Additive functions in boolean models of gene regulatory network modules.

Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred Boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity and solution space, thus making it easier to investigate.

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a "covarion-like" pattern of correlated changes in evolutionary rates, and switches in conserved residues ("conserved but different"). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than "constant but different," but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.

The role of nonhematopoietic MHC class II expression in immune responses and tolerance

Si les rôles fonctionnels de diverses cellules immunitaires infiltrant des tissus enflammés sont assez bien compris, par contre, étonnamment, on connaît bien moins la capacité des cellules non hématopoïétiques résidant dans des tissus, à moduler l'activité biologique des cellules immunitaires immigrantes, et donc le résultat de la réponse immunitaire. La présentation des antigènes, dans le contexte des molécules du CMH de classe II (CMHII) à la surface des cellules présentatrices d'antigènes (CPA) professionnelles à une sous- population de lymphocytes T, est cruciale pour le développement des réponses immunitaires protectives spécifiques de l'antigène. En général, l'expression de CMHII est réservée aux CPAs. Toutefois, au cours des pathologies inflammatoires spécifiques d'organe, telles que l'auto-immunité ou la maladie inflammatoire de l'intestin, l'expression de CMHII est également induite par la cytokine interféron (IFN)-y sur des cellules non hématopoïétiques qui résident dans des tissus enflammés. Les conséquences de ce phénomène sont encore peu comprises. Dans cette étude, nous avons utilisé une souche de souris génétiquement modifiées, qui n'a pas la capacité d'induire l'expression de CMHII sur les cellules non hématopoïétiques, mais a maintenu la régulation normale d'expression de CMHII sur les cellules hématopoïétiques. Nous avons appliqué ces souris à différents modèles d'inflammation intestinale et à un modèle de maladie qui imite la maladie auto-immune de l'inflammation du muscle cardiaque (myocardite) chez l'homme. Nous avons pu montrer que, au cours de l'inflammation intestinale, l'expression du CMHII nonhématopoïétique, ou encore l'expression du CMHII par les cellules épithéliales de l'intestin, confère une protection contre la maladie, en réduisant les cellules immunitaires inflammatoires et en augmentant les cellules Τ régulatrices anti-inflammatoires. Ces résultats pourraient expliquer l'échec des traitements d'anti-IFN-γ dans les maladies intestinales inflammatoires chez l'homme. En revanche, dans la myocardite auto-immune, nos résultats indiquent que la présentation d'antigènes par les cellules non hématopoïétiques du coeur est nécessaire pour l'apparition de la pathologie cardiaque, comme nos souris sont résistantes à la maladie. Toutefois, cela n'est pas dû à un défaut d'activation des lymphocytes T, car les lymphocytes Τ des souris mutantes sont parfaitement capables de promouvoir la maladie après le transfert adoptif dans des animaux de type naturel. Nos résultats suggèrent que, durant les maladies inflammatoires spécifiques d'organe, la présentation d'antigène par des cellules non hématopoïétiques module et contribue au résultat de la réponse immunitaire d'une manière opposée, conférant soit la protection contre la maladie ou sa promotion. Nos résultats pourraient ouvrir la voie à des thérapies qui prennent en compte la contribution de la présentation d'antigènes par les cellules non hématopoïétiques, au cours des maladies inflammatoires spécifiques d'organe. - Les molécules du CMH de classe II (CMHII) sont fondamentales pour la présentation des antigènes aux lymphocytes Τ CD4+, car elles permettent le développement des réponses immunitaires spécifiques de l'antigène. Il est largement admis que l'expression de CMHII est réservée aux cellules présentatrices d'antigènes (CPA). Cependant, dans des conditions inflammatoires, l'expression de CMHII est en principe également induite par l'interféron (IFN)-y sur les cellules non hématopoïétiques, telles que les cellules épithéliales et les cardiomyocytes. Une controverse existe jusqu'à présent au sujet de la fonction de cette présentation d'antigènes non professionnelle, pour savoir si elle favorise la tolérance ou l'immunité dépendante des lymphocytes Τ in vivo. Pour répondre à cette question, nous avons testé des souris qui ne sont pas capables d'induire l'expression du CMHII sur les cellules non hématopoïétiques (souris PIV-/- K14 CIITA Tg) parmi différents modèles murins de pathologies inflammatoires, à savoir les modèles de vaccination pour induire des réponses spécifiques d'antigènes des lymphocytes B, plusieurs modèles de colite et un modèle de myocardite auto-immune expérimental (EAM). Pour cela, nous avons administré à ces souris un modèle de colite atténuée, induite par une infection chronique à Helicobacter hepaticus et par l'administration d'anticorps monoclonaux bloquant le récepteur de l'interleukine (IL)-10 (anti-IL-10R). Dans ce système, nous avons pu observer que l'expression abrogée de CMHII a aggravé la colite bactérienne, soit par les cellules non