A hormonal regulatory module that provides flexibility to tropic responses.

Plants orient their growth depending on directional stimuli such as light and gravity, in a process known as tropic response. Tropisms result from asymmetrical accumulation of auxin across the responding organ relative to the direction of the stimulus, which causes differential growth rates on both sides of the organ. Here, we show that gibberellins (GAs) attenuate the gravitropic reorientation of stimulated hypocotyls of dark-grown Arabidopsis (Arabidopsis thaliana) seedlings. We show that the modulation occurs through induction of the expression of the negative regulator of auxin signaling INDOLE-3-ACETIC ACID INDUCIBLE19/MASSUGU2. The biological significance of this regulatory mechanism involving GAs and auxin seems to be the maintenance of a high degree of flexibility in tropic responses. This notion is further supported by observations that GA-deficient seedlings showed a much lower variance in the response to gravity compared to wild-type seedlings and that the attenuation of gravitropism by GAs resulted in an increased phototropic response. This suggests that the interplay between auxin and GAs may be particularly important for plant orientation under competing tropic stimuli.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

The de facto independence of regulatory agencies and its consequences for policy making and regulatory outcomes

This dissertation focuses on the practice of regulatory governance, throughout the study of the functioning of formally independent regulatory agencies (IRAs), with special attention to their de facto independence. The research goals are grounded on a "neo-positivist" (or "reconstructed positivist") position (Hawkesworth 1992; Radaelli 2000b; Sabatier 2000). This perspective starts from the ontological assumption that even if subjective perceptions are constitutive elements of political phenomena, a real world exists beyond any social construction and can, however imperfectly, become the object of scientific inquiry. Epistemologically, it follows that hypothetical-deductive theories with explanatory aims can be tested by employing a proper methodology and set of analytical techniques. It is thus possible to make scientific inferences and general conclusions to a certain extent, according to a Bayesian conception of knowledge, in order to update the prior scientific beliefs in the truth of the related hypotheses (Howson 1998), while acknowledging the fact that the conditions of truth are at least partially subjective and historically determined (Foucault 1988; Kuhn 1970). At the same time, a sceptical position is adopted towards the supposed disjunction between facts and values and the possibility of discovering abstract universal laws in social science. It has been observed that the current version of capitalism corresponds to the golden age of regulation, and that since the 1980s no government activity in OECD countries has grown faster than regulatory functions (Jacobs 1999). Following an apparent paradox, the ongoing dynamics of liberalisation, privatisation, decartelisation, internationalisation, and regional integration hardly led to the crumbling of the state, but instead promoted a wave of regulatory growth in the face of new risks and new opportunities (Vogel 1996). Accordingly, a new order of regulatory capitalism is rising, implying a new division of labour between state and society and entailing the expansion and intensification of regulation (Levi-Faur 2005). The previous order, relying on public ownership and public intervention and/or on sectoral self-regulation by private actors, is being replaced by a more formalised, expert-based, open, and independently regulated model of governance. Independent regulation agencies (IRAs), that is, formally independent administrative agencies with regulatory powers that benefit from public authority delegated from political decision makers, represent the main institutional feature of regulatory governance (Gilardi 2008). IRAs constitute a relatively new technology of regulation in western Europe, at least for certain domains, but they are increasingly widespread across countries and sectors. For instance, independent regulators have been set up for regulating very diverse issues, such as general competition, banking and finance, telecommunications, civil aviation, railway services, food safety, the pharmaceutical industry, electricity, environmental protection, and personal data privacy. Two attributes of IRAs deserve a special mention. On the one hand, they are formally separated from democratic institutions and elected politicians, thus raising normative and empirical concerns about their accountability and legitimacy. On the other hand, some hard questions about their role as political actors are still unaddressed, though, together with regulatory competencies, IRAs often accumulate executive, (quasi-)legislative, and adjudicatory functions, as well as about their performance.

ENaC and its regulatory proteins as drug targets for blood pressure control.

