Mechanisms of Arsenic Detoxification and Resistance

Arsenic is a ubiquitous environmental toxic substance. As a consequence of continual exposure to arsenic, nearly every organism, from Escherichia coli to humans have evolved arsenic detoxification pathways. One of the pathways is extrusion of arsenic from inside the cells, thereby conferring resistance. The R773 arsRDABC operon in E. coli encodes an ArsAB efflux pump that confers resistance to arsenite. ArsA is the catalytic subunit of the pump, while ArsB forms the oxyanion conducting pathway. ArsD is an arsenite metallochaperone that binds arsenite and transfers it to ArsA. The interaction of ArsA and ArsD allows for resistance to As(III) at environmental concentrations. The interaction between ArsA ATPase and ArsD metallochaperone was examined. A quadruple mutant in the arsD gene encoding a K2A/K37A/K62A/K104A ArsD is unable to interact with ArsA. An error-prone mutagenesis approach was used to generate random mutations in the arsA gene that restored interaction with the quadruple arsD mutant in yeast two-hybrid assays. Three such mutants encoding Q56R, F120I and D137V ArsA were able to restore interaction with the quadruple ArsD mutant. Structural models generated by in silico docking suggest that an electrostatic interface favors reversible interaction between ArsA and ArsD. Mutations in ArsA that propagate changes in hydrogen bonding and salt bridges to the ArsA-ArsD interface also affect their interactions. The second objective was to examine the mechanism of arsenite resistance through methylation and subsequent volatilization. Microbial ArsM (As(III) S-adenosylmethyltransferase) catalyzes the formation of trimethylarsine as the volatile end product. The net result is loss of arsenic from cells. The gene for CrArsM from the eukaryotic green alga Chlamydomonas reinhardtii was chemically synthesized and expressed in E. coli. The purified protein catalyzed the methylation of arsenite into methyl-, dimethyl- and trimethyl products. Synthetic purified CrArsM was crystallized in an unliganded form. Biochemical and biophysical studies conducted on CrArsM sheds new light on the pathways of biomethylation. While in microbes ArsM detoxifies arsenic, the human homolog, hAS3MT, converts inorganic arsenic into more toxic and carcinogenic forms. An understanding of the enzymatic mechanism of ArsM will be critical in deciphering its parallel roles in arsenic detoxification and carcinogenesis.

O comportamento pró-social de crianças com sintomatologia do transtorno da conduta

Pro-social behaviors are seen regularly throughout our daily lives, as we often witness people giving alms, helping a neighbor move, donating blood, or taking care of a friend's children, among others. From an evolutionary perspective, such behaviors occur because they have a high adaptive value to our species, precisely due to our high degree of dependence on group living for survival. Probably, for this same reason, since children have shown a preference for prosocial behaviors over antisocial behaviors, this preference becomes more visible as we grow. However, children with symptoms of conduct disorder show a pattern of aggressive, impulsive and more selfish behaviors than children without such symptoms. Furthermore, these children also experience environments in which antisocial behaviors are more frequent and intense compared to the general population. Priming experiments are one way of measuring the influence of simple environmental cues on our behavior. For example, driving faster when listening to music, religious people help more on religious elements, like the bible, and children are more cooperative after playing games of an educational nature. Thus, the objectives of the current study were to: evaluate whether there is any difference in generosity, through sharing behavior, among children with and without symptoms of conduct disorder; analyze the influence of prosocial priming on sharing behavior on children with and without symptoms of conduct disorder; and finally, analyze from an evolutionary perspective, the reasons given by children with and without symptoms of conduct disorder for sharing or not sharing with their best friend in a classroom environment. To address this question, the teachers of these children were asked to respond to an inventory that was designed to signal the presence or absence of symptoms of conduct disorder. Children identified as having or not having symptoms of conduct disorder could then undergo an experimental (with priming) or control (no priming) condition. Under the experimental condition, the children were asked to watch two short videos showing scenes of helping and sharing among peers, to perform a distraction activity, and finally to chose two of four different materials presented by the researcher and decide how much of these two materials they would like to share with their best friend in the classroom. Then the children were asked about their reasons for sharing or not sharing. Children subjected to the control condition performed the same activities as in the xi experimental condition, but did not watch the video first. The results showed a notable difference in the effect of priming in accordance with the child's stage of development; a difference in the amount of material donated to a best friend by children with and without symptoms of conduct disorder, and a change in this observed difference with the influence of pro-social priming; and finally, a convergence in the thinking of children regarding their reasons for sharing with evolutionary theory. The results of this study also indicate the importance of individual factors, developmental stage, environmental and evolutionary conditions in the pro-social behavior of children with and without symptoms of conduct disorder.