hématopoïétiques, soit exclusivement par les cellules épithéliales intestinales (CEI) dans un autre modèle murin (souris plV_fl/fl vil-Cre Tg). Ce phénotype du côlon a été associé à une augmentation des fréquences de cellules immunitaires innées, de lymphocytes Th1 CD4+, et d'expression des cytokines et de chimiokines pro-inflammatoires, y compris l'IFN-γ. Notamment, l'expression défectueuse de CMHII non hématopoïétique a également réduit les cellules Τ régulatrices (Treg) Forkhead box P3 (FoxP3)+, sans influencer les fréquences des cellules innées lymphoïdes et des cellules Th17. Ces résultats suggèrent un rôle tolérogène de CEIs CMHII+ qui contribue à l'homéostasie immunitaire intestinale. En revanche, dans le modèle d'EAM, les souris ayant subi une ablation de CMHII non hématopoïétique étaient résistantes à l'induction de la maladie, alors que la progression de la pathologie cardiaque, dans les souris de type naturel ou hétérozygotes, a été accompagnée par une régulation positive de l'expression de CMHII du myocarde. Cependant, l'inflammation cardiaque pourrait être transférée de manière adoptive depuis des souris amorcées PIV-/- K14 CIITA Tg vers des souris de type naturel, indiquant l'absence de défaut intrinsèque d'amorçage des cellules T CD4+ dans notre modèle de souris. Ces observations impliquent un rôle à jouer pour des cellules CMHII+ non hématopoïétiques résidentes du coeur, dans la promotion active de ΙΈΑΜ. En conclusion, nos résultats, provenant de diverses pathologies inflammatoires spécifiques d'organes, suggèrent un rôle complexe et divergent, soit tolérogène, soit immunogène/ pathologique, pour l'expression de CMHII non hématopoïétique au cours des pathologies inflammatoires. L'expression non professionnelle de CMHII semble influencer le résultat des réponses immunitaires en fonction de différents facteurs, tels que le tissu cible, le(s) type(s) de cellule(s) non hématopoïétique(s) participante(s) et l'origine de l'inflammation. Nos résultats pourraient potentiellement ouvrir la voie à des applications thérapeutiques, qui tiennent compte de la contribution de la présentation d'antigènes par des CPAs non professionnelles, au cours de l'inflammation spécifique d'organe. - MHC class II (MHCII) molecules are fundamental for the presentation of antigens to CD4+ Τ cells, allowing the development of antigen-specific immune responses. It is widely accepted that MHCII expression is restricted to antigen-presenting cells (APC). However, under inflammatory conditions, MHCII expression is typically also induced by interferon (IFN)-y on nonhematopoietic cells such as epithelial cells and cardiomyocytes. So far, it remains controversial whether this nonprofessional antigen-presentation function promotes CD4+ Τ cell-dependent tolerance or immunity in vivo. To address this issue, we utilised mice which lack inducible MHCII expression on nonhematopoietic cells (pIV-/- K14 CIITA Tg mice) in different mouse models of inflammatory pathologies, namely immunisation models to induce antigen-specific Β cell responses, various colitis models and a model of experimental autoimmune myocarditis (EAM). In an attenuated model of colitis induced by chronic Helicobacter hepaticus infection and treatment with anti-interleukin (IL)-10 receptor (anti-IL-10R) monoclonal blocking antibody, we observed that abrogated MHCII expression by nonhematopoietic cells or, in an alternative tamoxifen-inducible mouse model (plV_fl/fl vil-Cre Tg mice), exclusively by intestinal epithelial cells (IEC), exacerbated bacterial-driven colitis, which was associated with increased colonic frequencies of innate immune cells, CD4+ Th1 cells and expression of proinflammatory cytokines and chemokines, including IFN-γ. Notably, defective nonhematopoietic MHCII expression also resulted in reduced Forkhead box P3 (FoxP3)+ regulatory Τ (Treg) cells without influencing innate lymphoid cell (ILC) and Th17 cell frequencies. These findings suggest a tolerogenic role of MHClT lECs to contribute to intestinal immune homeostasis. In contrast, in the EAM model, mice ablated of nonhematopoietic MHCII were resistant to disease induction, whereas progression of cardiac pathology in WT and heterozygous control mice was accompanied by upregulation of myocardial MHCII expression. However, cardiac inflammation could be adoptively transferred from primed pIV-/- K14 CIITA Tg mice into WT mice, indicating no intrinsic defect of CD4+ Τ activation in our mouse model. These observations imply a role for MHCIT heart-resident nonhematopoietic cells in actively promoting EAM. In conclusion, our findings from different organ-specific inflammatory pathologies suggest a complex and diverging role - either tolerogenic or immunogenic/ pathologic - for nonhematopoietic MHCII expression during inflammatory pathologies: Nonprofessional MHCII expression appears to influence the outcome of immune responses depending on 7 factors such as the target tissue, participating non hematopoietic cell type(s) and the origin of inflammation. Our findings may potentially open the way to therapeutic applications taking into account the contribution of antigen presentation by nonprofessional, tissue-resident APCs during organ-specific inflammation.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

