Transformation of Medicago truncatula with the arginine decarboxylase gene to modify polyamine metabolism toward water deficit resistance

Dissertation submitted to obtain a Ph.D. (Doutoramento) degree in Biology at the Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa

Towards modification of Medicago truncatula epigenome: genome editing with engineered nucleases

Periodic drought is the primary limitation of plant growth and crop yield. The rise of water demand caused by the increase in world population and climate change, leads to one of the biggest challenges of modern agriculture: to increase food and feed production. De novo DNA methylation is a process regulated by small interfering RNA (siRNAs), which play a role in plant response and adaptation to abiotic stress. In the particular case of water deficit, growing evidences suggest a link between the siRNA pathways and drought response in the model legume Medicago truncatula. As a first step to understand the role of DNA methylation under water stress, we have set up several bioinformatics and molecular methodologies allowing the design of Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems and the assembly of TALENs (transcription activator-like effector nucleases), to target both dicer-like 3 (MtDCL3) and RNA-Dependent RNA polymerase (MtRDR2), enzymes of the RNA-directed DNA methylation pathway. TALENs efficiency was evaluated prior to plant transformation by a yeast-based assay using two different strategies to test TALENs activity: Polyacrylamide gel electrophoresis (PAGE) and Single strand conformation polymorphisms (SSCP). In this assay, yeast cells triple transformation emerged as good and rapid alternative to laborious yeast mating strategies. PAGE analysis might be a valuable tool to test TALENs efficacy in vivo if we could increase TALENs activity. SSCP-based approach proved to be ineffective due to the generation of several false positives. TALENs and CRISPR/Cas9 system constructed and designed in this work will in the future certainly enable the successful disruption of DCL3 and RDR2 genes and shed the light on the relationship between plant stress resistance and epigenetic regulation mediated by siRNAs in M.truncatula.

Heavy-metal resistance in Marinobacter aquaeolei 617 insights into copper resistance

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Biotecnologia

Ecophysiology of Ruditapes decussatus

The physiological responses of the clam R. decussatus from the Ria Formosa, southern Portugal, were examined in relation to normoxia, hypoxia (11, 6, 3 and 1.2 kPa) and anoxia; acute elevation of temperature (at 20, 27 and 32 °C), and its effect on the resistance to air exposure (at 20, 28 and 35 °C); current velocity (0.6, 3, 8 17, 24 and 36 cm. s-1) and turbidity (10, 100 and 300 mg. l-1 dry weight of particulate matter), and the efficiency of this species in retaining particles of different size (at 10 and 100 mg. l-1); and to copper contamination considering both short-term acute exposure to high levels (0.1-10 mg Cu. l-1) and chronic environmental levels (0.01 mg Cu. l-1). Clearance rates, respiration rates, absorption efficiency and excretion rates were assessed through the physiological energetics in terms of the energy budget and scope for growth (SFG). Stress independent respiration rates (R) and clearance rates (CR) were observed in relation to hypoxia down to 12 kPa and 6 kPa, respectively. Anoxic rates were 3.6 % of normoxic rates. Scope for growth was greatly reduced under extreme hypoxia (14 % of SFG in normoxia). Respiration rate was temperature independent in the range 20-32 °C but the decline in clearance rate resulted in negative SFG at 32 °C. Gaping during air exposure and the maintenance of faster aerobic metabolism led to 100 % mortality in 20 hours at 35 °C, 4 days at 28 °C and 5 days at 20 °C. Low current velocities (≤ 8 cm. s-1) supported high clearance rates. Shear stresses ≥ 0.9 Pa induced sediment movement and disturbed the feeding processes resulting in decreased clearance rates (at 36 cm. s-1, is 10 % of maximum CR). The observed ability of jetting out depleted water at a different level than the one of the inhalant current results is an important adaptation of clams to the slow currents of sheltered environments. Ingestion at high seston concentrations (> 100 mg. l-1) is controled by reducing the amount filtered, lowering CR (to 30 % of CR at low seston loads) and producing pseudofeces. Observed efficient retention of particles (70-100 %) in the range 3 to 8 μm is beneficial when algal cells are diluted by fine silt particles as it is likely to occur in the clams natural environment. R. decussatus in the short term escaped the exposure to copper by valve closure and therefore acute tests are not applicable to adult clams of this species. At environmental levels chronic exposure to copper did not induce lethal effects during the exposure period (20 days), but scope for growth was reduced to c. 30 %, indicating sustained impairment of physiological functions. The sensitivity of the physiological energetics and the integrated scope for growth measurement in assessing stress effects caused by natural environmental factors was highlighted.