Generosidade e cooperação de crianças monitoradas e não monitoradas: a interação entre a condição socioeconômica e o ambiente escolar

Studies have shown that a person's socioeconomic status (SES) and the environment in which they are inserted modulate their pro-sociality. While children studying in schools with a more affluent student body tend to be more generous, adults with high SES in both real and experimental situations tend to be more selfish, greedy and individualistic. Another factor that influences pro-sociality is monitoring. When we do something under the supervision of another person, we tend to be more generous and cooperative, compared to situations in which no one is watching, even if the "observer" is a drawing of eyes. This monitoring effect occurs in both adults and children. To date, no studies have investigated whether the SES and the environment influence the pro-sociality of the children. There have also been no studies on how the monitoring effect might be influenced by SES and the environment (in this case, whether the environment is a public or private school). Given this context, our main objective was to investigate whether the generosity and cooperation of monitored and unmonitored kids is modulated by these factors. To this end, we did eight matches of the public goods, under monitoring and control conditions, with 249 children from the ages of 7 to 10 years enrolled in public and private schools in Natal, state of Rio Grande do Norte (Brazil). The SES of each child's family was assessed according to the Economic Classification Criterion of Brazil (2013). Contrary to our predictions, SES, school environment and experimental conditions did not significantly influence cooperation and generosity behavior when analyzed separately. We discuss whether the influences of resource and experimental design adopted for the current study and the historical and economic conditions of Brazil might explain these observations. Interestingly, when SES and school environment were analyzed together, an effect of monitoring on generosity and cooperation was detected. More specifically, monitoring had the effect of decreasing generosity among children with greater SES in private schools; and increased cooperation among children with greater SES in public schools. These results suggest that there is an influence of monitoring on the pro-sociality of children in relation to their SES and acquaintanceship environments. We argue that these observations may be explained by different preoccupations with reputation, according to the environment in which a child is inserted.

Genetic and Molecular Basis of Encapsulation and Capsule Diversity in Kingella kingae

Kingella kingae is a bacterial pathogen that is increasingly recognized as an etiology of septic arthritis, osteomyelitis, bacteremia, and endocarditis in young children. The pathogenesis of K. kingae disease starts with bacterial adherence to the respiratory epithelium of the posterior pharynx. Previous work has identified type IV pili and a trimeric autotransporter protein called Knh (Kingella NhhA homolog) as critical factors for adherence to human epithelial cells. Additional studies established that the presence of a polysaccharide capsule interferes with Knh-mediated adherence. Given the inhibitory role of capsule during adherence we sought to uncover the genes involved in capsule expression to understand how capsule is elaborated on the cell surface. Additionally, this work aimed to further characterize capsule diversity among K. kingae clinical isolates and to investigate the relationship between capsule type and site of isolation.

We first set out to identify the carbohydrates present in the K. kingae capsule present in the prototype strain 269-492. Glycosyl composition and NMR analysis of surface extractable polysaccharides demonstrated two distinct polysaccharides, one consisting of GalNAc and Kdo with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and the other containing galactose alone with the structure →5)-β-Galf-(1→.

To discern the two polysaccharides we disrupted the ctrA gene required for surface localization of the K. kingae polysaccharide capsule and observed a loss of GalNAc and Kdo but no effect on the presence of Gal in bacterial surface extracts. In contrast, deletion of the pamABCDE locus involved in production of a reported galactan exopolysaccharide eliminated Gal but had no effect on the presence of GalNAc and Kdo in surface extracts. These results established that K. kingae strain KK01 produces a polysaccharide capsule with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and a separate exopolysaccharide with the structure →5)-β-Galf-(1→.

