I. Coenzyme B12 as a hydroformylation-type catalyst. Part II. Mechanisms of hydrogen transfer in the methylmalonyl coenzyme a mutase reaction

Part I

The mechanism of the hydroformylation reaction was studied. Using cobalt deuterotetracarbonyl and 1-pentene as substrates, the first step in the reaction, addition of cobalt tetracarbonyl to an olefin, was shown to be reversible.

Part II

The role of coenzyme B₁₂ in the isomerization of methylmalonyl coenzyme A to succinyl coenzyme A by methylmalonyl coenzyme A mutase was studied. The reaction was allowed to proceed to partial completion using a mixture of methylmalonyl coenzyme A and 4, 4, 4-tri-²H-methylmalonyl coenzyme A as substrate. The deuterium distribution in the product, succinyl coenzyme A, was shown to best fit a model in which hydrogen is transferred from C-4 of methylmalonyl coenzyme A to C-5’ of the adenosyl moiety of coenzyme B₁₂ in the rate determining step. The three hydrogens at the 5’-adenosyl position of the coenzyme B₁₂ intermediate are then able to become enzymatically equivalent before hydrogen is transferred from the coenzyme B₁₂ intermediate to form succinyl coenzyme A.

Phytoplankton periodicity: its motivation, mechanisms and manipulation

This review summarizes some recent work to find a generalized explanation of phytoplankton periodicity in lakes. Much of the observational and experimental evidence is drawn from work centred on the large enclosures (Lund Tubes) installed in Blelham Tarn, English Lake District. Observations on the phytoplankton in the tubes are related to the periodic changes that occur in natural lakes and it is suggested that such changes have common patterns, that they are due to common causes, that they are affected by similar processes and that they are therefore predictable and, potentially, manipulable.

Control mechanisms in the human binocular oculomotor system

A study of human eye movements was made in order to elucidate the nature of the control mechanism in the binocular oculomotor system.

We first examined spontaneous eye movements during monocular and binocular fixation in order to determine the corrective roles of flicks and drifts. It was found that both types of motion correct fixational errors, although flicks are somewhat more active in this respect. Vergence error is a stimulus for correction by drifts but not by flicks, while binocular vertical discrepancy of the visual axes does not trigger corrective movements.

Second, we investigated the non-linearities of the oculomotor system by examining the eye movement responses to point targets moving in two dimensions in a subjectively unpredictable manner. Such motions consisted of hand-limited Gaussian random motion and also of the sum of several non-integrally related sinusoids. We found that there is no direct relationship between the phase and the gain of the oculomotor system. Delay of eye movements relative to target motion is determined by the necessity of generating a minimum afferent (input) signal at the retina in order to trigger corrective eye movements. The amplitude of the response is a function of the biological constraints of the efferent (output) portion of the system: for target motions of narrow bandwidth, the system responds preferentially to the highest frequency; for large bandwidth motions, the system distributes the available energy equally over all frequencies. Third, the power spectra of spontaneous eye movements were compared with the spectra of tracking eye movements for Gaussian random target motions of varying bandwidths. It was found that there is essentially no difference among the various curves. The oculomotor system tracks a target, not by increasing the mean rate of impulses along the motoneurons of the extra-ocular muscles, but rather by coordinating those spontaneous impulses which propagate along the motoneurons during stationary fixation. Thus, the system operates at full output at all times.

Fourth, we examined the relative magnitude and phase of motions of the left and the right visual axes during monocular and binocular viewing. We found that the two visual axes move vertically in perfect synchronization at all frequencies for any viewing condition. This is not true for horizontal motions: the amount of vergence noise is highest for stationary fixation and diminishes for tracking tasks as the bandwidth of the target motion increases. Furthermore, movements of the occluded eye are larger than those of the seeing eye in monocular viewing. This effect is more pronounced for horizontal motions, for stationary fixation, and for lower frequencies.

Finally, we have related our findings to previously known facts about the pertinent nerve pathways in order to postulate a model for the neurological binocular control of the visual axes.

The ecological impact of different mechanisms of chronic sub-lethal toxicity on feeding and respiratory physiology

Sub-lethal toxicity tests, such as the scope-for-growth test, reveal simple relationships between measures of contaminant concentration and effect on respiratory and feeding physiology. Simple models are presented to investigate the potential impact of different mechanisms of chronic sub-lethal toxicity on these physiological processes. Since environmental quality is variable, even in unimpacted environments, toxicants may have differentially greater impacts in poor compared to higher quality environments. The models illustrate the implications of different degrees and mechanisms of toxicity in response to variability in the quality of the feeding environment, and variability in standard metabolic rate. The models suggest that the relationships between measured degrees of toxic stress, and the maintenance ration required to maintain zero scope-for-growth, may be highly nonlinear. In addition it may be possible to define critical levels of sub-lethal toxic effect above which no environment is of sufficient quality to permit prolonged survival.

Propaganda de medicamentos. É possível regular ?

