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.

The immunological synapse and actin assembly: a regulatory role for PKC theta.

Engagement of the T cell receptor leads to the accumulation of filamentous actin, which is necessary for the formation of the immunological synapse and subsequent T cell activation. In the December issue of Molecular Cell, Sasahara et al. provide new insights into the link between the T cell receptor and actin assembly in the immunological synapse, and reveal a critical regulatory role for PKC theta in this process.

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Regulation of horizontal gene transfer of the catabolic island ICEclc

ICEclc is a mobile genetic element found in two copies on the chromosome of the bacterium Pseudomonas knackmussii B13. ICEclc harbors genes encoding metabolic pathways for the degradation of chlorocatechols (CLC) and 2-aminophenol (2AP). At low frequencies, ICEclc excises from the chromosome, closes into a circular DNA molecule which can transfer to another bacterium via conjugation. Once in the recipient cell, ICEclc can reintegrate into the chromosome by site-specific recombination. This thesis aimed at identifying the regulatory network underlying the decisions for ICEclc horizontal transfer (HGT). The first chapter is an introduction on integrative and conjugative elements (ICEs) more in general, of which ICEclc is one example. In particular I emphasized the current knowledge of regulation and conjugation machineries of the different classes of ICE. In the second chapter, I describe a transcriptional analysis using microarrays and other experiments to understand expression of ICEclc in exponential and stationary phase. By overlaying transcriptomic profiles with Northern hybridizations and RT- PCR data, we established a transcription map for the entire core region of ICEclc, a region assumed to encode the ICE conjugation process. We also demonstrated how transcription of the ICEclc core is maximal in stationary phase, which correlates to expression of reporter genes fused to key ICEclc promoters. In the third chapter, I present a transcriptome analysis of ICEclc in a variety of different host species, in order to explore whether there are species-specific differences. In the fourth chapter, I focus on the role of a curious ICEclc-encoded TetR-type transcriptional repressor. We find that this gene, which we name mfsR, not only controls its own expression but that of a set of genes for a putative multi-drug efflux pump (mfsABC) as well. By using a combination of biochemical and molecular biology techniques, I could show that MfsR specifically binds to operator boxes in two ICEclc promoters (PmfsR and PmfsA), inhibiting the transcription of both the mfsR and mfsABC-orf38184 operons. Although we could not detect a clear phenotype of an mfsABC deletion, we discuss the implications of pump gene reorganizations in ICEclc and close relatives. In the fifth chapter, we find that mfsR not only controls its own expression and that of the mfsABC operon, but is also indirectly controlling ICEclc transfer. Using gene deletions, microarrays, transfer assays and microscopy-based reporter fusions, we demonstrate that mfsR actually controls a small operon of three regulatory genes. The last gene of this mfsR operon, orf17162, encodes a LysR-type activator that when deleted strongly impairs ICEclc transfer. Interestingly, deletion of mfsR leads to transfer competence in almost all cells, thereby overruling the bistability process in the wild-type. In the final sixth chapter, I discuss the relevance of the present thesis and the resulting perspectives for future studies.

Promoter architecture of mouse olfactory receptor genes.

Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice.