Having established that K. kingae produces a capsule comprised of GalNAc and Kdo, we next set out to identify the genetic determinants of capsule through a transposon mutagenesis screen. In addition to the previously identified ctrABCD operon, lipA, lipB, and a putative glycosyltransferase termed csaA (capsule synthesis region A gene A) were found to be essential for the production of surface-localized capsule. The ctr operon, lipA, lipB, and csaA were found to be present at unlinked locations throughout the genome, which is atypical for gram-negative organisms that elaborate a capsule dependent on an ABC-type transporter for surface localization. Through examining capsule localization in the ctrA, lipA, lipB, and csaA mutant strains, we determined that the ctrABCD, lipA/lipB, and csaA gene products respectively function in capsule export, assembly, and synthesis, respectively. The GalNAc transferase and Kdo transferase domains found in CsaA further support its role in catalyzing the synthesis of the GalNAc-Kdo capsule in the K. kingae prototype strain.

To investigate the capsule diversity that exists in K. kingae we screened a panel of strains isolated from patients with invasive disease or healthy carriers for the csaA capsule synthesis locus. We discovered that Kingella kingae expresses one of 4 capsule synthesis loci (csa, csb, csc, or csd) associated with a capsule consisting of Kdo and GalNAc (type a), Kdo and GlcNAc (type b), Kdo and ribose (type c), and GlcNAc and galactose (type d), respectively. Cloning of the csa, csb, csc, or csd locus into the empty flanking gene region in a non-encapsulated mutant (creation of an isogenic capsule swap) was sufficient to produce either the type a, type b, or type c capsule, respectively, further supporting the role of these loci in expression of a specific polysaccharide linkage. Capsule type a and capsule type b accounted for 96% of invasive strains. Conversely, capsule type c and capsule type d were found disproportionately among carrier isolates, suggesting that capsule type is important in promoting invasion and dissemination.

In conclusion, we discovered that Kingella kingae expresses a polysaccharide capsule and an exopolysaccharide on its surface that require distinct genetic loci for surface localization. Further investigation into genetic determinants of encapsulation revealed the loci ctrABCD, lipA/lipB, and a putative glycosyltransferase are required for capsule expression, with the gene products having roles in capsule export, assembly, and synthesis, respectively. The putative glycosyltransferase CsaA was determined to be a bifunctional enzyme with both GalNAc-transferase and Kdo-transferase activity. Furthermore, we discovered a total of 4 capsule types expressed in clinical isolates of K. kingae, each with a distinct capsule synthesis locus. The variation in the proportion of capsule types found between invasive strains and carriage strains suggest that capsule type is important in promoting invasion and dissemination. Taken together, this work expands our knowledge of the capsule types expressed among K. kingae carrier and invasive isolates and provides insights into the common genetic determinants of capsule expression. These contributions may lead to selecting clinically relevant capsule types to develop into a capsule based vaccine to prevent K. kingae colonization.

Genomics and virulence factors of Fusobacterium necrophorum

Fusobacterium necrophorum, a Gram negative, anaerobic bacterium, is a common cause of acute pharyngitis and tonsillitis and a rare cause of more severe infections of the head and neck. At the beginning of the project, there was no available genome sequence for F. necrophorum. The aim of this project was to sequence the F. necrophorum genome and identify and study its putative virulence factors contained using in silico and in vitro analysis. Type strains JCM 3718 and JCM 3724,F. necrophorum subspecies necrophorum (Fnn) and funduliforme (Fnf), respectively, and strain ARU 01 (Fnf), isolated from a patient with LS, were commercially sequenced by Roche 454 GS-FLX+ next generation sequencing and assembled into contigs using Roche GS Assembler. Sequence data was annotated semi-automatically, using the xBASE pipeline, BLASTp and Pfam. The F. necrophorum genome was determined to be approximately 2.1 – 2.3 Mb in size, with an estimated 1,950 ORFs and includes genes for a leukotoxin, ecotin, haemolysin, haemagglutinin, haemin receptor, adhesin and type Vb and Vc secretion systems. The prevalence of the leukotoxin gene was investigated in strains JCM 3718, JCM 3724 and ARU 01, as well as a clinical collection of 25 Fnf strains, identified using biochemical and molecular tests. The leukotoxin operon was found to be universal within the strain collection by PCR. HL-60 cells subjected to aliquots of concentrated high molecular weight culture supernatant, predicted to contain the secreted leukotoxins of strains JCM 3718, JCM 3724 and ARU 01, were killed in a dose-dependent manner. The cytotoxic effect of the leukotoxin against human donor white blood cells was also tested to validate the HL-60 assay. The differences in the results between the two assays were not statistically significant. Ecotin, a serine protease inhibitor, was found to be present in 100 % of the strain collection and had a highly conserved sequence with primary and secondary binding sites exposed on opposing sides of the protein. During enzyme inhibition studies, a purified recombinant F. necrophorum ecotin protein inhibited human neutrophil elastase, a protease that degrades bacteria at inflammation sites, and human plasma kallikrein, a component of the host clotting cascade. The recombinant ecotin also prolonged human plasma clotting times by up to 7-fold for the extrinsic pathway, and up to 40-fold for the intrinsic pathway. The genome sequence data provides important information about F. necrophorum type strains and enables comparative study between strains and subspecies. Results from the leukotoxin and ecotin assays can be used to build up an understanding of how the organism behaves during infection.