The influence of geometric factors on the wall shear stress distribution in realistic human coronary arteries

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Biomédica. A presente dissertação foi desenvolvida no Erasmus Medical Center em Roterdão, Holanda

Contributo para o estudo da influência do stress na resposta imunitária à vacina contra a gripe em profissionais de saúde

Resumo: Os profissionais de saúde podem estar expostos a vários factores indutores de stress crónico nomeadamente de natureza profissional destacando-se, entre os seus possíveis efeitos, a diminuição da resposta de anticorpos após administração de vacinas, entre as quais, a vacina contra a gripe. Uma vez que os trabalhadores da saúde estão expostos a factores indutores de stress e, simultaneamente, a agentes biológicos cujos efeitos poderão ser prevenidos pela vacinação, é pertinente estudar a influência do stress na resposta imunitária à vacina contra a gripe em enfermeiros. Constituíram objectivos deste trabalho: (1) estudar a associação entre a presença de stress crónico em enfermeiros hospitalares e a “insuficiente” resposta imunitária à vacina contra a gripe, avaliada um mês após a vacinação (T1); (2) estudar a associação entre a presença de stress crónico em enfermeiros hospitalares e a redução dos títulos de anticorpos dirigidos às hemaglutininas seis meses após a vacinação (T6) e (3) identificar algumas características das unidades de internamento e do trabalho dos participantes que possam estar associadas à presença de stress crónico e estudar a sua possível associação com a resposta imunitária à vacina contra a gripe. Realizou-se um estudo caso-controlo incorporado num estudo de coortes e a amostra em estudo foi constituída por 136 enfermeiros saudáveis (83,8% sexo feminino; média de idades de 33anos) de um hospital universitário. Realizaram-se entrevistas individuais e aplicaram-se as versões portuguesas dos questionários The General Health Questionnaire (GHQ12) e Maslach Burnout Inventory – Human Services Survey (MBI-HSS) para determinação da presença de stress crónico pelo método da triangulação, no início do estudo (T0) e realizou-se a recolha de dados relativos à caracterização de elementos de trabalho nas unidades de internamento. Foi administrada a vacina contra a gripe e determinou-se os títulos de anticorpos dirigidos às hemaglutininas de cada estirpe componentes da vacina contra a gripe utilizada em 2007, antes da vacinação, um mês e seis meses após a vacinação. Não se encontrou associação, ao nível de significância de 5%, entre a presença de stress e a “insuficiente” resposta à vacina contra a gripe, avaliada pela taxa de indivíduos que apresentaram um aumento, ao fim de um mês, inferior a quatro vezes os títulos de anticorpos antes da vacinação. No entanto, encontrou-se uma maior proporção de indivíduos com stress no grupo de participantes em que ocorreu uma diminuição do título de anticorpos dirigidos à hemaglutinina AH1 (ac AH1) em T6, quando comparado com o respectivo grupo controlo. A diferença entre grupos foi estatisticamente significativa, quando se avaliou a presença de stress pelo método da triangulação usando a entrevista (p=0,006), pelo método da triangulação usando o GHQ12 (p=0,045) e ainda usando a combinação dos três critérios (p=0,001). Após análise multivariada, verificou-se que a associação entre a presença de XXVI stress e a redução dos ac AH1 em T6 manteve significado estatístico (respectivamente, p= 0,010, p= 0,042 e p=0,002) e apresentou odds ratio ajustados, em função de cada um dos métodos de avaliação da presença de stress, de 3,643, de 2,733 e de 5,223. A quantidade de trabalho percepcionada como sobrecarga constituiu o factor indutor de stress mais vezes referido (58,8% da amostra e 61,8% dos enfermeiros de unidades de internamento), seguida dos conflitos entre profissionais. O contacto com o sofrimento e a morte de doentes foram identificados em quarto lugar pela amostra, mas em segundo pelos enfermeiros de unidades de internamento. Nesses, verificou-se uma associação positiva entre trabalhar em Serviços onde o número de doentes falecidos foi muito elevado e a presença de stress, medido pelo