Simulation-based systematic review of imatinib population pharmacokinetics and PK-PD relationships in chronic myeloid leukemia (CML) patients

Objectives: Several population pharmacokinetic (PPK) and pharmacokinetic-pharmacodynamic (PK-PD) analyses have been performed with the anticancer drug imatinib. Inspired by the approach of meta-analysis, we aimed to compare and combine results from published studies in a useful way - in particular for improving the clinical interpretation of imatinib concentration measurements in the scope of therapeutic drug monitoring (TDM). Methods: Original PPK analyses and PK-PD studies (PK surrogate: trough concentration Cmin; PD outcomes: optimal early response and specific adverse events) were searched systematically on MEDLINE. From each identified PPK model, a predicted concentration distribution under standard dosage was derived through 1000 simulations (NONMEM), after standardizing model parameters to common covariates. A "reference range" was calculated from pooled simulated concentrations in a semi-quantitative approach (without specific weighting) over the whole dosing interval. Meta-regression summarized relationships between Cmin and optimal/suboptimal early treatment response. Results: 9 PPK models and 6 relevant PK-PD reports in CML patients were identified. Model-based predicted median Cmin ranged from 555 to 1388 ng/ml (grand median: 870 ng/ml and inter-quartile range: 520-1390 ng/ml). The probability to achieve optimal early response was predicted to increase from 60 to 85% from 520 to 1390 ng/ml across PK-PD studies (odds ratio for doubling Cmin: 2.7). Reporting of specific adverse events was too heterogeneous to perform a regression analysis. The general frequency of anemia, rash and fluid retention increased however consistently with Cmin, but less than response probability. Conclusions: Predicted drug exposure may differ substantially between various PPK analyses. In this review, heterogeneity was mainly attributed to 2 "outlying" models. The established reference range seems to cover the range where both good efficacy and acceptable tolerance are expected for most patients. TDM guided dose adjustment appears therefore justified for imatinib in CML patients. Its usefulness remains now to be prospectively validated in a randomized trial.

Les symbioses agro-industrielles en Afrique de l'Ouest : évaluation du potentiel d'une nouvelle stratégie pour un développement durable