Regulation of the Gac/Rsm pathway in "Pseudomonas fluorescens" CHA0

SUMMARY : Two-component systems are key mediators implicated in the response of numerous bacteria to a wide range of signals and stimuli. The two-component system comprised of the sensor kinase GacS and the response regulator GacA is broadly distributed among γ-proteobacteria bacteria and fulfils diverse functions such as regulation of carbon storage and expression of virulence. In Pseudomonas fluorescens, a soil bacterium which protects plants from root-pathogenic fungi and nematodes, the GacS/GacA two-component system has been shown to be essential for the production of secondary metabolites and exoenzymes required for the biocontrol activity of the bacterium. The regulatory cascade initiated by GacS/GacA consists of two translational repressor proteins, RsmA and RsmE, as well as three GacAcontrolled small regulatory RNAs RsmX, RsmY and RsmZ, which titrate RsmA and RsmE to allow the expression of biocontrol factors. Genetic analysis revealed that two additional sensor kinases termed RetS and Lads were involved as negative and positive control elements, respectively, in the Gac/Rsm pathway in P. fluoresens CHAO. Furthermore, it could be proposed that RetS and Lads interact with GacS, thereby modulating the expression of antibiotic compounds and hydrogen cyanide, as well as the rpoS gene encoding the stress and stationary phase sigma factor σ. Temperature was found to be an important environmental cue that influences the Gac/Rsm network. Indeed, the production of antibiotic compounds and hydrogen cyanide was reduced at 35°C, by comparison with the production at 30°C. RetS was identified to be involved in this temperature control. The small RNA RsmY was confirmed to be positively regulated by GacA and RsmA/RsmE. Two essential regions were identified in the rsmY promoter by mutational analysis, the upstream activating sequence (UAS) and the linker sequence. Although direct experimental evidence is still missing, several observations suggest that GacA may bind to the UAS, whereas the linker region would be recognized by intermediate RsmA/RsmEdependent repressors and/or activators. In conclusion, this work has revealed new elements contributing to the function of the signal transduction mechanisms in the Gac/Rsm pathway. RESUME : Les systèmes ä deux composants sont des mécanismes d'une importance notoire que beaucoup de bactéries utilisent pour faire face et répondre aux stimuli environnementaux. Le système à deux composants comprenant le senseur GacS et le régulateur de réponse GacA est très répandu chez les γ-protéobactéries et remplit des fonctions aussi diverses que la régulation du stockage de carbone ou l'expression de la virulence. Chez Pseudomonas fluorescens CHAO, une bactérie du sol qui protège les racines des plantes contre des attaques de champignons et nématodes pathogènes, le système à deux composants GacS/GacA est essentiel à la production de métabolites secondaires et d'exoenzymes requis pour l'activité de biocontrôle de la bactérie. La cascade régulatrice initiée pas GacS/GacA fait intervenir deux protéines répresseur de traduction, RsmA et RsmE, ainsi que trois petits ARNs RsmX, RsmY et RsmZ, dont la production est contrôlée par GacA. Ces petits ARNs ont pour rôle de contrecarrer l'action des protéines répressseur de la traduction, ce qui permet l'expression de facteurs de biocontrôle. Des analyses génétiques ont révélé la présence de deux senseurs supplémentaires, appelés Rets et Lads, qui interviennent dans la cascade Gac/Rsm de P. fluorescens. L'impact de ces senseurs est, respectivement, négatif et positif. Ces interactions ont apparenunent lieu au niveau de GacS et permettent une modulation de l'expression des antibiotiques et de l'acide cyanhydrique, ainsi que du gène rpoS codant pour le facteur sigma du stress. La température s'est révélée être un facteur environnemental important qui influence la cascade Gac/Rsm. Il s'avère en effet que la production d'antibiotiques ainsi que d'acide cyanhydrique est moins importante à 35°C qu'à 30°C. L'implication du senseur Rets dans ce contrôle par la température a pu être démontrée. La régulation positive du petit ARN RsmY par GacA et RsmA/RsmE a pu être confirmée; par le biais d'une analyse mutationelle, deux régions essentielles ont pu être mises en évidence dans la région promotrice de rsmY. Malgré le manque de preuves expérimentales directes, certains indices suggèrent que GacA puisse directement se fixer sur une des deux régions (appelée UAS), tandis que la deuxième région (appelée linker) serait plutôt reconnue par des facteurs intermédiaires (activateurs ou répresseurs) dépendant de RsmA/RsmE. En conclusion, ce travail a dévoilé de nouveaux éléments permettant d'éclairer les mécanismes de transduction des signaux dans la cascade Gac/Rsm.

Human invariant V alpha 24-J alpha Q TCR supports the development of CD1d-dependent NK1.1+ and NK1.1- T cells in transgenic mice.