método da triangulação usando a entrevista (p=0,039), usando o GHQ12 (p=0,019), usando a escala de exaustão emocional do MBI-HSS (p=0,012) e pela combinação dos três métodos (p=0,014). Verificou-se também uma associação positiva entre a presença de stress, identificada pelo método da triangulação usando a escala de exaustão emocional do MBI-HSS, e o trabalho em serviços de internamento onde a percentagem de doentes idosos (p=0,025) e a taxa de letalidade (p=0,036) foram elevadas. Contudo, não se encontrou associação entre a exposição muito frequente ao sofrimento e à morte de doentes e a redução do título de ac AH1 em T6. Possivelmente, a exposição a esse factor indutor de stress, apesar de estar relacionada com a presença de stress nos enfermeiros de serviços de internamento, não foi suficientemente intenso para, por si só, estar associada à redução do título de ac AH1 em T6. A associação encontrada entre a presença de stress crónico e a redução do título de anticorpos AH1 em T6 vem apoiar a resposta à questão de investigação inicialmente colocada de que o stress poderá influenciar negativamente a manutenção dos títulos de anticorpos, mesmo em indivíduos adultos não idosos. Assim, o risco de um enfermeiro com stress apresentar redução do título de anticorpos dirigidos à hemaglutinina da estirpe AH1N1 – A/Solomon Islands/3/2006 ao fim dos seis meses do estudo, foi 3,6, 2,7 ou 5,2 vezes superior ao de um enfermeiro sem stress, consoante o critério de stress ter sido determinado, respectivamente, pelo método da triangulação usando a entrevista, pelo método da triangulação utilizando o GHQ12 ou pela combinação dos três critérios. Summary: Health workers may be exposed to various factors causing chronic stress namely those related directly to their activity, in particular the decrease in the capacity of the response of antibodies after the administration of the vaccines, amongst others the Influenza vaccine. Since health workers are exposed to factors causing stress and at the same time biological agents, whose effects may be prevented through vaccination, it is important to study the influence of stress in the immunity response to the Influenza vaccine on nurses. The aims of this study are: (1) to examine the relation between chronic stress in hospital nurses and the “insufficient” immunity response to the Influenza vaccine, assessed at one month after vaccination (T1); (2) to examine the relation between chronic stress in hospital nurses and the decrease of the hemagglutinin titles of antibodies six months after vaccination (T6); (3) to identify some characteristics of internment units and the work of the participants that may be related to the presence of chronic stress and to study its possible relation with the immunity response to the Influenza vaccine. A control-case study, integrated in a coortes study, was carried out and the sample under analysis consisted of 136 healthy nurses (83,8% female; average age 33 years old) from a university hospital. Several individual interviews were conducted and the portuguese versions of General Health Questionnaire (GHQ12) and Maslach Burnout Inventory – Human Services Survey (MBI-HSS) was applied in order to determine the presence of chronic stress, using the triangulation method at the beginning of the study (T0). Data concerning the particular features of the internment units was collected. The Influenza vaccine was administered and the titles of hemagglutinin antibodies of each strain composing the Influenza vaccine used in 2007, before vaccination, and a month and six months after vaccination, were determined. There was no statistically relevant (5%) relation between stress and the “insufficient” immune response to the Influenza vaccine, according to the rate of individuals that showed, after a month, a level of antibodies concentration lower than four times the level prior to the vaccination. Nevertheless, there was a greater number of individuals with stress in the group of participants in which there was a decrease of the hemagglutinin titles of antibodies AH1 (ac AH1) in T6, when compared to the control group under study. The difference between groups was statistically