Bouyid v Belgium: The “minimum level of severity” and Human Dignity's Role in Article 3 ECHR

The Grand Chamber of the European Court of Human Rights recently delivered an important judgment on Article 3 ECHR in the case of Bouyid v Belgium. In Bouyid, the Grand Chamber was called upon to consider whether slaps inflicted on a minor and an adult in police custody were in breach of Article 3 ECHR, which provides that ‘No one shall be subjected to torture or to inhuman or degrading treatment or punishment’. Overruling the Chamber judgment in the case, the Grand Chamber ruled by 14 votes to 3 that there had been a substantive violation of Article 3 in that the applicants had been subjected to degrading treatment by members of the Belgian police; it found that there had been a breach of the investigative duty under Article 3 also. In this comment, I focus on the fundamental basis of disagreement between the majority of the Grand Chamber and those who found themselves in dissent, on the question of whether there had been a substantive breach of Article 3. The crux of the disagreement lay in the understanding and application of the test of ‘minimum level of severity’, which the ECtHR has established as decisive of whether a particular form of ill-treatment crosses the Article 3 threshold, seen also in light of Article 3’s absolute character, which makes it non-displaceable – that is, immune to trade-offs of the type applicable in relation to qualified rights such as privacy and freedom of expression. I consider the way the majority of the Grand Chamber unpacked and applied the concept of dignity – or ‘human dignity’ – towards finding a substantive breach of Article 3, and briefly distil some of the principles underpinning the understanding of human dignity emerging in the Court’s analysis.

Molecular reconstruction of a genetic code alteration

The genetic code establishes the rules that govern gene translation into proteins. It was established more than 3.5 billion years ago and it is one of the most conserved features of life. Despite this, several alterations to the standard genetic code have been discovered in both prokaryotes and eukaryotes, namely in the fungal CTG clade where a unique seryl transfer RNA (tRNACAG Ser) decodes leucine CUG codons as serine. This tRNACAG Ser appeared 272±25 million years ago through insertion of an adenosine in the middle position of the anticodon of a tRNACGA Ser gene, which changed its anticodon from 5´-CGA-3´ to 5´-CAG-3´. This most dramatic genetic event restructured the proteome of the CTG clade species, but it is not yet clear how and why such deleterious genetic event was selected and became fixed in those fungal genomes. In this study we have attempted to shed new light on the evolution of this fungal genetic code alteration by reconstructing its evolutionary pathway in vivo in the yeast Saccharomyces cerevisiae. For this, we have expressed wild type and mutant versions of the C. albicans tRNACGA Ser gene into S. cerevisiae and evaluated the impact of the mutant tRNACGA Ser on fitness, tRNA stability, translation efficiency and aminoacylation kinetics. Our data demonstrate that these mutants are expressed and misincorporate Ser at CUGs, but their expression is repressed through an unknown molecular mechanism. We further demonstrate, using in vivo forced evolution methodologies, that the tRNACAG Ser can be easily inactivated through natural mutations that prevent its recognition by the seryl-tRNA synthetase. The overall data show that repression of expression of the mistranslating tRNACAG Ser played a critical role on the evolution of CUG reassignment from Leu to Ser. In order to better understand the evolution of natural genetic code alterations, we have also engineered partial reassignment of various codons in yeast. The data confirmed that genetic code ambiguity affects fitness, induces protein aggregation, interferes with the cell cycle and results in nuclear and morphologic alterations, genome instability and gene expression deregulation. Interestingly, it also generates phenotypic variability and phenotypes that confer growth advantages in certain environmental conditions. This study provides strong evidence for direct and critical roles of the environment on the evolution of genetic code alterations.

Identification of molecules and pathways regulating mistranslation in Candida albicans

Candida albicans is the major fungal pathogen in humans, causing diseases ranging from mild skin infections to severe systemic infections in immunocompromised individuals. The pathogenic nature of this organism is mostly due to its capacity to proliferate in numerous body sites and to its ability to adapt to drastic changes in the environment. Candida albicans exhibit a unique translational system, decoding the leucine-CUG codon ambiguously as leucine (3% of codons) and serine (97%) using a hybrid serine tRNA (tRNACAGSer). This tRNACAGSer is aminoacylated by two aminoacyl tRNA synthetases (aaRSs): leucyl-tRNA synthetase (LeuRS) and seryl-tRNA synthetase (SerRS). Previous studies showed that exposure of C. albicans to macrophages, oxidative, pH stress and antifungals increases Leu misincorporation levels from 3% to 15%, suggesting that C. albicans has the ability to regulate mistranslation levels in response to host defenses, antifungals and environmental stresses. Therefore, the hypothesis tested in this work is that Leu and Ser misincorporation at CUG codons is dependent upon competition between the LeuRS and SerRS for the tRNACAGSer. To test this hypothesis, levels of the SerRS and LeuRS were indirectly quantified under different physiological conditions, using a fluorescent reporter system that measures the activity of the respective promoters. Results suggest that an increase in Leu misincorporation at CUG codons is associated with an increase in LeuRS expression, with levels of SerRS being maintained. In the second part of the work, the objective was to identify putative regulators of SerRS and LeuRS expression. To accomplish this goal, C. albicans strains from a transcription factor knock-out collection were transformed with the fluorescent reporter system and expression of both aaRSs was quantified. Alterations in the LeuRS/SerRS expression of mutant strains compared to wild type strain allowed the identification of 5 transcription factors as possible regulators of expression of LeuRS and SerRS: ASH1, HAP2, HAP3, RTG3 and STB5. Globally, this work provides the first step to elucidate the molecular mechanism of regulation of mistranslation in C. albicans.