Hypertension is a serious medical problem affecting millions of people worldwide. A key protein regulating blood pressure is the Epithelial Na(+) Channel (ENaC). In accord, loss of function mutations in ENaC (PHA1) cause hypotension, whereas gain of function mutations (Liddle syndrome) result in hypertension. The region mutated in Liddle syndrome, called the PY motif (L/PPxY), serves as a binding site for the ubiquitin ligase Nedd4-2, a C2-WW-Hect E3 ubiquitin ligase. Nedd4-2 binds the ENaC-PY motif via it WW domains, ubiquitylates the channel and targets it for endocytosis, a process impaired in Liddle syndrome due to poor binding of the channel to Nedd4-2. This leads to accumulation of active channels at the cell surface and increased Na(+) (and fluid) absorption in the distal nephron, resulting in elevated blood volume and blood pressure. Compounds that destabilize cell surface ENaC, or enhance Nedd4-2 activity in the kidney, could potentially serve as drug targets for hypertension. In addition, recent discoveries of regulation of activation of ENaC by proteases such as furin, prostasin and elastase, which cleave the extracellular domain of this channel leading to it activation, as well as the identification of inhibitors that block the activity of these proteases, provide further avenues for drug targeting of ENaC and the control of blood pressure.

Progesterone/RANKL is a major regulatory axis in the human breast.

Estrogens and progesterones are major drivers of breast development but also promote carcinogenesis in this organ. Yet, their respective roles and the mechanisms underlying their action in the human breast are unclear. Receptor activator of nuclear factor κB ligand (RANKL) has been identified as a pivotal paracrine mediator of progesterone function in mouse mammary gland development and mammary carcinogenesis. Whether the factor has the same role in humans is of clinical interest because an inhibitor for RANKL, denosumab, is already used for the treatment of bone disease and might benefit breast cancer patients. We show that progesterone receptor (PR) signaling failed to induce RANKL in PR(+) breast cancer cell lines and in dissociated, cultured breast epithelial cells. In clinical specimens from healthy donors and intact breast tissue microstructures, hormone response was maintained and RANKL expression was under progesterone control, which increased RNA stability. RANKL was sufficient to trigger cell proliferation and was required for progesterone-induced proliferation. The findings were validated in vivo where RANKL protein expression in the breast epithelium correlated with serum progesterone levels and the protein was expressed in a subset of luminal cells that express PR. Thus, important hormonal control mechanisms are conserved across species, making RANKL a potential target in breast cancer treatment and prevention.

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.

MOTIVATION: Combinatorial interactions of transcription factors with cis-regulatory elements control the dynamic progression through successive cellular states and thus underpin all metazoan development. The construction of network models of cis-regulatory elements, therefore, has the potential to generate fundamental insights into cellular fate and differentiation. Haematopoiesis has long served as a model system to study mammalian differentiation, yet modelling based on experimentally informed cis-regulatory interactions has so far been restricted to pairs of interacting factors. Here, we have generated a Boolean network model based on detailed cis-regulatory functional data connecting 11 haematopoietic stem/progenitor cell (HSPC) regulator genes. RESULTS: Despite its apparent simplicity, the model exhibits surprisingly complex behaviour that we charted using strongly connected components and shortest-path analysis in its Boolean state space. This analysis of our model predicts that HSPCs display heterogeneous expression patterns and possess many intermediate states that can act as 'stepping stones' for the HSPC to achieve a final differentiated state. Importantly, an external perturbation or 'trigger' is required to exit the stem cell state, with distinct triggers characterizing maturation into the various different lineages. By focusing on intermediate states occurring during erythrocyte differentiation, from our model we predicted a novel negative regulation of Fli1 by Gata1, which we confirmed experimentally thus validating our model. In conclusion, we demonstrate that an advanced mammalian regulatory network model based on experimentally validated cis-regulatory interactions has allowed us to make novel, experimentally testable hypotheses about transcriptional mechanisms that control differentiation of mammalian stem cells. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Policy Credibility and Delegation to Independent Regulatory Agencies: A Comparative Empirical Analysis

Independent regulatory agencies are one of the main institutional features of the 'rising regulatory state' in Western Europe. Governments are increasingly willing to abandon their regulatory competencies and to delegate them to specialized institutions that are at least partially beyond their control. This article examines the empirical consistency of one particular explanation of this phenomenon, namely the credibility hypothesis, claiming that governments delegate powers so as to enhance the credibility of their policies. Three observable implications are derived from the general hypothesis, linking credibility and delegation to veto players, complexity and interdependence. An independence index is developed to measure agency independence, which is then used in a multivariate analysis where the impact of credibility concerns on delegation is tested. The analysis relies on an original data set comprising independence scores for thirty-three regulators. Results show that the credibility hypothesis can explain a good deal of the variation in delegation. The economic nature of regulation is a strong determinant of agency independence, but is mediated by national institutions in the form of veto players.

Synchronous versus asynchronous modeling of gene regulatory networks.

MOTIVATION: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene-gene, protein-protein and gene-protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes. RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process. AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.