relevant when assessing the presence of stress by triangulation method using the interview (p=0,006), by triangulation method using the GHQ12 (p=0,045) and by the combination of the three criteria (p=0,001). After multivariate analysis, it was verified that the XXVIII relation between the presence of stress and the reduction of the ac AH1 in T6 was statistically relevant (respectively, p= 0,010, p= 0,042 and p=0,002) and the odds ratio were, according to each of the methods used to assess the presence of stress, 3,643, 2,733 and 5,223. Overwork was the most emphasised stress-causing factor (58,8% of the sample and 61,8% of the nurses working in the Internment Units), followed by conflicts arousing among co-workers. Witnessing the suffering and death of patients was ranked as the fourth cause of stress, but the second by the nurses of the internment units. The former revealed a positive connection between working in the services, where there was a high rate of deaths, and the presence of stress, when assessing the presence of stress by triangulation method using the interview (p=0,039), the GHQ12 (p=0,019), the MBI-HSS emotional exhaustion scale (p=0,012) and by the combination of the three criteria (p=0,014).There was also a connection between the presence of stress, identified by the method of triangulation using the MBI-HSS emotional exhaustion scale, and working in the internment units, where the percentage of elderly people (p=0,025) and the mortality rate (p=0,036) were high. However, there was no connection between frequent exposure to suffering and death in patients and the reduction of ac AH1 titles, in T6. Although one can establish a connection between stress in nurses working in the internment units and the aforementioned stress-causing factor, the exposure to that factor was not, per se, intense enough to reduce the ac AH1 title in T6. The relation found between the presence of chronic stress and the reduction of AH1 antibodies titles in T6, corroborates the hypothesis that stress can negatively influence the title of antibodies, even in non-elderly adults. Thus, and according to the criteria used to define stress, by the triangulation method using the interview, by the triangulation method using the GHQ12 or the combination of the three criteria respectively, the risk of a nurse suffering from stress showing a reduction in the title of hemagglutinin antibodies for the strain AH1N1 – A/Solomon Islands/3/2006 six-month after Influenza vaccine was 3,6, 2,7 or 5,2 times greater than on a nurse suffering from no stress at all. Résumé: Les professionnels de la santé peuvent être exposés à différents facteurs inducteurs de stress chronique de nature professionnelle. On remarque, parmi les effets possibles, une baisse de la réponse des anticorps après l´administration de vaccins, comme en particulier, le vaccin de la grippe. Lorsque les professionnels de la santé ont été exposés à des facteurs inducteurs de stress, et de manière simultanée, à des agents biologiques dont les effets pourront être prévenus par la vaccination, il est pertinent d´étudier l´influence du stress dans la réponse immunitaire au vaccin de la grippe chez les infirmiers. Ils ont constitué des objectifs d´études et de discussion : (1) étudier l´association entre la présence de stress chronique chez les infirmiers, en milieu hospitalier, et la “insuffisant” réponse immunitaire au vaccin de la grippe, vérifiée à un mois après la vaccination (T1); (2) étudier l´association entre la présence de stress chronique chez les infirmiers, en milieu hospitalier, et la réduction de la teneur des anticorps dirigé à la hémaglutinina six mois après la vaccination (T6) (3) identifier certaines caractéristiques des unités d´internement, et étudier les aspects du travail des participants, qui puissent être associée à la présence de stress chronique et étudier sa possible association avec la réponse immunitaire au vaccin de la grippe. Une étude cas-contrôle incorporée dans une étude de groupe a été réalisée et un échantillon, pour étude, a été constitué par 136 infirmiers sains (83,8% de sexe féminin, âge moyen 33 ans) travaillant dans un hôpital universitaire. Des