A sizable fraction of T cells expressing the NK cell marker NK1.1 (NKT cells) bear a very conserved TCR, characterized by homologous invariant (inv.) TCR V alpha 24-J alpha Q and V alpha 14-J alpha 18 rearrangements in humans and mice, respectively, and are thus defined as inv. NKT cells. Because human inv. NKT cells recognize mouse CD1d in vitro, we wondered whether a human inv. V alpha 24 TCR could be selected in vivo by mouse ligands presented by CD1d, thereby supporting the development of inv. NKT cells in mice. Therefore, we generated transgenic (Tg) mice expressing the human inv. V alpha 24-J alpha Q TCR chain in all T cells. The expression of the human inv. V alpha 24 TCR in TCR C alpha(-/-) mice indeed rescues the development of inv. NKT cells, which home preferentially to the liver and respond to the CD1d-restricted ligand alpha-galactosylceramide (alpha-GalCer). However, unlike inv. NKT cells from non-Tg mice, the majority of NKT cells in V alpha 24 Tg mice display a double-negative phenotype, as well as a significant increase in TCR V beta 7 and a corresponding decrease in TCR V beta 8.2 use. Despite the forced expression of the human CD1d-restricted TCR in C alpha(-/-) mice, staining with mCD1d-alpha-GalCer tetramers reveals that the absolute numbers of peripheral CD1d-dependent T lymphocytes increase at most by 2-fold. This increase is accounted for mainly by an increased fraction of NK1.1(-) T cells that bind CD1d-alpha-GalCer tetramers. These findings indicate that human inv. V alpha 24 TCR supports the development of CD1d-dependent lymphocytes in mice, and argue for a tight homeostatic control on the total number of inv. NKT cells. Thus, human inv. V alpha 24 TCR-expressing mice are a valuable model to study different aspects of the inv. NKT cell subset.

Selective absence of CD8+ TCRalpha beta+ intestinal epithelial cells in transgenic mice expressing beta2-microglobulin-associated ligands exclusively on thymic cortical epithelium.

Whereas interactions between the TCRalpha beta and self MHC:peptide complexes are clearly required for positive selection of mature CD4(+) and CD8(+) T cells during intrathymic development, the role of self or foreign ligands in maintaining the peripheral T cell repertoire is still controversial. In this report we have utilized keratin 14-beta2-microglobulin (K14-beta2m)-transgenic mice expressing beta2m-associated ligands exclusively on thymic cortical epithelial cells to address the possible influence of TCR:ligand interactions in peripheral CD8(+) T cell homeostasis. Our data indicate that CD8(+) T cells in peripheral lymphoid tissues are present in normal numbers in the absence of self MHC class I:peptide ligands. Surprisingly, however, steady state homeostasis of CD8(+) T cells in the intestinal epithelium is severely affected by the absence of beta2m-associated ligands. Indeed TCRalpha beta(+) IEL subsets expressing CD8alpha beta or CD8alpha alpha are both dramatically reduced in K14-beta2m mice, suggesting that the development, survival or expansion of CD8(+) IEL depends upon interaction of the TCR with MHC class I:peptide or other beta2m-associated ligands elsewhere than on thymic cortical epithelium. Collectively, our data reveal an unexpected difference in the regulation of CD8(+) T cell homeostasis by beta2m-associated ligands in the intestine as compared to peripheral lymphoid organs.

Having Your Cake and Eating It, Too: Can Regulatory Agencies Be Both Independent and Accountable?

Independent regulatory agencies (IRAs) were created in various sectors and on different governmental levels to implement liberalization policies. This paper investigates the link between IRAs' independence, which is said to promote regulatory credibility and the use of technical expertise, and their accountability, which is related to the need for controlling and legitimizing independent regulators. The literature on the regulatory state anticipates a positive relation between the independence and accountability of IRAs, but systematic empirical evidence is still lacking. To tackle this question, this paper measures and compares the independence and the accountability of IRAs in three differentially liberalized sectors in Switzerland (telecommunications, electricity and railways). With the application of Social Network Analysis, this piece of research shows that IRAs can be de facto independent and accountable at the same time, but the two features do not necessarily co-evolve in the same direction.