A Motivação do Envolvimento dos Bombeiros em Atividades de Voluntariado: um estudo de caso.

Este estudo teve como principal objetivo a análise dos fatores determinantes que levaram os bombeiros voluntários de uma corporação para a prática de voluntariado. Nesta investigação, começamos por fazer um enquadramento teórico sobre as perspetivas e tipos de motivação do voluntariado, focando-nos depois em alguns aspetos da sua prática em Portugal. A componente empírica deste estudo apoiou-se numa análise quantitativa a 92 questionários realizados a bombeiros voluntários, adaptados de um estudo realizado por Ward e Mckillop (2011) com uma escala do tipo Likert de 1 a 7 pontos. A análise da distribuição por sexo apontou uma proporção de homens superior à das mulheres (63 = 68,5% vs. 29 = 31,5%), com idades compreendidas entre os 17 e os 71 anos, sendo a média das mesmas de 37,77 anos (dp = ± 12,1). No que concerne ao estado civil, dos inquiridos (35 = 38%) são casados. Quanto à escolaridade, a moda estatística situou-se no secundário (52 = 56,5%). Os itens que compuseram a escala de motivação para o voluntariado apresentaram pontuações superiores a 4 pontos numa escala do tipo Likert de 7 pontos. A escala constituída por 17 itens relaciona os diferentes tipos de motivação, designadamente, social, interesse, prazer, material-egoísta, egoísta, altruísta, necessidade e dever moral. Estes itens foram avaliados nas seguintes variáveis: sexo, classe etária, escolaridade e antiguidade. As conclusões retiradas deste estudo revelaram, dominantemente, motivações do tipo altruísta e social, para a prática do voluntariado. Estes resultados basearam-se nos valores das significâncias estatísticas (p). Quanto à motivação dos elementos do sexo masculino e do sexo feminino, verificaram-se em ambas maiores percentagens no tipo de motivação altruísta. Na análise realizada consoante a classe etária, as respostas que obtiveram maior percentagem foram relativamente ao item altruísta. No que concerne à escolaridade, os inquiridos com ensino básico e secundário apresentaram um maior número de respostas nos itens altruísta e social. Nos licenciados o item com maior percentagem foi o dever moral. Na análise feita relativamente à interseção entre a motivação e os anos de voluntariado, obtiveram-se índices de motivação muito diferenciados, entre os quais interesse, prazer, social, egoísta, material-egoísta e necessidade. / This study aimed to the analysis of the determining factors that led the volunteer firefighters of a corporation to practice voluntary. In this investigation, we begin by making a theoretical framework on the perspectives and types of volunteer motivation, focusing us then in some aspects of their practice in Portugal. The empirical component of the study was supported on a quantitative analysis of 92 questionnaires by volunteer firefighters, adapted from a study by Ward & McKillop (2011) with a Likert scale from 1 to 7 points. The gender distribution, of the analysis indicated a ratio of greater than men to women (63 = 68.5% vs. 29 = 31.5%), aged between 17 and 71 years, and the average of 37 to 77 years (SD = ± 12.1). With regard to marital status (35 = 38%) are married. As for education, the statistical mode stood in the secondary on (52 = 56.5%). The items comprising the motivation scale for volunteering had scores greater than 4 points on a Likert scale of 7 points. The scale consists of 17 items lists the different types of motivation, namely social, interest, pleasure, material-selfish, selfish, selfless, necessity and moral duty. These items were evaluated in the following variables: gender, age group, education level and years of service. Conclusions from this study revealed mainly motivations of altruistic and social type for volunteering. These results were based on the values of statistical significance (p). Both male and female elements replied with the highest percentage for the type of altruistic motivation. In the analysis carried out according to age group, the answers with the greatest percentage were relative to the altruistic item. With regard to education respondents with elementary and high school education had a higher number of responses in altruistic and social items. At University graduate level the item with the highest percentage was the moral duty. In the analysis regarding the intersection between motivation and years of volunteering very different motivation indices were obtained including interest, pleasure, social, selfish, material-selfish and need.