entretiens individuels ont été réalisés et les versions portugaises des questionnaires de General Health Questionnaire (GHQ12) et Maslach Burnout Inventory- Human Service Survey (MBI-HSS) ont été utilisés pour déterminer la présence de stress chronique grâce à la méthode de triangulation, au début de l´étude (T0) et un relevé de données relatives à la caractérisation d´éléments de travail dans les unités d´internement a été fait. Le vaccin de la grippe a été administré et les teneurs en anticorps dirigés aux hémaglutininas de chaque composant du vaccin de la grippe pour 2007 ont été déterminés, avant la vaccination et un mois et six mois après. On n´a pas trouvé d´association, à un niveau significatif de au moins 5%, entre la présence de stress et la “insuffisant” réponse au vaccin de la grippe, évaluée par le taux d´individus qui ont présenté une augmentation, à la fin du mois, inférieur à quatre fois la teneur des anticorps par rapport à avant la vaccination. Cependant , on a trouvé une plus grande proportion d´individus victimes de stress dans le groupe des participants où il y a eu une baisse de la teneur des anticorps dirigé à la hémaglutinina AH1 (ac AH1) en T6, après comparaison avec le respectif groupe de contrôle. La différence entre les groupes a été statistiquement significative lorsqu´on a vérifié la présence de stress grâce à la méthode de triangulation, en utilisant l´entretien (p=0,006), par la méthode de triangulation en utilisant le GHQ12 (p=0,045) et en utilisant aussi la combinaison des trois critères (p=0,001). Après une analyse XXX multivariée, on a vérifié que l´association entre la présence de stress et la réduction des ac AH1 en T6 a conservé un signifié statistique (respectivement, p=0,010, p=0,042 et p=0,002) et a présenté des odds ratio ajustés, en fonction de chacune des méthodes de vérification de la présence de stress de 3,643, de 2,733 et de 5,223. La quantité de travail perçue comme une surcharge constitue le facteur inducteur de stress le plus souvent cité (58,8% de l´échantillon et 61,8% des infirmiers des unités d´internement), suivi par les conflits entre professionnels. Le contact avec la souffrance et la mort des patients a été placé en quatrième position par l´échantillon, mais en deuxième position par les infirmiers des unités d´internement. Dans ces cas, on a vérifié une association évidente entre le fait de travailler dans des services où le nombre de patients décédés a été très élevé et la présence de stress, identifiée par la méthode de triangulation, en utilisant l´entretien (p=0,039), le GHQ12 (p=0,019), l´échelle de fatigue émotionnelle du MBI-HSS (p=0,012) et en utilisant aussi la combinaison des trois critères (p=0,014). On a aussi vérifié une association positive entre la présence de stress, identifiée par la méthode de triangulation, en utilisant l´échelle de fatigue émotionnelle du MBI-HSS et le travail dans des services d´internement où le pourcentage de malade âgés (p=0,025) et le taux de mortalité ont été élevés (p=0,036). Malgré tout, on n´a pas trouvé d´association entre l´exposition très fréquente à la souffrance et à la mort des patients et la réduction de la teneur de ac AH1 en T6. Probablement l´exposition à ce facteur inducteur de stress, bien qu´elle soit liée à la présence de stress chez les infirmiers des services d´internement, n´a pas été suffisamment intense pour, en elle-même, être associée à la réduction de la teneur ac AH1 enT6. L´association trouvée entre la présence de stress chronique et la réduction de la teneur des anticorps AH1 en T6 vient renforcer l´hypothèse que le stress pourra influencer négativement la manutention des teneurs en anticorps même chez les individus adultes jeunes. Donc le risque qu´un infirmier stressé présente une réduction de la teneur en anticorps dirigés à la hémaglutinina de le composant AH1N1-A/Solomon Island/3/2006 à la fin des six mois d´études a été 3,6, 2,7 ou 5,2 fois supérieure à celui d´un infirmier sans stress, après avoir déterminé le critère de stress, respectivement par la méthode de triangulation utilisant l´entretien, par la méthode de triangulation utilisant le GHQ12 ou par la combinaison des trois critères.