Neuronal in vitro models for the estimation of acute systemic toxicity.

The objective of the EU funded integrated project "ACuteTox" is to develop a strategy in which general cytotoxicity, together with organ-specific endpoints and biokinetic features, are taken into consideration in the in vitro prediction of oral acute systemic toxicity. With regard to the nervous system, the effects of 23 reference chemicals were tested with approximately 50 endpoints, using a neuronal cell line, primary neuronal cell cultures, brain slices and aggregated brain cell cultures. Comparison of the in vitro neurotoxicity data with general cytotoxicity data generated in a non-neuronal cell line and with in vivo data such as acute human lethal blood concentration, revealed that GABA(A) receptor function, acetylcholine esterase activity, cell membrane potential, glucose uptake, total RNA expression and altered gene expression of NF-H, GFAP, MBP, HSP32 and caspase-3 were the best endpoints to use for further testing with 36 additional chemicals. The results of the second analysis showed that no single neuronal endpoint could give a perfect improvement in the in vitro-in vivo correlation, indicating that several specific endpoints need to be analysed and combined with biokinetic data to obtain the best correlation with in vivo acute toxicity.

From deep seated slope deformation to rock avalanche: Destabilization and transportation models of the Sierre landslide (Switzerland)

Sackung is a widespread post-glacial morphological feature affecting Alpine mountains and creating characteristic geomorphological expression that can be detected from topography. Over long time evolution, internal deformation can lead to the formation of rapidly moving phenomena such as a rock-slide or rock avalanche. In this study, a detailed description of the Sierre rock-avalanche (SW Switzerland) is presented. This convex-shaped postglacial instability is one of the larger rock-avalanche in the Alps, involving more than 1.5 billion m3 with a run-out distance of about 14 km and extremely low Fahrböschung angle. This study presents comprehensive analyses of the structural and geological characteristics leading to the development of the Sierre rock-avalanche. In particular, by combining field observations, digital elevation model analyses and numerical modelling, the strong influence of both ductile and brittle tectonic structures on the failure mechanism and on the failure surface geometry is highlighted. The detection of pre-failure deformation indicates that the development of the rock avalanche corresponds to the last evolutionary stage of a pre-existing deep seated gravitational slope instability. These analyses accompanied by the dating and the characterization of rock avalanche deposits, allow the proposal of a destabilization model that clarifies the different phases leading to the development of the Sierre rock avalanche.

Redox dysregulation and oxidative stress in schizophrenia: genetic and functional anomalies of glutathione synthesis in patients and experimental models involving GABA interneurons and NMDA receptors

