Numerical Groundwater Model to Assess the Fate of Nitrates in the Coastal Aquifer of Arborea (Sardinia, Italy)

The Arborea plain in Sardinia (Italy) is classified as a nitrate vulnerable zone (NVZ). In the present study, the individual work steps that are necessary to progress from the existing 3D hydrogeological model to a 3D numerical groundwater model using the interactive finite-element simulation system FEFLOW 7.4 are shown. The results of the transient flow model highlight the influence of the drainage network on the overall groundwater management: the total water volume drained by the ditches accounted for approximately 58% of the annual outflow volume. The numerical transport simulations conducted from 2012 to 2020 using hypothetical field-based nitrate input scenarios globally underestimated the high concentrations that were observed in the NVZ. However, as observed in the field, the computed nitrate concentrations in December 2020 still varied strongly in space, from several mg L−1 to several hundreds of mg L−1. The origin of these remaining local hotspots is not yet known. The modeling of rainfall fluctuations under the influence of climate change revealed a general long-term decline in the groundwater level of several tens of centimeters in the long term and, in conjunction with a zero-nitrate scenario, led to a significant decrease in nitrate pollution. Although hotspots were attenuated, the concentrations at several monitoring wells still exceeded the limit value of 50 mg L−1

A perfect palindrome in the Escherichia coli chromosome forms DNA hairpins on both leading- and lagging-strands

DNA palindromes are hotspots for DNA double strand breaks, inverted duplications and intra-chromosomal translocations in a wide spectrum of organisms from bacteria to humans. These reactions are mediated by DNA secondary structures such as hairpins and cruciforms. In order to further investigate the pathways of formation and cleavage of these structures, we have compared the processing of a 460 base pair (bp) perfect palindrome in the Escherichia coli chromosome with the same construct interrupted by a 20 bp spacer to form a 480 bp interrupted palindrome. We show here that the perfect palindrome can form hairpin DNA structures on the templates of the leading- and lagging-strands in a replication-dependent reaction. In the presence of the hairpin endonuclease SbcCD, both copies of the replicated chromosome containing the perfect palindrome are cleaved, resulting in the formation of an unrepairable DNA double-strand break and cell death. This contrasts with the interrupted palindrome, which forms a hairpin on the lagging-strand template that is processed to form breaks, which can be repaired by homologous recombination

Regulation and Role of Arabidopsis CUL4-DDB1A-DDB2 in Maintaining Genome Integrity upon UV Stress

Plants use the energy in sunlight for photosynthesis, but as a consequence are exposed to the toxic effect of UV radiation especially on DNA. The UV-induced lesions on DNA affect both transcription and replication and can also have mutagenic consequences. Here we investigated the regulation and the function of the recently described CUL4-DDB1-DDB2 E3 ligase in the maintenance of genome integrity upon UV-stress using the model plant Arabidopsis. Physiological, biochemical, and genetic evidences indicate that this protein complex is involved in global genome repair (GGR) of UV-induced DNA lesions. Moreover, we provide evidences for crosstalks between GGR, the plant-specific photo reactivation pathway and the RAD1-RAD10 endonucleases upon UV exposure. Finally, we report that DDB2 degradation upon UV stress depends not only on CUL4, but also on the checkpoint protein kinase Ataxia telangiectasia and Rad3-related (ATR). Interestingly, we found that DDB1A shuttles from the cytoplasm to the nucleus in an ATR-dependent manner, highlighting an upstream level of control and a novel mechanism of regulation of this E3 ligase

Identification and Characterization of Alternative Promoters, Transcripts and Protein Isoforms of Zebrafish R2 Gene

Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the de novo synthesis of deoxyribonucleoside triphosphates. Expression of RNR subunits is closely associated with DNA replication and repair. Mammalian RNR M2 subunit (R2) functions exclusively in DNA replication of normal cells due to its S phase-specific expression and late mitotic degradation. Herein, we demonstrate the control of R2 expression through alternative promoters, splicing and polyadenylation sites in zebrafish. Three functional R2 promoters were identified to generate six transcript variants with distinct 5′ termini. The proximal promoter contains a conserved E2F binding site and two CCAAT boxes, which are crucial for the transcription of R2 gene during cell cycle. Activity of the distal promoter can be induced by DNA damage to generate four transcript variants through alternative splicing. In addition, two novel splice variants were found to encode distinct N-truncated R2 isoforms containing residues for enzymatic activity but no KEN box essential for its proteolysis. These two N-truncated R2 isoforms remained in the cytoplasm and were able to interact with RNR M1 subunit (R1). Thus, our results suggest that multilayered mechanisms control the differential expression and function of zebrafish R2 gene during cell cycle and under genotoxic stress