Deciphering the role of Yap4 phosphorylation under stress conditions

The existence of molecular mechanisms of response, repair and adaptation, many of which are greatly conserved across nature, gives to the cell with the plasticity it requires to adjust to its ever-changing environment, a homeostatic event that is termed the stress response. In the budding yeast Saccharomyces cerevisiae there is a particular family of transcription factors, the Yap family, which has been shown to have a relevant role in yeast adaptation to several stress conditions. In particular, Yap1 is the major regulator of the transcriptional response to oxidative stress and Yap2 and Yap8 play important roles upon cadmium and arsenic exposure, respectively.(...)

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

Estrogen receptor dependent genetic and epigenetic factors of tamoxifen resistance

Resumo: A decisão da terapêutica hormonal no tratamento do cancro da mama baseiase na determinação do receptor de estrogénio alfa por imunohistoquímica (IHC). Contudo, a presença deste receptor não prediz a resposta em todas as situações, em parte devido a limitações do método IHC. Investigámos se a expressão dos genes ESR1 e ESR2, bem como a metilação dos respectivos promotores, pode estar relacionada com a evolução desfavorável de uma proporção de doentes tratados com tamoxifeno assim como com a perda dos receptores de estrogénio alfa (ERα) e beta (ERß). Amostras de 211 doentes com cancro da mama diagnosticado entre 1988 e 2004, fixadas em formalina e preservadas em parafina, foram utilizadas para a determinação por IHC da presença dos receptores ERα e ERß. O mRNA total do gene ESR1 e os níveis específicos do transcrito derivado do promotor C (ESR1_C), bem como dos transcritos ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 foram avaliados por Real-time PCR. Os promotores A e C do gene ESR1 e os promotores 0K e 0N do gene ESR2 foram investigados por análise de metilação dos dinucleotidos CpG usando bisulfite-PCR para análise com enzimas de restrição, ou para methylation specific PCR. Atendendo aos resultados promissores relacionados com a metilação do promotor do gene ESR1, complementamos o estudo com um método quantitativo por matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) suportado pelo software Epityper para a medição da metilação nos promotores A e C. Fez-se a avaliação da estabilidade do mRNA nas linhas celulares de cancro da mama MCF-7 e MDA-MB-231 tratadas com actinomicina D. Baixos níveis do transcrito ESR1_C associaram-se a uma melhor sobrevivência global (p = 0.017). Níveis elevados do transcrito ESR1_C associaram-se a uma resposta inferior ao tamoxifeno (HR = 2.48; CI 95% 1.24-4.99), um efeito mais pronunciado em doentes com tumores de fenótipo ERα/PgR duplamente positivo (HR = 3.41; CI 95% 1.45-8.04). A isoforma ESR1_C mostrou ter uma semi-vida prolongada, bem como uma estrutura secundária da região 5’UTR muito mais relaxada em comparação com a isoforma ESR1_A. A análise por Western-blot mostrou que ao nível da 21 proteína, a selectividade de promotores é indistinguivel. Não se detectou qualquer correlação entre os níveis das isoformas do gene ESR2 ou entre a metilação dos promotores do gene ESR2, e a detecção da proteína ERß. A metilação do promotor C do gene ESR1, e não do promotor A, foi responsável pela perda do receptor ERα. Estes resultados sugerem que os níveis do transcrito ESR1_C sejam usados como um novo potencial marcador para o prognóstico e predição de resposta ao tratamento com tamoxifeno em doentes com cancro da mama. Abstract: The decision of endocrine breast cancer treatment relies on ERα IHC-based assessment. However, ER positivity does not predict response in all cases in part due to IHC methodological limitations. We investigated whether ESR1 and ESR2 gene expression and respective promoter methylation may be related to non-favorable outcome of a proportion of tamoxifen treated patients as well as to ERα and ERß loss. Formalin-fixed paraffin-embedded breast cancer samples from 211 patients diagnosed between 1988 and 2004 were submitted to IHC-based ERα and ERß protein determination. ESR1 whole mRNA and promoter C specific transcript levels, as well as ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 transcripts were assessed by real-time PCR. ESR1 promoters A and C, and ESR2 promoters 0N and 0K were investigated by CpG methylation analysis using bisulfite-PCR for restriction analysis, or methylation specific PCR. Due to the promising results related to ESR1 promoter methylation, we have used a quantification method by matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS) together with Epityper software to measure methylation at promoters A and C. mRNA stability was assessed in actinomycin D treated MCF-7 and MDA-MB-231 cells. ERα protein was quantified using transiently transfected breast cancer cells. Low ESR1_C transcript levels were associated with better overall survival (p = 0.017). High levels of ESR1_C transcript were associated with non-favorable response in tamoxifen treated patients (HR = 2.48; CI 95% 1.24-4.99), an effect that was more pronounced in patients with ERα/PgR double-positive tumors (HR = 3.41; CI 95% 1.45-8.04). The ESR1_C isoform had a prolonged mRNA half-life and a more relaxed 5’UTR structure compared to ESR1_A isoform. Western-blot analysis showed that at protein level, the promoter selectivity is undistinguishable. There was no correlation between levels of ESR2 isoforms or ESR2 promoter methylation and ERß protein staining. ESR1 promoter C CpG methylation and not promoter A was responsible for ERα loss. We propose ESR1_C levels as a putative novel marker for breast cancer prognosis and prediction of tamoxifen response.