Objective: Converging evidence speak in favor of an abnormal susceptibility to oxidative stress in schizophrenia. A decreased level of glutathione (GSH), the principal non-protein antioxidant and redox regulator, was observed both in cerebrospinal-fluid and prefrontal cortex of schizophrenia patients (Do et al., 2000). Results: Schizophrenia patients have an abnormal GSH synthesis most likely of genetic origin: Two independent case-control studies showed a significant association between schizophrenia and a GAG trinucleotide repeat (TNR) polymorphism in the GSH key synthesizing enzyme glutamate-cysteine-ligase (GCL) catalytic subunit (GCLC) gene. The most common TNR genotype 7/7 was more frequent in controls, whereas the rarest TNR genotype 8/8 was three times more frequent in patients. The disease-associated genotypes correlated with a decrease in GCLC protein expression, GCL activity and GSH content. Such a redox dysregulation during development could underlie the structural and functional anomalies in connectivity: In experimental models, GSH deficit induced anomalies similar to those observed in patients. (a) morphology: In animal models with GSH deficit during the development we observed in prefrontal cortex a decreased dendritic spines density in pyramidal cells and an abnormal development of parvalbumine (but not of calretinine) immunoreactive GABA interneurones in anterior cingulate cortex. (b) physiology: GSH depletion in hippocampal slices induces NMDA receptors hypofunction and an impairment of long term potentiation. In addition, GSH deficit affected the modulation of dopamine on NMDA-induced Ca 2+ response in cultured cortical neurons. While dopamine enhanced NMDA responses in control neurons, it depressed NMDA responses in GSH-depleted neurons. Antagonist of D2-, but not D1-receptors, prevented this depression, a mechanism contributing to the efficacy of antipsychotics. The redox sensitive ryanodine receptors and L-type calcium channels underlie these observations. (c) cognition: Developing rats with low [GSH] and high dopamine lead deficit in olfactory integration and in object recognition which appears earlier in males that females, in analogy to the delay of the psychosis onset between man and woman. Conclusion: These clinical and experimental evidence, combined with the favorable outcome of a clinical trial with N-Acetyl Cysteine, a GSH precursor, on both the negative symptoms (Berk et al., submitted) and the mismatch negativity in an auditory oddball paradigm supported the proposal that a GSH synthesis impairment of genetic origin represent, among other factors, one major risk factor in schizophrenia.

Redox dysregulation in the pathophysiology of schizophrenia and bipolar disorder: insights from animal models.

Abstract Significance: Schizophrenia (SZ) and bipolar disorder (BD) are classified as two distinct diseases. However, accumulating evidence shows that both disorders share genetic, pathological, and epidemiological characteristics. Based on genetic and functional findings, redox dysregulation due to an imbalance between pro-oxidants and antioxidant defense mechanisms has been proposed as a risk factor contributing to their pathophysiology. Recent Advances: Altered antioxidant systems and signs of increased oxidative stress are observed in peripheral tissues and brains of SZ and BD patients, including abnormal prefrontal levels of glutathione (GSH), the major cellular redox regulator and antioxidant. Here we review experimental data from rodent models demonstrating that permanent as well as transient GSH deficit results in behavioral, morphological, electrophysiological, and neurochemical alterations analogous to pathologies observed in patients. Mice with GSH deficit display increased stress reactivity, altered social behavior, impaired prepulse inhibition, and exaggerated locomotor responses to psychostimulant injection. These behavioral changes are accompanied by N-methyl-D-aspartate receptor hypofunction, elevated glutamate levels, impairment of parvalbumin GABA interneurons, abnormal neuronal synchronization, altered dopamine neurotransmission, and deficient myelination. Critical Issues: Treatment with the GSH precursor and antioxidant N-acetylcysteine normalizes some of those deficits in mice, but also improves SZ and BD symptoms when given as adjunct to antipsychotic medication. Future Directions: These data demonstrate the usefulness of GSH-deficient rodent models to identify the mechanisms by which a redox imbalance could contribute to the development of SZ and BD pathophysiologies, and to develop novel therapeutic approaches based on antioxidant and redox regulator compounds. Antioxid. Redox Signal. 18, 1428-1443.

Protective and Aggravating Effects of Nlrp3 Inflammasome Activation in IBD Models: Influence of Genetic and Environmental Factors.