(Photo)physical properties of new molecular glasses end-capped with thiophene rings composed of diimide and imine units

New symmetrical arylene bisimide derivatives formed by using electron-donating-electron-accepting systems were synthesized. They consist of a phthalic diimide or naphthalenediimide core and imine linkages and are end-capped with thiophene, bithiophene, and (ethylenedioxy)thiophene units. Moreover, polymers were obtained from a new diamine, N,N′-bis(5- aminonaphthalenyl)naphthalene-1,4,5,8-dicarboximide and 2,5- thiophenedicarboxaldehyde or 2,2′-bithiophene-5,5′-dicarboxaldehyde. The prepared azomethine diimides exhibited glass-forming properties. The obtained compounds emitted blue light with the emission maximum at 470 nm. The value of the absorption coefficient was determined as a function of the photon energy using spectroscopic ellipsometry. All compounds are electrochemically active and undergo reversible electrochemical reduction and irreversible oxidation processes as was found in cyclic voltammetry and differential pulse voltammetry (DPV) studies. They exhibited a low electrochemically (DPV) calculated energy band gap (Eg) from 1.14 to 1.70 eV. The highest occupied molecular orbital and lowest unoccupied molecular orbital levels and Eg were additionally calculated theoretically by density functional theory at the B3LYP/6-31G(d,p) level. The photovoltaic properties of two model compounds as the active layer in organic solar cells in the configuration indium tin oxide/poly(3,4-(ethylenedioxy)thiophene):poly(styrenesulfonate)/active layer/Al under an illumination of 1.3 mW/cm2 were studied. The device comprising poly(3-hexylthiophene) with the compound end-capped with bithiophene rings showed the highest value of Voc (above 1 V). The conversion efficiency of the fabricated solar cell was in the range of 0.69-0.90%

Geochemical modeling of isotopic fractionation : implementation in reactive transport code Hytec and environmental applications

L’éventail des processus géochimiques modélisés par les codes de transport réactif a vocation à s’élargir de plus en plus et permet à ces codes de traiter des problématiques de nature différente (stockage de déchets radioactifs, exploitation minière, pollutions, etc.). Cette dernière décennie a vu l’essor de la modélisation des fractionnements isotopiques par les codes de transport réactif. Cette fonctionnalité permet d’ajouter au suivi de réactions géochimiques leur impact sur la composition isotopique des espèces chimiques. Néanmoins, l’hypothèse classiquement utilisée lors de ces modélisations repose sur l’existence d’un isotope majoritaire au sein des isotopes de l’élément d’intérêt. Ces travaux menés à MINES ParisTech contiennent les développements mathématiques réalisés afin de vérifier que la méthodologie reste valide pour un ensemble d’hypothèses moins contraignantes, vérifiées dans la majorité des systèmes naturels. Plusieurs applications ont été réalisées avec Hytec, code de transport réactif développé à MINES ParisTech. La comparaison de résultats dans le cadre d’un benchmark a permis de valider l’emploi de cette méthodologie avec Hytec. Ensuite, un modèle de dégradation et de migration de solvants chlorés dans un système aquifère-aquitard a été mis au point et permet de simuler les signatures isotopiques du carbone et du chlore au sein de ces composés. Les résultats ont montré que le suivi de la composition isotopique des solvants dans l’aquifère peut renseigner sur leur potentielle dégradation dans l’aquitard. Par ailleurs, ces travaux montrent l’importance de la configuration du modèle numérique utilisé ainsi que le potentiel offert par la modélisation des fractionnements isotopiques combinée à la polyvalence d’Hytec.The scope of geochemical processes modeled by reactive transport codes is widening and allows these codes to address different type of problematics (radioactive waste storage, mining, contamination, etc.). The last decade saw the rise of the isotopic fractionation modeling with reactive transport codes. This functionality allows tracing geochemical processes in amore precise way, using geochemical reactions and the isotopic fractionation they induce. However, the traditionally used hypothesis to model isotopic fractionation relies on the existence of a major isotope for the studied element. This work, prepared at MINES ParisTech, contains mathematical developments to support the methodology a set of less constraining hypotheses, easily verified in the majority of natural systems. Several application cases were performed with Hytec, are active transport code developed at MINES ParisTech. The comparison of isotopic fractionation simulation results in a benchmark study acts as a validation of this methodology with Hytec.Then, a model of degradation and migration of chlorinated solvents in an aquifer-aquitard system was built step by step. This model allows simulating the isotopic signatures of carbon and chlorine in these components. Results showed that data extracted from the aquifer brings information about the reactivity of the aquitard regarding the solvent degradation. Furthermore, results also highlight the importance of the choice of model parameters and the potential of isotopic fractionation modeling combined to theversatility of Hytec