RésuméCette thèse traite de l'utilisation des concepts de Symbiose Industrielle dans les pays en développement et étudie le potentiel de cette stratégie pour stimuler un développement régional durable dans les zones rurales d'Afrique de l'Ouest. En particulier, lorsqu'une Symbiose Industrielle est instaurée entre une usine et sa population alentour, des outils d'évaluation sont nécessaires pour garantir que le projet permette d'atteindre un réel développement durable. Les outils existants, développés dans les pays industrialisés, ne sont cependant pas complètement adaptés pour l'évaluation de projets dans les pays en développement. En effet, les outils sont porteurs d'hypothèses implicites propres au contexte socio-économique dans lequel ils ont été conçus.L'objectif de cette thèse est de développer un cadre méthodologique pour l'évaluation de la durabilité de projets de Symbiose Industrielle dans les pays en développement.Pour ce faire, je m'appuie sur une étude de cas de la mise en place d'une Symbiose Industrielle au nord du Nigéria, à laquelle j'ai participé en tant qu'observatrice dès 2007. AshakaCem, une usine productrice de ciment du groupe Lafarge, doit faire face à de nombreuses tensions avec la population rurale alentour. L'entreprise a donc décidé d'adopter une nouvelle méthode inspirée des concepts de Symbiose Industrielle. Le projet consiste à remplacer jusqu'à 10% du carburant fossile utilisé pour la cuisson de la matière crue (calcaire et additifs) par de la biomasse produite par les paysans locaux. Pour ne pas compromettre la fragile sécurité alimentaire régionale, des techniques de lutte contre l'érosion et de fertilisation naturelle des sols sont enseignées aux paysans, qui peuvent ainsi utiliser la culture de biomasse pour améliorer leurs cultures vivrières. A travers cette Symbiose Industrielle, l'entreprise poursuit des objectifs sociaux (poser les bases nécessaires à un développement régional), mais également environnementaux (réduire ses émissions de CO2 globales) et économiques (réduire ses coûts énergétiques). Elle s'ancre ainsi dans une perspective de développement durable qui est conditionnelle à la réalisation du projet.A travers l'observation de cette Symbiose et par la connaissance des outils existants je constate qu'une évaluation de la durabilité de projets dans les pays en développement nécessite l'utilisation de critères d'évaluation propres à chaque projet. En effet, dans ce contexte, l'emploi de critères génériques apporte une évaluation trop éloignée des besoins et de la réalité locale. C'est pourquoi, en m'inspirant des outils internationalement reconnus comme l'Analyse du Cycle de Vie ou la Global Reporting Initiative, je définis dans cette thèse un cadre méthodologique qui peut, lui, être identique pour tous les projets. Cette stratégie suit six étapes, qui se réalisent de manière itérative pour permettre une auto¬amélioration de la méthodologie d'évaluation et du projet lui-même. Au cours de ces étapes, les besoins et objectifs en termes sociaux, économiques et environnementaux des différents acteurs sont déterminés, puis regroupés, hiérarchisés et formulés sous forme de critères à évaluer. Des indicateurs quantitatifs ou qualitatifs sont ensuite définis pour chacun de ces critères. Une des spécificités de cette stratégie est de définir une échelle d'évaluation en cinq graduations, identique pour chaque indicateur, témoignant d'un objectif totalement atteint (++) ou pas du tout atteint (--).L'application de ce cadre méthodologique à la Symbiose nigériane a permis de déterminer quatre critères économiques, quatre critères socio-économiques et six critères environnementaux à évaluer. Pour les caractériser, 22 indicateurs ont été définis. L'évaluation de ces indicateurs a permis de montrer que le projet élaboré atteint les objectifs de durabilité fixés pour la majorité des critères. Quatre indicateurs ont un résultat neutre (0), et un cinquième montre qu'un critère n'est pas atteint (--). Ces résultats s'expliquent par le fait que le projet n'en est encore qu'à sa phase pilote et n'a donc pas encore atteint la taille et la diffusion optimales. Un suivi sur plusieurs années permettra de garantir que ces manques seront comblés.Le cadre méthodologique que j'ai développé dans cette thèse est un outil d'évaluation participatif qui pourra être utilisé dans un contexte plus large que celui des pays en développement. Son caractère générique en fait un très bon outil pour la définition de critères et indicateurs de suivi de projet en terme de développement durable.SummaryThis thesis examines the use of industrial symbiosis in developing countries and studies its potential to stimulate sustainable regional development in rural areas across Western Africa. In particular, when industrial symbiosis is instituted between a factory and the surrounding population, evaluation tools are required to ensure the project achieves truly sustainable development. Existing tools developed in industrialized countries are not entirely suited to assessing projects in developing countries. Indeed, the implicit hypotheses behind such tools reflect the socioeconomic context in which they were designed. The goal of this thesis is to develop a methodological framework for evaluating the sustainability of industrial symbiosis projects in developing countries.To accomplish this, I followed a case study about the implementation of industrial symbiosis in northern Nigeria by participating as an observer since 2007. AshakaCem, a cement works of Lafarge group, must confront many issues associated with violence committed by the local rural population. Thus, the company decided to adopt a new approach inspired by the concepts of industrial symbiosis.The project involves replacing up to 10% of the fossil fuel used to heat limestone with biomass produced by local farmers. To avoid jeopardizing the fragile security of regional food supplies, farmers are taught ways to combat erosion and naturally fertilize the soil. They can then use biomass cultivation to improve their subsistence crops. Through this industrial symbiosis, AshakaCem follows social objectives (to lay the necessary foundations for regional development), but also environmental ones (to reduce its overall CO2 emissions) and economical ones (to reduce its energy costs). The company is firmly rooted in a view of sustainable development that is conditional upon the project's execution.By observing this symbiosis and by being familiar with existing tools, I note that assessing the sustainability of projects in developing countries requires using evaluation criteria that are specific to each project. Indeed, using generic criteria results in an assessment that is too far removed from what is needed and from the local reality. Thus, by drawing inspiration from such internationally known tools as Life Cycle Analysis and the Global Reporting Initiative, I define a generic methodological framework for the participative establishment of an evaluation methodology specific to each project.The strategy follows six phases that are fulfilled iteratively so as to improve the evaluation methodology and the project itself as it moves forward. During these phases, the social, economic, and environmental needs and objectives of the stakeholders are identified, grouped, ranked, and expressed as criteria for evaluation. Quantitative or qualitative indicators are then defined for each of these criteria. One of the characteristics of this strategy is to define a five-point evaluation scale, the same for each indicator, to reflect a goal that was completely reached (++) or not reached at all (--).Applying the methodological framework to the Nigerian symbiosis yielded four economic criteria, four socioeconomic criteria, and six environmental criteria to assess. A total of 22 indicators were defined to characterize the criteria. Evaluating these indicators made it possible to show that the project meets the sustainability goals set for the majority of criteria. Four indicators had a neutral result (0); a fifth showed that one criterion had not been met (--). These results can be explained by the fact that the project is still only in its pilot phase and, therefore, still has not reached its optimum size and scope. Following up over several years will make it possible to ensure these gaps will be filled.The methodological framework presented in this thesis is a highly effective tool that can be used in a broader context than developing countries. Its generic nature makes it a very good tool for defining criteria and follow-up indicators for sustainable development.