Background: Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation due to dysregulation of the mucosal immune system. The cytokines IL-1β and IL-18 appear early in intestinal inflammation and their pro-forms are processed via the caspase-1-activating multiprotein complex, the Nlrp3 inflammasome. Previously, we reported that the uptake of dextran sodium sulfate (DSS) by macrophages activates the Nlrp3 inflammasome and that Nlrp3(-/-) mice are protected in the acute DSS colitis model. Of note, other groups have reported opposing effects in regards to DSS susceptibility in Nlrp3(-/-) mice. Recently, mice lacking inflammasomes were found to develop a distinct intestinal microflora. Methods: To reconcile the contradicting observations, we investigated the role of Nlrp3 deficiency in two different IBD models: acute DSS colitis and TNBS (2,4,6-trinitrobenzene sulfonic acid)-induced colitis. In addition, we investigated the impact of the intestinal flora on disease severity by performing cohousing experiments of wild-type and Nlrp3(-/-) mice, as well as by antibiotic treatment. Results: Nlrp3(-/-) mice treated with either DSS or TNBS exhibited attenuated colitis and lower mortality. This protective effect correlated with an increased frequency of CD103+ lamina propria dendritic cells expressing a tolerogenic phenotype in Nlrp3(-/-) mice in steady state conditions. Interestingly, after cohousing, Nlrp3(-/-) mice were as susceptible as wild-type mice, indicating that transmission of endogenous bacterial flora between the two mouse strains might increase susceptibility of Nlrp3(-/-) mice towards DSS-induced colitis. Accordingly, treatment with antibiotics almost completely prevented colitis in the DSS model. Conclusions: The composition of the intestinal microflora significantly influences disease severity in IBD models comparing wild-type and Nlrp3(-/-) mice. This observation may - at least in part - explain contradictory results concerning the role of the inflammasome in different labs. Further studies are required to define the role of the Nlrp3 inflammasome in noninflamed mucosa under steady state conditions and in IBD.

Establishment of animal models to analyze the kinetics and distribution of human tumor antigen-specific CD8⁺ T cells.

Many patients develop tumor antigen-specific T cell responses detectable in peripheral blood mononuclear cells (PBMCs) following cancer vaccine. However, measurable tumor regression is observed in a limited number of patients receiving cancer vaccines. There is a need to re-evaluate systemically the immune responses induced by cancer vaccines. Here, we established animal models targeting two human cancer/testis antigens, NY-ESO-1 and MAGE-A4. Cytotoxic T lymphocyte (CTL) epitopes of these antigens were investigated by immunizing BALB/c mice with plasmids encoding the entire sequences of NY-ESO-1 or MAGE-A4. CD8(+) T cells specific for NY-ESO-1 or MAGE-A4 were able to be detected by ELISPOT assays using antigen presenting cells pulsed with overlapping peptides covering the whole protein, indicating the high immunogenicity of these antigens in mice. Truncation of these peptides revealed that NY-ESO-1-specific CD8(+) T cells recognized D(d)-restricted 8mer peptides, NY-ESO-181-88. MAGE-A4-specific CD8(+) T cells recognized D(d)-restricted 9mer peptides, MAGE-A4265-273. MHC/peptide tetramers allowed us to analyze the kinetics and distribution of the antigen-specific immune responses, and we found that stronger antigen-specific CD8(+) T cell responses were required for more effective anti-tumor activity. Taken together, these animal models are valuable for evaluation of immune responses and optimization of the efficacy of cancer vaccines.

Orthotropic active strain models for the numerical simulation of cardiac biomechanics

An active strain formulation for orthotropic constitutive laws arising in cardiac mechanics modeling is introduced and studied. The passive mechanical properties of the tissue are described by the Holzapfel-Ogden relation. In the active strain formulation, the Euler-Lagrange equations for minimizing the total energy are written in terms of active and passive deformation factors, where the active part is assumed to depend, at the cell level, on the electrodynamics and on the specific orientation of the cardiac cells. The well-posedness of the linear system derived from a generic Newton iteration of the original problem is analyzed and different mechanical activation functions are considered. In addition, the active strain formulation is compared with the classical active stress formulation from both numerical and modeling perspectives. Taylor-Hood and MINI finite elements are employed to discretize the mechanical problem. The results of several numerical experiments show that the proposed formulation is mathematically consistent and is able to represent the main key features of the phenomenon, while allowing savings in computational costs.

Repression and Protest Structural Models and Strategic Interactions

The recent wave of upheavals and revolts in Northern Africa and the Middle East goes back to an old question often raised by theories of collective action: does repression act as a negative or positive incentive for further mobilization? Through a review of the vast literature devoted to this question, this article aims to go beyond theoretical and methodological dead-ends. The article moves on to non-Western settings in order to better understand, via a macro-sociological and dynamic approach, the causal effects between mobilizations and repression. It pleads for a meso- and micro-level approach to this issue: an approach that puts analytical emphasis both on protest organizations and on individual activists' careers.