Molecular engeneering of new conjugated systems for nonlinear optics,Multiphoton absorption and thermotropic polymorphism

Nous présentons dans ce travail la conception, la synthèse et les caractérisations photo-physiques et physico-chimiques de matériaux conjugués polyfonctionnels de type donneurs-donneurs , optimisés à la fois pour l'absorption multiphotonique et pour l'obtention d'un riche polymorphisme thermotrope. Ainsi, nous avons développé une nouvelle stratégie de synthèse modulaire axée sur la préparation de briques élémentaires conjuguées et solubles dans les solvants organiques usuels. Une fois ces briques élémentaires synthétisées, nous avons obtenu rapidement et efficacement par couplage croisé des séries de chromophores organiques uni-, bi- et tri-dimensionnels ayant des sous-structures à motifs uniques de type oligophénylène, oligophénylène-vinylène, oligophénylène-éthynylène, ainsi que des chromophores unidimensionnels à motifs mixtes. En association avec une étude théorique des propriétés d'absorption à deux photons par modélisation, cette approche synthétique nous a permis d'étudier l'influence de variations structurales minimes sur l'efficacité d'absorption à deux photons. Dans le cas des chromophores unidimensionnels nous introduisons la notion de dissymétrie, soit du système conjugué, soit des groupements terminaux donneurs. Nous proposons également une alternative au concept classique du chromophore unidimensionnel pour l'absorption à deux photons, en introduisant la notion de dimensionnalité coopérative. Enfin, nous avons étudié l'influence de l'augmentation progressive de l'anisotropie sur des systèmes mésomorphes symétriques et dissymétriques. Nous avons mis en évidence un polymorphisme thermodynamiquement stable et riche (mésophases lamellaire, colonnaire et cubique), voire atypique (mésophase tétragonale). Des modèles de l'organisation moléculaire au sein des phases sont proposés sur la base de résultats issus des études de diffraction des rayons X aux petits angles de Bragg.We report on the conception, synthesis, photo-physical and physicochemical characterizations of  push-push  polyfunctional conjugated materials optimised for multiphoton absorption and for a rich thermotropic polymorphism. So, we developed a new modular synthetic strategy centred on the preparation of conjugated building blocks which are soluble in usual organic solvents. By cross-coupling reaction, series of one-, two- and three-dimensional organic chromophores were obtained quickly and efficiently. Chromophores have oligophenylene, oligophenylenevinylene, oligophenyleneacetylene sub-structures or mixed motives. In association with a theoretical study of the two-photon absorption properties, this synthetic approach allowed us to study the influence of little structural modifications on the two-photon absorption efficiency. We present also a new conception of the one-dimensional chromophore, by introducing the notion of dissymmetry either of conjugated system or of the terminal donor groups. In addition we propose an alternative to the classical concept of the one-dimensional chromophores commonly used in non-linear optics, by introducing the notion of cooperative dimensionality. Finally, we have studied the influence of progressive increase of the anisotropy on symmetric and asymmetric mesomorphic systems. We have evidenced a rich and thermodynamically stable polymorphism (lamellar, columnar and cubic phases), even unusual (tetragonal mesophase). Models for the molecular organization within the mesophases are proposed on the basis of small Bragg angle X-ray diffraction studies

Molecular engeneering of new conjugated systems for nonlinear optics,Multiphoton absorption and thermotropic polymorphism

Nous présentons dans ce travail la conception, la synthèse et les caractérisations photo-physiques et physico-chimiques de matériaux conjugués polyfonctionnels de type donneurs-donneurs , optimisés à la fois pour l'absorption multiphotonique et pour l'obWe report on the conception, synthesis, photo-physical and physicochemical characterizations of  push-push  polyfunctional conjugated materials optimised for multiphoton absorption and for a rich thermotropic polymorphism. So, we developed a new modula