Expression of human estrogen receptor mutants in Xenopus oocytes: correlation between transcriptional activity and ability to form protein-DNA complexes.

The human estrogen receptor (hER) is a trans-acting regulatory protein composed of a series of discrete functional domains. We have microinjected an hER expression vector (HEO) into Xenopus oocyte nuclei and demonstrate, using Western blot assay, that the hER is synthesized. When nuclear extracts from oocytes were prepared and incubated in the presence of a 2.7 kb DNA fragment comprising the 5' end of the vitellogenin gene B2, formation of estrogen-dependent complexes could be visualized by electron microscopy over the estrogen responsive element (ERE). Of crucial importance is the observation that the complex formation is inhibited by the estrogen antagonist tamoxifen, is restored by the addition of the hormone and does not take place with extracts from control oocytes injected with the expression vector lacking the sequences encoding the receptor. The presence of the biologically active hER is confirmed in co-injection experiments, in which HEO is co-introduced with a CAT reporter gene under the control of a vitellogenin promoter containing or lacking the ERE. CAT assays and primer extensions analyses reveal that both the receptor and the ERE are essential for estrogen induced stimulation of transcription. The same approach was used to analyze selective hER mutants. We find that the DNA binding domain (region C) is essential for protein--DNA complex formation at the ERE but is not sufficient by itself to activate transcription from the reporter gene. In addition to region C, both the hormone binding (region E) and amino terminal (region A/B) domains are needed for an efficient transcription activation.(ABSTRACT TRUNCATED AT 250 WORDS)

Protective effects of hypercapnic acidosis on ventilator-induced lung injury.

To investigate whether respiratory acidosis modulates ventilator-induced lung injury (VILI), we perfused (constant flow) 21 isolated sets of normal rabbit lungs, ventilated them for 20 min (pressure controlled ventilation [PCV] = 15 cm H(2)O) (Baseline) with an inspired CO(2) fraction adjusted for the partial pressure of CO(2) in the perfusate (PCO(2) approximately equal to 40 mm Hg), and then randomized them into three groups. Group A (control: n = 7) was ventilated with PCV = 15 cm H(2)O for three consecutive 20-min periods (T1, T2, T3). In Group B (high PCV/normocapnia; n = 7), PCV was given at 20 (T1), 25 (T2), and 30 (T3) cm H(2)O. The targeted PCO(2) was 40 mm Hg in Groups A and B. Group C (high PCV/hypercapnia; n = 7) was ventilated in the same way as Group B, but the targeted PCO(2) was approximately equal to 70 to 100 mm Hg. The changes (from Baseline to T3) in weight gain (Delta WG: g) and in the ultrafiltration coefficient (Delta K(f) = gr/min/ cm H(2)O/100g) and the protein and hemoglobin concentrations in bronchoalveolar lavage fluid (BALF) were used to assess injury. Group B experienced a significantly greater Delta WG (14.85 +/- 5.49 [mean +/- SEM] g) and Delta K(f) (1.40 +/- 0.49 g/min/cm H(2)O/100 g) than did either Group A (Delta WG = 0.70 +/- 0.43; Delta K(f) = 0.01 +/- 0.03) or Group C (Delta WG = 5.27 +/- 2.03 g; Delta K(f) = 0.25 +/- 0.12 g/min/cm H(2)O/ 100 g). BALF protein and hemoglobin concentrations (g/L) were higher in Group B (11.98 +/- 3.78 g/L and 1.82 +/- 0.40 g/L, respectively) than in Group A (2.92 +/- 0.75 g/L and 0.38 +/- 0.15 g/L) or Group C (5.71 +/- 1.88 g/L and 1.19 +/- 0.32 g/L). We conclude that respiratory acidosis decreases the severity of VILI in this model.