Dialectique des regards - l’autre et la construction du récit de soi dans l’auto-filmage pathographique

Le présent mémoire entend analyser la pratique de l’auto-filmage dans deux films : La Pudeur ou l’impudeur (Hervé Guibert) et Tarnation (Jonathan Caouette). Nous regroupons ces long-métrages sous l’étiquette « auto-filmage pathographique ». Le malade, s’émancipant de l’imagerie médicale et des pratiques cinématographiques institutionnelles, reprend l’image filmique à son compte, aidé en cela par une technologie toujours plus ergonomique. Cette résurgence de l’image du corps malade dans le champ social ne se fait pas sans heurt ; l’exposition de corps décharnés et agoniques convoque un imaginaire catastrophiste et contredit les rituels d’effacement du corps auxquels procède la société occidentale. La forme que prend le récit de soi dans l’auto-filmage pathographique dépend de la maladie qui affecte chaque créateur. Nous observons une redéfinition de la sincérité, en lien avec l’exercice autobiographique. Il s’agit d’utiliser, dans l’auto-filmage pathographique, certains procédés fictionnels pour créer un discours sur soi-même dont la véracité repose sur d’autres critères que ceux communément admis. L’auto-filmage pathographique suppose en ce sens un véritable changement d’attitude et la mise en place de techniques de soi. Il induit une forme de réconciliation avec sa propre identité physique et psychique. En cela, l’écriture filmique de soi est un agent transformateur de la vie et un exercice spirituel. Les réalisateurs ne sont cependant pas uniquement tournés vers eux-mêmes. Chacun inclut quelques privilégiés au coeur de sa démarche. Le soin de soi, dans l’auto-filmage pathographique, ne se désolidarise pas du soin des autres. Auto-filmage et caméra subjective entretiennent un lien dialectique qui donne son sens à l’auto-filmage pathographique et voit leur antagonisme éclater. L’individu s’auto-filmant n’est pas seul ; sa démarche n’est pas qu’un solipsisme. Elle se voit dépassée par l’émergence de l’autre dans le champ ou parfois même, sa prise en main de la caméra.

FUNCTIONAL CHARACTERIZATION OF THE LINK BETWEEN CARBOHYDRATE METABOLISM AND THE PATHOGENESIS OF THE INVASIVE M1T1 GROUP A STREPTOCOCCUS

The Group A Streptococcus (GAS), or Streptococcus pyogenes, is a strict human pathogen that colonizes a variety of sites within the host. Infections can vary from minor and easily treatable, to life-threatening, invasive forms of disease. In order to adapt to niches, GAS utilizes environmental cues, such as carbohydrates, to coordinate the expression of virulence factors. Research efforts to date have focused on identifying how either components of the phosphoenolpyruvate-phosphotransferase system (PTS) or global transcriptional networks affect the regulation of virulence factors, but not the synergistic relationship between the two. The present study investigates the role of a putative PTS-fructose operon encoded by fruRBA and its role in virulence in the M1T1 strain 5448. Growth in fructose resulted in induction of fruRBA. RT-PCR showed that fruRBA formed an operon, which was repressed by FruR in the absence of fructose. Growth and carbon utilization profiles revealed that although the entire fruRBA operon was required for growth in fructose, FruA was the main fructose transporter. The ability of both ΔfruR and ΔfruB mutants to survive in whole human blood or neutrophils was impaired. However, the phenotypes were not reproduced in murine whole blood or in a mouse intraperitoneal infection, indicating a human-specific mechanism. While it is known that the PTS can affect activity of the Mga virulence regulator, further characterization of the mechanism by which sugars and its protein domains affect activity have not been studied. Transcriptional studies revealed that the core Mga regulon is activated more in a glucose-rich than a glucose-poor environment. This activation correlates with the differential phosphorylation of Mga at its PTS regulatory domains (PRDs). Using a 5448 mga mutant, transcriptome studies in THY or C media established that the Mga regulon reflects the media used. Interestingly, Mga regulates phage-encoded DNases in a low glucose environment. We also show that Mga activity is dependent on C-terminal amino acid interactions that aid in the formation of homodimers. Overall, the studies presented sought to define how external environmental cues, specifically carbohydrates, control complex regulatory networks used by GAS, contribute to pathogenesis, and aid in adaptation to various nutrient conditions encountered.