Malignant transformation of DMBA/TPA-induced papillomas and nevi in the skin of mice selectively lacking retinoid-X-receptor alpha in epidermal keratinocytes.

Retinoid-X-receptor alpha (RXRalpha), a member of the nuclear receptor (NR) superfamily, is a ligand-dependent transcriptional regulatory factor. It plays a crucial role in NR signalling through heterodimerization with some 15 NRs. We investigated the role of RXRalpha and its partners on mouse skin tumor formation and malignant progression upon topical DMBA/TPA treatment. In mutants selectively ablated for RXRalpha in keratinocytes, epidermal tumors increased in size and number, and frequently progressed to carcinomas. As keratinocyte-selective peroxisome proliferator-activated receptor gamma (PPARgamma) ablation had similar effects, RXRalpha/PPARgamma heterodimers most probably mediate epidermal tumor suppression. Keratinocyte-selective RXRalpha-null and vitamin-D-receptor null mice also exhibited more numerous dermal melanocytic growths (nevi) than control mice, but only nevi from RXRalpha mutant mice progressed to invasive human-melanoma-like tumors. Distinct RXRalpha-mediated molecular events appear therefore to be involved, in keratinocytes, in cell-autonomous suppression of epidermal tumorigenesis and malignant progression, and in non-cell-autonomous suppression of nevi formation and progression. Our study emphasizes the crucial role of keratinocytes in chemically induced epidermal and melanocytic tumorigenesis, and raises the possibility that they could play a similar role in UV-induced tumorigenesis, notably in nevi formation and progression to melanoma.

L'exploitation des eaux souterraines en Syrie centrale : construction de diagnostics et politiques d'intervention

Syrian dry areas have been for several millennia a place of interaction between human populations and the environment. If environmental constraints and heterogeneity condition the human occupation and exploitation of resources, socio-political, economic and historical elements play a fundamental role. Since the late 1980s, Syrian dry areas are viewed as suffering a serious water crisis, due to groundwater overdraft. The Syrian administration and international development agencies believe that groundwater overexploitation is also leading to a decline of agricultural activities and to poverty increase. Action is thus required to address these problems.However, the overexploitation diagnosis needs to be reviewed. The overexploitation discourse appears in the context of Syria's opening to international organizations and to the market economy. It echoes the international discourse of "global water crisis". The diagnosis is based on national indicators recycling old Soviet data that has not been updated. In the post-Soviet era, the Syrian national water policy seems to abandon large surface water irrigation projects in favor of a strategy of water use rationalization and groundwater conservation in crisis regions, especially in the district of Salamieh.This groundwater conservation policy has a number of inconsistencies. It is justified for the administration and also probably for international donors, since it responds to an indisputable environmental emergency. However, efforts to conserve water are anecdotal or even counterproductive. The water conservation policy appears a posteriori as an extension of the national policy of food self-sufficiency. The dominant interpretation of overexploitation, and more generally of the water crisis, prevents any controversary approach of the status of resources and of the agricultural system in general and thus destroys any attempt to discuss alternatives with respect to groundwater management, allocation, and their inclusion in development programs.A revisited diagnosis of the situation needs to take into account spatial and temporal dimensions of the groundwater exploitation and to analyze the co-evolution of hydrogeological and agricultural systems. It should highlight the adjustments adopted to cope with environmental and economic variability, changes of water availability and regulatory measures enforcements. These elements play an important role for water availability and for the spatial, temporal, sectoral allocation of water resource. The groundwater exploitation in the last century has obviously had an impact on the environment, but the changes are not necessarily catastrophic.The current groundwater use in central Syria increases the uncertainty by reducing the ability of aquifers to buffer climatic changes. However, the climatic factor is not the only source of uncertainty. The high volatility of commodity prices, fuel, land and water, depending on the market but also on the will (and capacity) of the Syrian State to preserve social peace is a strong source of uncertainty. The research should consider the whole range of possibilities and propose alternatives that take into consideration the risks they imply for the water users, the political will to support or not the local access to water - thus involving a redefinition of the economic and social objectives - and finally the ability of international organizations to reconsider pre-established diagnoses.