Dynamical modeling and analysis of large cellular regulatory networks.

The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

Capsule permeability via polymer and protein ingress/egress.

Static incubation tests, where microcapsules and beads are contacted with polymer and protein solutions, have been developed for the characterization of permselective materials applied for bioartificial organs and drug delivery. A combination of polymer ingress, detected by size-exclusion chromatography, and protein ingress/ egress, assessed by gel electrophoresis, provides information regarding the diffusion kinetics, molar mass cutoff(MMCO) and permeability. This represents an improvement over existing permeability measurements that are based on the diffusion of a single type of solute. Specifically, the permeability of capsules based on alginate, cellulose sulfate, polymethylene-co-guanidine were characterized as a function of membrane thickness. Solid alginate beads were also evaluated. The MMCO of these capsules was estimated to be between 80 and 90 kDa using polymers, and between 116-150 kDa with proteins. Apparently, the globular shape of the proteins (radius of gyration (Rg) of 4.2-4.6 nm) facilitates their passage through the membrane, comparatively to the polysaccharide coil conformation (Rg of 6.5-8.3 nm). An increase of the capsule membrane thickness reduced these values. The MMCO of the beads, which do not have a membrane limiting their permselective properties, was higher, between 110 and 200 kDa with dextrans, and between 150 and 220 kDa with proteins. Therefore, although the permeability estimated with biologically relevant molecules is generally higher due to their lower radius of gyration, both the MMCO of synthetic and natural watersoluble polymers correlate well, and can be used as in vitro metrics for the immune protection ability of microcapsules and microbeads. This article shows, to the authors' knowledge, the first reported concordance between permeability measures based on model natural and biological macromolecules.

The eukaryotic promoter database (EPD).

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes a description of the initiation site mapping data, exhaustive cross-references to the EMBL nucleotide sequence database, SWISS-PROT, TRANSFAC and other databases, as well as bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements. EPD can be accessed at http://www.epd.isb-sib.ch

The NLRP3 inflammasome in health and disease: the good, the bad and the ugly.

While interleukin (IL)-1β plays an important role in combating the invading pathogen as part of the innate immune response, its dysregulation is responsible for a number of autoinflammatory disorders. Large IL-1β activating platforms, known as inflammasomes, can assemble in response to the detection of endogenous host and pathogen-associated danger molecules. Formation of these protein complexes results in the autocatalysis and activation of caspase-1, which processes precursor IL-1β into its secreted biologically active form. Inflammasome and IL-1β activity is required to efficiently control viral, bacterial and fungal pathogen infections. Conversely, excess IL-1β activity contributes to human disease, and its inhibition has proved therapeutically beneficial in the treatment of a spectrum of serious, yet relatively rare, heritable inflammasomopathies. Recently, inflammasome function has been implicated in more common human conditions, such as gout, type II diabetes and cancer. This raises the possibility that anti-IL-1 therapeutics may have broader applications than anticipated previously, and may be utilized across diverse disease states that are linked insidiously through unwanted or heightened inflammasome activity.