Studies on the genetics of artemisinin resistance in malaria

A existência de estirpes de Plasmodium falciparum resistentes a multiplos fármacos é um dos problemas mais graves no controlo da malária. Novos fármacos, como a artemisinina (ART) e seus derivados são cada vez mais utilizados no tratamento da malaria e muito embora até ao momento não haja registos de fármaco-resistência estável à ART o seu surgimento seria desastroso devido á falta de alternativas. A investigação apresentada nesta tese descreve a selecção de resistência estável à ART e ao artesunato (ATN) utilizando um modelo roedor de malária, o parasita Plasmodium chabaudi chabaudi (Plasmodium chabaudi). Dois clones de Plasmodium chabaudi diferentes, AS-15CQ e AS-30CQ, foram inoculados em murganhos que por sua vez foram tratados na presença de concentrações sucessivamente crescentes de ATN e ART, sendo que no final do processo de seleção de resistência, os parasitas obtidos apresentavam uma resistência de 6 e 15 vezes superior ao ATN e à ART, respectivamente, em relação aos parasitas iniciais. Os clones obtidos foram nomeados respectivamente AS-ATN (obtido a partir de AS-15CQ por seleção com pressão de ATN) e AS-ART (obtido a partir de AS-30CQ por seleção com pressão de ART). A resistência obtida durante o processo de seleção é estável após clonagem, congelamento/descongelamento, passagem sanguínea na ausência de pressão de fármaco e transmissão natural através do mosquito vector. A sequência nucleotídica e o número de cópias dos genes previamente descritos na literatura como moduladores putativos de resistência à ART e seus derivados: mdr1, cg10, tctp e atp6; foi comparada entre parasitas resistentes e sensíveis, não tendo sido encontradas nenhumas alterações, quer na sequência quer no número de cópias destes genes. Posteriormente, numa tentativa de identificar os genes envolvidos na resistância à ART e ao ATN a técnica de Linkage Group Selection (LGS) foi utilizada. Para tal dois cruzamentos genéticos foram realizados. Estes cruzamentos foram realizados entre os clones fármaco-resistentes; AS-ART e AS-ATN e um clone geneticamente distinto dos anteriores e sensível aos fármacos em estudos, AJ. Após realização do LGS quatro loci genéticos; nos cromossomas de P. chabaudi 1, 2, 6 e 8 foram encontrados associados à resistência. Atendendo a que, a selecção no cromossoma 2 era a mais forte, este locus foi submetido a subsequentes análises genéticas, tendo sido encontradas duas mutações diferentes (V739F e V770F) num gene que codifica para um enzima de desubiquitinação (gene ubp-1).