Identificação de genes em Chromobacterium violaceum relacionados à resposta ao estresse

The sequencing of the genome of Chromobacterium violaceum identified one single circular chromosome of 4.8 Mb, in which approximately 40% of the founded ORFs are classified as hypothetical conserved or hypothetical. Some genic regions of biotechnological and biological interest had been characterized, e. g., environmental detoxification and DNA repair genes, respectively. Given this fact, the aim of this work was to identify genes of C. violaceum related to stress response, as the ones involved with mechanisms of DNA repair and/or genomic integrity maintenance. For this, a genomic library of C. violaceum was built in Escherichia coli strain DH10B (RecA-), in which clones were tested to UVC resistance, resulting in five candidates clones. In the PLH6A clone were identified four ORFs (CV_3721 to 3724). Two ORFs, CV_3722 and CV_3724, were subcloned and a synergic complementation activity was observed. The occurrence of an operon was confirmed using cDNA from C. violaceum in a RT-PCR assay. Further, it was observed the induction of the operon after the treatment with UVC. Thus, this operon was related to the stress response in C. violaceum. The mutagenesis assay with rifampicin after the treatment with UVC light showed high frequency of mutagenicity for the ORF CV_3722 (Pol III δ subunit). In this way, we propose that the C. violaceum δ subunit can act in DH10B in the translesion synthesis using Pol IV in a RecA independent-manner pathway. In growth curve assays other four clones (PLE1G, PLE7B, PLE10B and PLE12H) were able to complement the function at the dose 5 J/m2 and in mutagenicity assays PLE7B, PLE10B and PLE12H showed frequencies of mutation with significant differences upon the control (DH10B), demonstrating that in some way they are involved with the stress response in C. violaceum. These clones appear to be interrelated, probably regulated by a messenger molecule (eg., nucleotide c-di-GMP) and/or global regulatory molecule (eg., σS subunit of RNA polymerase).The results obtained contribute for a better genetic knowledge of this specie and its response mechanisms to environmental stress.

Proteômica diferencial da Chromobacterium violaceum em resposta ao estresse oxidativo induzido por peróxido de hidrogênio

The β-proteobacterium Chromobacterium violaceum is a Gram-negative, free-living, saprophytic and opportunistic pathogen that inhabits tropical and subtropical ecosystems among them, in soil and water of the Amazon. It has great biotechnological potential, and because of this potential, its genome was completely sequenced in 2003. Genome analysis showed that this bacterium has several genes with functions related to the ability to survive under different kinds of environmental stresses. In order to understand the physiological response of C. violaceum under oxidative stress, we applied the tool of shotgun proteomics. Thus, colonies of C. violaceum ATCC 12472 were grown in the presence and absence of 8 mM H2O2 for two hours, total proteins were extracted from bacteria, subjected to SDS-PAGE, stained and hydrolysed. The tryptic peptides generated were subjected to a linear-liquid chromatography (LC) followed by mass spectrometer (LTQ-XL-Orbitrap) to obtain quantitative and qualitative data. A shotgun proteomics allows to compare directly in complex samples, differential expression of proteins and found that in C. Violaceum, 131 proteins are expressed exclusively in the control condition, 177 proteins began to be expressed under oxidative stress and 1175 proteins have expression in both conditions. The results showed that, under the condition of oxidative stress, this bacterium changes its metabolism by increasing the expression of proteins capable of combating oxidative stress and decreasing the expression of proteins related processes bacterial growth and catabolism (transcription, translation, carbon metabolism and fatty acids). A tool with of proteomics as an approach of integrative biology provided an overview of the metabolic pathways involved in the response of C. violaceum to oxidative stress, as well as significantly amplified understanding physiological response to environmental stress. Biochemical and "in silico" assays with the hypothetical ORF CV_0868 found that this is part of an operon. Phylogenetic analysis of superoxide dismutase, protein belonging to the operon also showed that the gene is duplicated in genome of C. violaceum and the second copy was acquired through a horizontal transfer event. Possibly, not only the SOD gene but also all genes comprising this operon were obtained in the same manner. It was concluded that C. violaceum has complex, efficient and versatile mechanisms in oxidative stress response