A conceptual framework to assess the effectiveness of HIV prevention

Aim: The relative effectiveness of different methods of prevention of HIV transmission is a subject of debate that is renewed with the integration of each new method. The relative weight of values and evidence in decision-making is not always clearly defined. Debate is often confused, as the proponents of different approaches address the issue at different levels of implementation. This paper defines and delineates the successive levels of analysis of effectiveness, and proposes a conceptual framework to clarify debate. Method / Issue: Initially inspired from work on contraceptive effectiveness, a first version of the conceptual framework was published in 1993 with definition of the Condom Effectiveness Matrix (Spencer, 1993). The framework has since integrated and further developed thinking around distinctions made between efficacy and effectiveness and has been applied to HIV prevention in general. Three levels are defined: theoretical effectiveness (ThE), use-effectiveness (UseE) and population use-effectiveness (PopUseE). For example, abstinence and faithfulness, as proposed in the ABC strategy, have relatively high theoretical effectiveness but relatively low effectiveness at subsequent levels of implementation. The reverse is true of circumcision. Each level is associated with specific forms of scientific enquiry and associated research questions: basic and clinical sciences with ThE; clinical and social sciences with UseE; epidemiology and social, economic and political sciences with PopUseE. Similarly, the focus of investigation moves from biological organisms, to the individual at the physiological and then psychological, social and ecological level, and finally takes as perspective populations and societies as a whole. The framework may be applied to analyse issues on any approach. Hence, regarding consideration of HIV treatment as a means of prevention, examples of issues at each level would be: ThE: achieving adequate viral suppression and non-transmission to partners; UseE: facility and degree of adherence to treatment and medical follow-up; PopUseE: perceived validity of strategy, feasibility of achieving adequate population coverage. Discussion: Use of the framework clarifies the questions that need to be addressed at all levels in order to improve effectiveness. Furthermore, the interconnectedness and complementary nature of research from the different scientific disciplines and the relative contribution of each become apparent. The proposed framework could bring greater rationality to the prevention effectiveness debate and facilitate communication between stakeholders.