New insights into the regulatory mechanisms of the NALP3 inflammasome

Résumé : Les vertébrés ont recours au système immunitaire inné et adaptatif pour combattre les pathogènes. La découverte des récepteurs Toll, il y a dix ans, a fortement augmenté l'intérêt porté à l'immunité innée. Depuis lors, des récepteurs intracellulaires tels que les membres de la famille RIG-like helicase (RLHs) et NOD-like receptor (NLRs) ont été décrits pour leur rôle dans la détection des pathogènes. L'interleukine-1 beta (IL-1β) est une cytokine pro-inflammatoire qui est synthétisée sous forme de précurseur, la proIL-1β. La proIL-1β requiert d'être clivée par la caspase-1 pour devenir active. La caspase-1 est elle-même activée par un complexe appelé inflammasome qui peut être formé par divers membres de la famille NLR. Plusieurs inflammasomes ont été décrits tels que le NALP3 inflammasome ou l'IPAF inflammasome. Dans cette étude nous avons identifié la co-chaperone SGT1 et la chaperone HSP90 comme partenaires d'interaction de NALP3. Ces deux protéines sont bien connues chez les plantes pour leurs rôles dans la régulation des gènes de résistance (gène R) qui sont structurellement apparentés à la famille NLR. Nous avons pu montrer que SGT1 et HSP90 jouent un rôle similaire dans la régulation de NALP3 et des protéines R. En effet, nous avons démontré que les deux protéines sont nécessaires pour l'activité du NALP3 inflammasome. De plus, la HSP90 est également requise pour la stabilité de NALP3. En se basant sur ces observations, nous avons proposé un modèle dans lequel SGT1 et HSP90 maintiennent NALP3 inactif mais prêt à percevoir un ligand activateur qui initierait la cascade inflammatoire. Nous avons également montré une interaction entre SGT1 et HSP90 avec plusieurs NLRs. Cette observation suggère qu'un mécanisme similaire pourrait être impliqué dans la régulation des membres de la famille des NLRs. Ces dernières années, plusieurs PAMPs mais également des DAMPs ont été identifiés comme activateurs du NALP3 inflammasome. Dans la seconde partie de cette étude, nous avons identifié la réponse au stress du réticulum endoplasmique (RE) comme nouvel activateur du NALP3 inflammasome. Cette réponse est initiée lors de l'accumulation dans le réticulum endoplasmique de protéines ayant une mauvaise conformation ce qui conduit, en autre, à l'arrêt de la synthèse de nouvelles protéines ainsi qu'une augmentation de la dégradation des protéines. Les mécanismes par lesquels la réponse du réticulum endoplasmique induit l'activation du NALP3 inflammasome doivent encore être déterminés. Summary : Vertebrates rely on the adaptive and the innate immune systems to fight pathogens. Awarness of the importance of the innate system increased with the identification of Toll-like receptors a decade ago. Since then, intracellular receptors such as the RIG-like helicase (RLH) and the NOD-like receptor (NLR) families have been described for their role in the recognition of microbes. Interleukin- 1ß (IL-1ß) is a key mediator of inflammation. This proinflammatory cytokine is synthesised as an inactive precursor that requires processing by caspase-1 to become active. Caspase-1 is, itself, activated in a complex termed the inflammasome that can be formed by members of the NLR family. Various inflammasome complexes have been described such as the IPAF and the NALP3 inflammasome. In this study, we have identified the co-chaperone SGT1 and the chaperone HSP90 as interacting partners of NALP3. SGT1 and HSP90 are both known for their role in the activity of plant resistance proteins (R proteins) which are structurally related to the NLR family. We have shown that HSP90 and SGT1 play a similar role in the regulation of NALP3 and in the regulation of plant R proteins. Indeed, we demonstrated that both HSP90 and SGT1 are essential for the activity of the NALP3 inflammasome complex. In addition, HSP90 is required for the stability of NALP3. Based on these observations, we have proposed a model in which SGT1 and HSP90 maintain NALP3 in an inactive but signaling-competent state, ready to receive an activating ligand that induces the inflammatory cascade. An interaction between several NLR members, SGTI and HSP90 was also shown, suggesting that similar mechanisms could be involved in the regulation of other NLRs. Several pathogen-associated molecular patterns (PAMPs) but also danger associated molecular patterns (DAMPs) have been identified as NALP3 activators. In the second part of this study, we have identified the ER stress response as a new NALP3 activator. The ER stress response is activated upon the accumulation of unfolded protein in the endoplasmic reticulum and results in a block in protein synthesis and increased protein degradation. The mechanisms of ER stress-mediated NALP3 activation remain to be determined.