Flow resistance in open-channel flows with mobile hydraulically rough beds

River Flow 2008, Vol.1

Studies on the genetics of artemisinin resistance in malaria

A existência de estirpes de Plasmodium falciparum resistentes a multiplos fármacos é um dos problemas mais graves no controlo da malária. Novos fármacos, como a artemisinina (ART) e seus derivados são cada vez mais utilizados no tratamento da malaria e muito embora até ao momento não haja registos de fármaco-resistência estável à ART o seu surgimento seria desastroso devido á falta de alternativas. A investigação apresentada nesta tese descreve a selecção de resistência estável à ART e ao artesunato (ATN) utilizando um modelo roedor de malária, o parasita Plasmodium chabaudi chabaudi (Plasmodium chabaudi). Dois clones de Plasmodium chabaudi diferentes, AS-15CQ e AS-30CQ, foram inoculados em murganhos que por sua vez foram tratados na presença de concentrações sucessivamente crescentes de ATN e ART, sendo que no final do processo de seleção de resistência, os parasitas obtidos apresentavam uma resistência de 6 e 15 vezes superior ao ATN e à ART, respectivamente, em relação aos parasitas iniciais. Os clones obtidos foram nomeados respectivamente AS-ATN (obtido a partir de AS-15CQ por seleção com pressão de ATN) e AS-ART (obtido a partir de AS-30CQ por seleção com pressão de ART). A resistência obtida durante o processo de seleção é estável após clonagem, congelamento/descongelamento, passagem sanguínea na ausência de pressão de fármaco e transmissão natural através do mosquito vector. A sequência nucleotídica e o número de cópias dos genes previamente descritos na literatura como moduladores putativos de resistência à ART e seus derivados: mdr1, cg10, tctp e atp6; foi comparada entre parasitas resistentes e sensíveis, não tendo sido encontradas nenhumas alterações, quer na sequência quer no número de cópias destes genes. Posteriormente, numa tentativa de identificar os genes envolvidos na resistância à ART e ao ATN a técnica de Linkage Group Selection (LGS) foi utilizada. Para tal dois cruzamentos genéticos foram realizados. Estes cruzamentos foram realizados entre os clones fármaco-resistentes; AS-ART e AS-ATN e um clone geneticamente distinto dos anteriores e sensível aos fármacos em estudos, AJ. Após realização do LGS quatro loci genéticos; nos cromossomas de P. chabaudi 1, 2, 6 e 8 foram encontrados associados à resistência. Atendendo a que, a selecção no cromossoma 2 era a mais forte, este locus foi submetido a subsequentes análises genéticas, tendo sido encontradas duas mutações diferentes (V739F e V770F) num gene que codifica para um enzima de desubiquitinação (gene ubp-1).

Studies on resistance and response to vancomycin in Enterococcus faecalis: a last resort antibiotic

Dissertation presented to obtain a Ph.D. degree in Biochemistry by Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa.

Positive Epistasis Drives the Acquisition of Multidrug Resistance

The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact-epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment the cost of multiple resistance is smaller than expected, a signature of pervasive positive epistasis among alleles that confer resistance to antibiotics. Competition assays reveal that the cost of resistance to a given antibiotic is dependent on the presence of resistance alleles for other antibiotics. Surprisingly we find that a significant fraction of resistant mutations can be beneficial in certain resistant genetic backgrounds, that some double resistances entail no measurable cost, and that some allelic combinations are hotspots for rapid compensation. These results provide additional insight as to why multi-resistant bacteria are so prevalent and reveal an extra layer of complexity on epistatic patterns previously unrecognized, since it is hidden in genome-wide studies of genetic interactions using gene knockouts.

Enterococcus and biocides: mechanisms of tolerance and selection for vancomycin resistance

Dissertation presented to obtain a Doctoral degree in Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.