Characterization of the effects of IL-17F on CHO cell line generation

CHO is the most commonly used mammalian host for the generation of cell lines allowing for the production of high quality therapeutic proteins. The generation of such cell lines is a lengthy and resource-intensive process requiring extensive screening in order to isolate candidates with optimal characteristics, such as growth, stability and productivity. For this reason, the biotechnology industry invests much effort in attempts to optimize CHO expression systems in order to streamline and shorten the cell line selection process. Based on preliminary observations of a facilitated selection of CHO-GS cell lines expressing members of the IL-17 cytokine family, this study investigates the use of IL-17F as a novel enhancing factor for CHO cell line generation. Using two different CHO expression systems (exploiting GS and DHFR-based selection), we demonstrated that IL-17F expression caused a significant increase in the occurrence of colonies during the selection process. All colonies selected produced substantial amounts of IL-17F, suggesting that benefits were conferred, during selection, to those cells expressing the cytokine. Furthermore, transgene expression levels were significantly increased when the selection pressure was raised to a level that would not normally be permissive for colony selection (i.e. 100 |o.M MSX for the CHO-GS expression system or 1000 nM MTX for the CHO-DHFR system). Finally, IL-17F expression was also found to enhance the rate of appearance of clones during single cell subcloning in the absence of selection pressure. Overall, these benefits have the potential to allow a substantial reduction in the length of cell line generation while significantly increasing cell line productivity. Nevertheless, we found that the high IL-17F expression levels required to convey enhancing effects was a limitation when attempting to co-express IL-17F and a recombinant soluble protein of therapeutic interest from independent CMV promoters within the same expression vector. In order to understand and overcome this limitation, studies were designed to characterize the IL-17F enhancing effect at the molecular and cellular level. Regular supplementation of recombinant biologically-active IL-17F into the culture medium during cell line selection was not able to reproduce the enhancing effects of endogenous IL-17F expression. In addition, increased IL-17F expression correlated with increased CHO-GS selection transgene expression at the single cell level. This data suggested a possible effect of IL-17F on viral promoter activity or transgene mRNA stability. It also provided direct evidence that the cells expressing the highest amounts of IL-17F obtained the most benefit. Overall data obtained from these study implied that IL-17F may act through an intracellular mechanism, possibly exerted during secretion. We therefore initiated experiments designed to determine the specific compartment(s) within which IL-17F triggers its effect. This work has identified IL-17F as a potentially powerful tool to optimize the CHO cell line generation process. The characterization of this enhancing effect at the molecular level has given us several insights into overcoming the current limitations, thus paving the way for the development of a viable technology that can be exploited within the biotechnology industry. - La CHO est la cellule hôte de mammifere la plus couramment utilisée dans la création de lignée cellulaire produisant des protéines thérapeutiques de haute qualité. La génération de ces lignées cellulaires est un processus long et exigeant l'utilisation de techniques de sélection robustes afin d'isoler des candidats possédants les caractéristiques optimales de croissance, de productivité et de stabilité d'expression. Les industries biopharmaceutiques ont investi beaucoup d'efforts afin d'optimiser les systèmes d'expression CHO dans le but raccourcir la longueur du procédé de sélection de lignées cellulaires et aussi d'en augmenter l'efficacité. A partir d'observations préliminaires obtenues lors de la génération de lignées cellulaires CHO- GS exprimant une cytokine appartenant à la famille des IL-17, nous avons réalisé une étude portant sur l'utilisation de l'IL-17F humaine (IL-17F) comme nouveau facteur d'optimisation pour la génération de lignées cellulaires CHO. Nous avons démontré, en utilisant les deux systèmes de sélection et d'expression CHO couramment utilisés (le premier exploitant la GS et l'autre basée sur la DHFR), que l'expression de l'IL-17F permet une augmentation significative de la fréquence d'apparition de colonies durant le processus de sélection de lignées cellulaires. Les différentes colonies sélectionnées expriment des quantités substantielles d'IL-17F, suggérant un effet bénéfique lors de la sélection qui serait exclusivement conféré aux cellules exprimant la cytokine. En outre, le niveau d'expression du transgene se trouve significativement augmenté lorsque la pression de sélection est portée à un niveau habituellement trop élevé pour permettre la sélection de colonies (soit 100 |JM MSX pour le système d'expression CHO-GS ou 1000 nM MTX pour le système CHO- DHFR). Enfin, l'expression d'IL-17F permet également d'améliorer la vitesse d'apparition de clones pendant une étape de sous-clonage en l'absence de pression de sélection. L'ensemble de ces effets bénéfiques permettent une réduction substantielle de la durée de génération de lignées cellulaires tout en augmentant considérablement la productivité des lignées obtenues. Néanmoins, nous avons constaté que la nécessité d'exprimer des niveaux élevés d'IL-17F afin obtenir l'ensemble de ses effets bénéfiques devient une contrainte lors de l'utilisation d'un vecteur d'expression composé de deux promoteurs CMV indépendants pour la co-expression de la cytokine et d'une protéine soluble présentant un intérêt thérapeutique. Afin de mieux comprendre et de surmonter cette limitation, plusieurs études ont été effectuées dans le but de mieux caractériser l'effet de IL-17F au niveau subcellulaire. L'apport régulier en IL-17F recombinante et biologiquement active dans le milieu de culture lors de la sélection de lignées cellulaires ne permet pas de reproduire les effets bénéfiques observés par l'expression endogène d'IL-17F. En outre, nous avons constaté que, lors de l'utilisation du système CHO- GS, l'augmentation d'expression de 1TL-17F est corrélée à un accroissement de l'expression du marqueur de sélection au niveau cellulaire. Ces résultats suggèrent un possible effet d'IL- 17F sur l'activité des promoteurs viraux et ainsi fournissent une preuve directe que les cellules exprimant de haut niveau d'IL-17F sont celles qui en profitent le plus. L'ensemble de ces observations mettrait en avant que l'effet d'IL-17F se ferait selon un mécanisme intracellulaire. Nous avons donc étudié le(s) compartiment(s) spécifique(s) dans lequel IL-17F pourrait exercer son effet. Ce travail a permis de définir IL-17F comme un puissant outil pour l'optimisation des procédés de génération de lignées cellulaires CHO. La caractérisation de cette amélioration de l'effet au niveau moléculaire nous a donné plusieurs indications sur la manière de dépasser les limitations actuelles, ouvrant ainsi la voie au développement d'une technologie viable qui peut être exploitée pars l'industrie biotechnologique.