A regulação da propaganda de medicamentos no Brasil incorpora quatro fragilidades: 1. A monitoração, fiscalização e punição de irregularidades são realizadas a posteriori do acometimento da infração (quando a população já foi submetida a risco sanitário); 2. As multas cobradas pela Anvisa têm valor irrisório frente aos investimentos do marketing farmacêutico; 3. Não há mecanismo que impeça que mesmo os valores irrisórios das multas sejam repassados aos preços dos produtos, onerando o consumidor; 4. A frase tida como de alerta - A PERSISTIREM OS SINTOMAS O MÉDICO DEVERÁ SER CONSULTADO - ao invés de conscientizar a população a respeito dos riscos da automedicação, estimula o uso de medicamentos sem receita, aconselhando a busca de um médico apenas no caso da persistência dos sintomas. Segundo dados da Anvisa e de estudos acadêmicos, 90% da publicidade exibida contém irregularidades. Assim, a RDC 102/2000 da Anvisa, que regulamenta o setor, se constitui em um aparente sistema de regulação, que beneficia o infrator e mantém a população sob risco. Este trabalho analisa o conceito e o uso dos mecanismos de marketing na busca de se elevar a comercialização de produtos farmacêuticos (no que se denomina produção de doenças), examina os conceitos de propaganda, medicamento, regulação e manipulação; percorre alguns estatutos internacionais referentes ao setor da publicidade de medicamentos (com foco nas diretivas da União Européia) e expõe a avaliação de organismos europeus de defesa do consumidor sobre o desempenho destas normas. Ao final, este estudo expõe as posições do setor regulado brasileiro (indústria, agências de publicidade e meios de comunicação) frente às posições de órgãos de defesa dos consumidores, da academia e da sociedade organizada no âmbito do SUS, para propor como alternativa um modelo regulador que supere as fragilidades do atual.

Efeitos de diferentes dietas hiperlipídicas na via L-arginina-óxido nítrico e no stress oxidativo em eritrócitos de camundongos C57BL/6

Introdução: o óxido nítrico (NO) é um gás inorgânico com uma meia-vida curta e tem um papel crítico na manutenção da homeostase vascular e fluidez sanguínea. O NO é sintetizado a partir do aminoácido L-arginina por uma família de enzimas NO sintases (NOS). Estudos têm mostrado que eritrócitos expressam NOS endotelial (eNOS) funcional, que serve como uma fonte de NO intraluminal. Além disso, eritrócitos participam da defesa antioxidante removendo os radicais livres e prevenindo o dano oxidativo às membranas biológicas e a destruição do NO. Dietas hiperlípidicas estão associadas a um risco aumentado de doença cardiovacular e síndrome metabólica, mas os exatos mecanismos não estão completamente esclarecidos. O objetivo deste estudo foi investigar os efeitos de diferentes dietas hiperlípidicas na via L-arginina-NO e o estresse oxidativo em eritrócitos de camundongos. Metodologia: camundongos machos C57BL/6 de três meses de idade receberam diferentes dietas por 10 semanas: dieta normolipídica ou dieta hiperlipídica contendo banha de porco (HB), óleo de oliva (HO), óleo de girassol (HG) ou óleo de canola (HC). Foram analisados o transporte de L-arginina mediado pelos transportadores catiônicos y+ e y+L, a atividade da NOS, a expressão da eNOS e da NOS induzível (iNOS), a formação de substâncias reativas ao ácido tiobarbitúrico (TBARS) e a atividade das enzimas antioxidantes catalase (CAT) e superóxido dismutase (SOD). Resultados: o transporte total de L-arginina estava aumentado no grupo HO em comparação aos controles e aos outros grupos com dieta hiperlipídica. Quando o transporte foi fracionado, o sistema y+ estava mais ativado no grupo HO em relação aos controles e outros grupos que receberam dieta hiperlipídica. O transporte de L-arginina via sistema y+L estava maior nos grupos HO, HG e HC comparados aos grupos controle e HB. Adicionalmente, a atividade basal da NOS e a expressão de eNOS estavam aumentadas em eritrócitos independente do tipo de dieta hiperlípidica insaturada. Observou-se uma maior expressão da iNOS no grupo HO comparado ao controle. Em contraste, o grupo HB apresentou uma inibição da via L-arginina-NO. A análise da peroxidação lipídica, através da formação de TBARS, e da atividade da enzima antioxidante CAT não revelou diferenças entre os grupos, ao contrário do grupo HO, que induziu uma ativação de outra enzima antioxidante, a SOD. Conclusões: o presente estudo proporciona a primeira evidência de que os sistemas y+ e y+L regulam o transporte aumentado de L-arginina em eritrócitos de camundongos do grupo HO. Além disso, todas as dietas hiperlipídicas insaturadas induzem um aumento da atividade basal da NOS associada a uma expressão elevada da eNOS. É possível que diferentes mudanças na composição lipídica da membrana plasmática induzidas pelas dietas possam afetar transportadores e enzimas nos eritrócitos. Além disso, a inibição da via L-arginina-NO no grupo HB pode contribuir para o desenvolvimento da aterosclerose, enquanto dietas hiperlipídicas insaturadas podem ter um efeito protetor via aumento da geração de NO.