Os efeitos das perceções de instrumentalização da avaliação de desempenho nas respostas face à organização

Doutoramento em Gestão

Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions

Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.

Trajectory Privacy Preservation in Mobile Wireless Sensor Networks

In recent years, there has been an enormous growth of location-aware devices, such as GPS embedded cell phones, mobile sensors and radio-frequency identification tags. The age of combining sensing, processing and communication in one device, gives rise to a vast number of applications leading to endless possibilities and a realization of mobile Wireless Sensor Network (mWSN) applications. As computing, sensing and communication become more ubiquitous, trajectory privacy becomes a critical piece of information and an important factor for commercial success. While on the move, sensor nodes continuously transmit data streams of sensed values and spatiotemporal information, known as ``trajectory information". If adversaries can intercept this information, they can monitor the trajectory path and capture the location of the source node. This research stems from the recognition that the wide applicability of mWSNs will remain elusive unless a trajectory privacy preservation mechanism is developed. The outcome seeks to lay a firm foundation in the field of trajectory privacy preservation in mWSNs against external and internal trajectory privacy attacks. First, to prevent external attacks, we particularly investigated a context-based trajectory privacy-aware routing protocol to prevent the eavesdropping attack. Traditional shortest-path oriented routing algorithms give adversaries the possibility to locate the target node in a certain area. We designed the novel privacy-aware routing phase and utilized the trajectory dissimilarity between mobile nodes to mislead adversaries about the location where the message started its journey. Second, to detect internal attacks, we developed a software-based attestation solution to detect compromised nodes. We created the dynamic attestation node chain among neighboring nodes to examine the memory checksum of suspicious nodes. The computation time for memory traversal had been improved compared to the previous work. Finally, we revisited the trust issue in trajectory privacy preservation mechanism designs. We used Bayesian game theory to model and analyze cooperative, selfish and malicious nodes' behaviors in trajectory privacy preservation activities.

VanB-type Enterococcus faecium clinical isolate successively inducibly resistant to, dependent on, and constitutively resistant to vancomycin

Three Enterococcus faecium strains isolated successively from the same patient, vancomycin-resistant strain BM4659, vancomycin-dependent strain BM4660, and vancomycin-revertant strain BM4661, were indistinguishable by pulsed-field gel electrophoresis and harbored plasmid pIP846, which confers VanB-type resistance. The vancomycin dependence of strain BM4660 was due to mutation P(175)L, which suppressed the activity of the host Ddl D-Ala:D-Ala ligase. Reversion to resistance in strain BM4661 was due to a G-to-C transversion in the transcription terminator of the vanRS(B) operon that lowered the free energy of pairing from -13.08 to -6.65 kcal/mol, leading to low-level constitutive expression of the resistance genes from the P(RB) promoter, as indicated by analysis of peptidoglycan precursors and of VanX(B) D,D-dipeptidase activity. Transcription of the resistance genes, studied by Northern hybridization and reverse transcription, initiated from the P(YB) resistance promoter, was inducible in strains BM4659 and BM4660, whereas it started from the P(RB) regulatory promoter in strain BM4661, where it was superinducible. Strain BM4661 provides the first example of reversion to vancomycin resistance of a VanB-type dependent strain not due to a compensatory mutation in the ddl or vanS(B) gene. Instead, a mutation in the transcription terminator of the regulatory genes resulted in transcriptional readthrough of the resistance genes from the P(RB) promoter in the absence of vancomycin.

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10-5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.