THE USE OF SIMULATIONS IN EVOLUTIONARY POPULATION GENETICS: APPLICATIONS ON HUMANS, OWLS AND VIRTUAL ORGANISMS

Summary (in English) Computer simulations provide a practical way to address scientific questions that would be otherwise intractable. In evolutionary biology, and in population genetics in particular, the investigation of evolutionary processes frequently involves the implementation of complex models, making simulations a particularly valuable tool in the area. In this thesis work, I explored three questions involving the geographical range expansion of populations, taking advantage of spatially explicit simulations coupled with approximate Bayesian computation. First, the neutral evolutionary history of the human spread around the world was investigated, leading to a surprisingly simple model: A straightforward diffusion process of migrations from east Africa throughout a world map with homogeneous landmasses replicated to very large extent the complex patterns observed in real human populations, suggesting a more continuous (as opposed to structured) view of the distribution of modern human genetic diversity, which may play a better role as a base model for further studies. Second, the postglacial evolution of the European barn owl, with the formation of a remarkable coat-color cline, was inspected with two rounds of simulations: (i) determine the demographic background history and (ii) test the probability of a phenotypic cline, like the one observed in the natural populations, to appear without natural selection. We verified that the modern barn owl population originated from a single Iberian refugium and that they formed their color cline, not due to neutral evolution, but with the necessary participation of selection. The third and last part of this thesis refers to a simulation-only study inspired by the barn owl case above. In this chapter, we showed that selection is, indeed, effective during range expansions and that it leaves a distinguished signature, which can then be used to detect and measure natural selection in range-expanding populations. Résumé (en français) Les simulations fournissent un moyen pratique pour répondre à des questions scientifiques qui seraient inabordable autrement. En génétique des populations, l'étude des processus évolutifs implique souvent la mise en oeuvre de modèles complexes, et les simulations sont un outil particulièrement précieux dans ce domaine. Dans cette thèse, j'ai exploré trois questions en utilisant des simulations spatialement explicites dans un cadre de calculs Bayésiens approximés (approximate Bayesian computation : ABC). Tout d'abord, l'histoire de la colonisation humaine mondiale et de l'évolution de parties neutres du génome a été étudiée grâce à un modèle étonnement simple. Un processus de diffusion des migrants de l'Afrique orientale à travers un monde avec des masses terrestres homogènes a reproduit, dans une très large mesure, les signatures génétiques complexes observées dans les populations humaines réelles. Un tel modèle continu (opposé à un modèle structuré en populations) pourrait être très utile comme modèle de base dans l'étude de génétique humaine à l'avenir. Deuxièmement, l'évolution postglaciaire d'un gradient de couleur chez l'Effraie des clocher (Tyto alba) Européenne, a été examiné avec deux séries de simulations pour : (i) déterminer l'histoire démographique de base et (ii) tester la probabilité qu'un gradient phénotypique, tel qu'observé dans les populations naturelles puisse apparaître sans sélection naturelle. Nous avons montré que la population actuelle des chouettes est sortie d'un unique refuge ibérique et que le gradient de couleur ne peux pas s'être formé de manière neutre (sans l'action de la sélection naturelle). La troisième partie de cette thèse se réfère à une étude par simulations inspirée par l'étude de l'Effraie. Dans ce dernier chapitre, nous avons montré que la sélection est, en effet, aussi efficace dans les cas d'expansion d'aire de distribution et qu'elle laisse une signature unique, qui peut être utilisée pour la détecter et estimer sa force.

Hyperoxemia in newborn infants: detection by pulse oximetry.