Intimate Ecologies: An exploration of the languages of contemporary exhibitions and making in museums and related cultural spaces in the UK

Intimate Ecologies considers the practice of exhibition-making over the past decade in formal museum and gallery spaces and its relationship to creating a concept of craft in contemporary Britain. Different forms of expression found in traditions of still life painting, film and moving image, poetic text and performance are examined to highlight the complex layers of language at play in exhibitions and within a concept of craft. The thesis presents arguments for understanding the value of embodied material knowledge to aesthetic experience in exhibitions, across a spectrum of human expression. These are supported by reference to exhibition case studies, critical and theoretical works from fields including social anthropology, architecture, art and design history and literary criticism and a range of individual, original works of art. Intimate Ecologies concludes that the museum exhibition, as a creative medium for understanding objects, becomes enriched by close study of material practice, and embodied knowledge that draws on a concept of craft. In turn a concept of craft is refreshed by the makers’ participation in shifting patterns of exhibition-making in cultural spaces that allow the layers of language embedded in complex objects to be experienced from different perspectives. Both art-making and the experience of objects are intimate, and infinitely varied: a vibrant ecology of exhibition-making gives space to this diversity.

Molecular structure and functional analysis of runx3 in zebrafish

Tese de doutoramento, Ciências Biomédicas, Universidade do Algarve, Departamento de Ciências Biomédicas e Medicina, 2014

Identification and molecular characterization of bone-related micrornas: functional implications

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2014

Identification of the cellular and molecular mechanism by which CD2AP, a regulator of neuronal intracellular transport contributes to the development of Alzheimer’s disease

Tese de mestrado. Biologia (Biologia Molecular e Genética). Universidade de Lisboa, Faculdade de Ciências,2014

Variation in protein expression levels in cell populations

Dissertation presented to obtain the Ph.D degree in Systems Biology

Of Structural Denial: A Narratological Study of the Structural Disintegration of the Novel Form

If an opening to the argument of this dissertation is of imperative necessity, one might tentatively begin with Herbert Quain, born in Roscommon, Ireland, author of the novels The God of the Labyrinth (1933) and April March (1936), the short-story collection Statements (1939), and the play The Secret Mirror (undated). To a certain extent, this idiosyncratic Irish author, who hailed from the ancient province of Connacht, may be regarded as a forerunner of the type of novels which will be considered in this dissertation. Quain was, after all, the unconscious creator of one of the first structurally disintegrated novels in the history of western literature, April March. His first novel, The God of the Labyrinth, also exhibits elements which are characteristic of structurally disintegrated fiction, for it provides the reader with two possible solutions to a mysterious crime. As a matter of fact, one might suggest that Quain’s debut novel offers the reader the possibility to ignore the solution to the crime and carry on living his or her readerly life, turning a blind eye to the novel itself. It may hence be argued that Quain’s first novel is in fact a compound of three different novels. It is self-evident that the structure of Quain’s oeuvre is of an experimental nature, combining geometrical precision with authorial innovation, and one finds in it a higher consideration for formal defiance than for the text itself. In other words, the means of expression are the concern of the author and not, interestingly, the textual content. April March, for example, is a novel which regresses back into itself, its first chapter focussing on an evening which is preceded by three possible evenings which, in turn, are each preceded by three other, dissimilar, possible evenings. It is a novel of backward-movement, and it is due to this process of branching regression that April March contains within itself at least nine possible novels. Structure, therefore, paradoxically controls the text, for it allows the text to expand or contract under its formal limitations. In other words, the formal aspects of the novel, usually associated with the restrictive device of a superior design, contribute to a liberation of the novel’s discourse. It is paradoxical only in the sense that the idea of structure necessarily entails the fixation of a narrative skeleton that determines how plot and discourse interact, something which Quain flouts for the purposes of innovation. In this sense, April March’s convoluted structure allows for multiple readings and interpretations of the same text, consciously germinating narratives within itself, producing different texts from a single, unique source. Thus, text and means of expression are bonded by a structural design that, rather than limiting, liberates the text of the novel.

Directed integration of new insulated lentiviral vectors to heterochromatin towards safer gene transfer to stem cells

The need for better gene transfer systems towards improved risk=benefit balance for patients remains a major challenge in the clinical translation of gene therapy (GT). We have investigated the improvement of integrating vectors safety in combining (i) new short synthetic genetic insulator elements (GIE) and (ii) directing genetic integration to heterochromatin. We have designed SIN-insulated retrovectors with two candidate GIEs and could identify a specific combination of insulator 2 repeats which translates into best functional activity, high titers and boundary effect in both gammaretro (p20) and lentivectors (DCaro4) (see Duros et al, abstract ibid). Since GIEs are believed to shield the transgenic cassette from inhibitory effects and silencing, DCaro4 has been further tested with chimeric HIV-1 derived integrases which comprise C-ter chromodomains targeting heterochromatin through either histone H3 (ML6chimera) or methylatedCpGislands (ML10). With DCaro4 only and both chimeras, a homogeneous expression is evidenced in over 20% of the cells which is sustained over time. With control lentivectors, less than 2% of cells express GFP as compared to background using a control double-mutant in both catalytic and ledgf binding-sites; in addition, a two-times increase of expression can be induced with histone deacetylase inhibitors. Our approach could significantly reduce integration into open chromatin sensitive sites in stem cells at the time of transduction, a feature which might significantly decrease subsequent genotoxicity, according to X-SCIDs patients data.Work performed with the support of EC-DG research within the FP6-Network of Excellence, CLINIGENE: LSHB-CT-2006-018933

Transfection of newt blastema mesenchyme using the techniques of lipofection and direct gene transfer

The regenerating amphibian limb provides a useful system for studying genes involved in the establishment of positional information. While a number of candidate genes that may playa role in pattern formation have been identified, their function in vivo is unknown in this system. To better ascertain the role of these genes, it would be useful to be able to alter their normal patterns of expression in vivo and to assess the effects of this misexpression on limb pattern. In order to achieve this, a method of introducing a plasmid containing the eDNA of a gene of interest into a newt blastema (a growth zone of mesenchymal progenitor cells) is needed. Unfortunately, most commonly used transfection techniques cannot be used with newt blastema cells. In this study, I have used the techniques of lipofection and direct gene transfer to introduce plasmid DNA containing reporter genes into the cells of a regenerating newt limb. The technique of lipofection was most effective when the blastema cells were transfected in vitro. The optimal ratio for transfection was shown to be 1:3 DNA:Lipofectin (W/w) , and an increase in the amount of DNA present in the mixture (1:3 ratio maintained) resulted in a corresponding increase in gene expression. The technique of direct gene transfer was used to transfect newt blastema cells with and without prior complex formation with Lipofectin. Injection of plasmid DNA alone provided the most 3 promising results. It was possible to introduce plasmid DNA containing the reporter gene ~-galactosidase and achieve significant gene expression in cells associated with the injection site. In the future, it would be interesting to use this technique to inject plasmid DNA containing a gene which may have a role in pattern formation into specific areas of the newt blastema and to analyze the resulting limb pattern that emerges.

The role of microRNAs and retinoid signaling during spinal cord regeneration in the adult newt.

The molecular events after spinal cord injury that lead to the establishment of a permissive environment and epimorphic regeneration remain unclear. Two molecular pathway regulators that may converge to create a spinal cord regeneration-permissive environment in the urodele are retinoic acid (RA) and microRNAs (miRNAs). Recent evidence suggests that RARβ-mediated signaling is necessary for tail and caudal spinal cord regeneration in the adult newt. MicroRNAs are attractive candidates as mediators of retinoid signaling during regeneration, as their pleiotropic effects are vital in situations where global changes in gene expression are required. Thus, the overall aim of this thesis was to determine if miRNAs are involved in tail and caudal spinal cord regeneration in the adult newt, and if they act as regulators and/or effectors of retinoid signaling during this process. I have demonstrated here, for the first time, that multiple miRNAs are dysregulated in response to spinal cord injury in the adult newt, as well as in response to inhibition of retinoid signaling. Two of these miRNAs, miR-133a and miR-1, appear to target RARβ2 transcripts both in vivo and in vitro. Inhibition of RA signaling via RARβ with a selective antagonist, LE135, alters the pattern of expression of these miRNAs, which leads to an inhibition of tail regeneration. These data are indicative of a negative feed back loop, albeit potentially an indirect one. I also aimed to examine which miRNAs are affected by inhibiting RA synthesis during regeneration, and provided a long list of miRNAs that are dysregulated. These data provide the foundation for future studies on the putative roles of these miRNAs, as well as their function in retinoid signaling. Overall, these studies provide the first evidence for a role for miRNAs as mediators of retinoid signaling during caudal spinal cord regeneration in any system.

The cumate gene-switch: a system for regulated expression in mammalian cells

Affiliation: Sophie Broussau, Amelie Pilotte & Bernard Massie : Départment de microbiologie et immunologie, Faculté de médecine, Université de Montréal

From Sisyphus’s Dilemma to Sisyphus’s Duty? A Meditation on the Regulation of Hate Propaganda in Relation to Hate Crimes and Genocide

Un résumé en français est également disponible.

La liberté d'expression et l'administration de la justice : le choc de deux paradigmes

"Thèse présentée à la Faculté des études supérieures En vue de l'obtention du grade de Docteur en droit (LL.D.)"