Pulse oximetry has been proposed as a noninvasive continuous method for transcutaneous monitoring of arterial oxygen saturation of hemoglobin (tcSO2) in the newborn infant. The reliability of this technique in detecting hyperoxemia is controversial, because small changes in saturation greater than 90% are associated with relatively large changes in arterial oxygen tension (PaO2). The purpose of this study was to assess the reliability of pulse oximetry using an alarm limit of 95% tcSO2 in detecting hyperoxemia (defined as PaO2 greater than 90 mm Hg) and to examine the effect of varying the alarm limit on reliability. Two types of pulse oximeter were studied alternately in 50 newborn infants who were mechanically ventilated with indwelling arterial lines. Three arterial blood samples were drawn from every infant during routine increase of inspired oxygen before intratracheal suction, and PaO2 was compared with tcSO2. The Nellcor N-100 pulse oximeter identified all 26 hyperoxemic instances correctly (sensitivity 100%) and alarmed falsely in 25 of 49 nonhyperoxemic instances (specificity 49%). The Ohmeda Biox 3700 pulse oximeter detected 13 of 35 hyperoxemic instances (sensitivity 37%) and alarmed falsely in 7 of 40 nonhyperoxemic instances (specificity 83%). The optimal alarm limit, defined as a sensitivity of 95% or more associated with maximal specificity, was determined for Nellcor N-100 at 96% tcSO2 (specificity 38%) and for Ohmeda Biox 3700 at 89% tcSO2 (specificity 52%). It was concluded that pulse oximeters can be highly sensitive in detecting hyperoxemia provided that type-specific alarm limits are set and a low specificity is accepted.

Synergistic effect of GDNF and NGF on axonal branching and elongation in vitro.

There is a clinical need to enhance functional recovery of injured peripheral nerves. Local administration of neurotrophic factors (NTFs) after surgical repair has been proposed for this purpose. Little is known, however, on the optimal local dose and dosing frequency of NTFs in a peripheral nerve defect. For increasing our knowledge on biologically relevant local NTFs concentrations and for making available an in vitro assay for assessing the bioactivity of NTFs in connection with implantable localized delivery systems, we developed in this study a bioassay for NTFs, which is based on dorsal root ganglion (DRG) explants from E9 (9 days old) chicken embryos. Axonal elongation and extent of axonal branching was analyzed microscopically after addition of glial cell line-derived neurotrophic factor (GDNF) and nerve growth factor (NGF), each alone and in combination. GDNF significantly promoted axonal elongation, but only little axonal branching, whereas NGF induced extensive axonal branching with modest axonal elongation. The combination of GDNF and NGF exerted a synergistic effect on the axonal elongation, axonal branching and growth kinetics. GDNF and NGF also enhanced the expression of their respective functional receptors Ret and TrkA on the DRG neurons. This information should be relevant for the development of implants containing NTFs and on drug therapy of damaged peripheral nerves.

Granzyme A is an interleukin 1 beta-converting enzyme.

Apoptosis is critically dependent on the presence of the ced-3 gene in Caenorhabditis elegans, which encodes a protein homologous to the mammalian interleukin (IL)-1 beta-converting enzyme (ICE). Overexpression of ICE or ced-3 promotes apoptosis. Cytotoxic T lymphocyte-mediated rapid apoptosis is induced by the proteases granzyme A and B. ICE and granzyme B share the rare substrate site of aspartic acid, after which amino acid cleavage of precursor IL-1 beta (pIL-1 beta) occurs. Here we show that granzyme A, but not granzyme B, converts pIL-1 beta to its 17-kD mature form. Major cleavage occurs at Arg120, four amino acids downstream of the authentic processing site, Asp116. IL-1 beta generated by granzyme A is biologically active. When pIL-1 beta processing is monitored in lipopolysaccharide-activated macrophage target cells attacked by cytotoxic T lymphocytes, intracellular conversion precedes lysis. Prior granzyme inactivation blocks this processing. We conclude that the apoptosis-inducing granzyme A and ICE share at least one downstream target substrate, i.e., pIL-1 beta. This suggests that lymphocytes, by means of their own converting enzyme, could initiate a local inflammatory response independent of the presence of ICE.

X-ray mosaic nanotomography of large microorganisms.

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state.