Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: Towards the design of higher-affinity inhibitors

<p>Abstract</p> <p>Background</p> <p>DNA polymerase beta (pol beta), the error-prone DNA polymerase of single-stranded DNA break repair as well as base excision repair pathways, is overexpressed in several tumors and takes part in chemotherapeutic agent resistance, like that of cisplatin, through translesion synthesis. For this reason pol beta has become a therapeutic target. Several inhibitors have been identified, but none of them presents a sufficient affinity and specificity to become a drug. The fragment-based inhibitor design allows an important improvement in affinity of small molecules. The initial and critical step for setting up the fragment-based strategy consists in the identification and structural characterization of the first fragment bound to the target.</p> <p>Results</p> <p>We have performed docking studies of pamoic acid, a 9 micromolar pol beta inhibitor, and found that it binds in a single pocket at the surface of the 8 kDa domain of pol beta. However, docking studies provided five possible conformations for pamoic acid in this site. NMR experiments were performed on the complex to select a single conformation among the five retained. Chemical Shift Mapping data confirmed pamoic acid binding site found by docking while NOESY and saturation transfer experiments provided distances between pairs of protons from the pamoic acid and those of the 8 kDa domain that allowed the identification of the correct conformation.</p> <p>Conclusion</p> <p>Combining NMR experiments on the complex with docking results allowed us to build a three-dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta.</p

Enhancing remediation of residual DNAPL in multilayer aquifers: Post-injection of alcohol-surfactant-polymer mixtures

Although polymer-surfactant injection is an effective remediation technology for multilayer aquifers contaminated by Dense Non-Aqueous Phase Liquids (DNAPL), the existence of residual DNAPL after treatment is inevitable. This study evaluates the efficiency of the post-injection of alcohol-surfactant-polymer (ASP) mixtures containing 1-propanol/1-hexanol, sodium dodecylbenzenesulfonate (SDBS), and xanthan in enhancing remediation of residual DNAPL in layered systems. A range of experimental devices, including batch, rheological measurements, centimetric 1D column, and decametric 2D tank experiments, were employed. Batch experiments revealed that the inclusion of 1-hexanol swelled the DNAPL volume due to alcohol partitioning. Conversely, with only 1-propanol present in the alcohol-surfactant (AS) mixture, DNAPL dissolved in the aqueous phase. The co-presence of 1-hexanol along with 1-propanol in AS mixture favored 1-propanol's partitioning into the DNAPL phase. Column experiments, following primary xanthan-SDBS (XS) injections, demonstrated that ASP mixtures with 1-hexanol (regardless of presence of 1-propanol) underwent a mobilization mechanism. DNAPL appeared in the effluent as an organic phase after the post-injection of 0.3 pore-volumes (PV), by a reduction trend in its density. In contrast, mixtures with solely 1-propanol exhibited a solubilization mechanism, with DNAPL dissolving in the aqueous phase and emerging in the effluent after approximately 1 PV. 2D tank experiments visualized mobilization and solubilization mechanisms in multilayered systems. Post-injection of the ASP mixture with solely 1-propanol led to DNAPL solubilization, demonstrated by a dark zone of varied DNAPL concentrations, followed by a clearer white zone indicating significant DNAPL dissolution. Injecting ASP mixture containing both 1-propanol and 1-hexanol mobilized swollen DNAPL ganglia throughout layers, with these droplets coalescing and migrating to the recovery point. The darkness of mobilized droplets was faded as more DNAPL was recovered. The solubilization ASP mixture enhanced the recovery factor by 0.02 while the mobilization ASP mixture led to a 0.08 increase in the recovery factor

PDRs4All IV. An embarrassment of riches: Aromatic infrared bands in the Orion Bar

(Abridged) Mid-infrared observations of photodissociation regions (PDRs) are dominated by strong emission features called aromatic infrared bands (AIBs). The most prominent AIBs are found at 3.3, 6.2, 7.7, 8.6, and 11.2 $\mu$m. The most sensitive, highest-resolution infrared spectral imaging data ever taken of the prototypical PDR, the Orion Bar, have been captured by JWST. We provide an inventory of the AIBs found in the Orion Bar, along with mid-IR template spectra from five distinct regions in the Bar: the molecular PDR, the atomic PDR, and the HII region. We use JWST NIRSpec IFU and MIRI MRS observations of the Orion Bar from the JWST Early Release Science Program, PDRs4All (ID: 1288). We extract five template spectra to represent the morphology and environment of the Orion Bar PDR. The superb sensitivity and the spectral and spatial resolution of these JWST observations reveal many details of the AIB emission and enable an improved characterization of their detailed profile shapes and sub-components. While the spectra are dominated by the well-known AIBs at 3.3, 6.2, 7.7, 8.6, 11.2, and 12.7 $\mu$m, a wealth of weaker features and sub-components are present. We report trends in the widths and relative strengths of AIBs across the five template spectra. These trends yield valuable insight into the photochemical evolution of PAHs, such as the evolution responsible for the shift of 11.2 $\mu$m AIB emission from class B$_{11.2}$ in the molecular PDR to class A$_{11.2}$ in the PDR surface layers. This photochemical evolution is driven by the increased importance of FUV processing in the PDR surface layers, resulting in a "weeding out" of the weakest links of the PAH family in these layers. For now, these JWST observations are consistent with a model in which the underlying PAH family is composed of a few species: the so-called 'grandPAHs'.Comment: 25 pages, 10 figures, to appear in A&

PDRs4All III: JWST's NIR spectroscopic view of the Orion Bar

(Abridged) We investigate the impact of radiative feedback from massive stars on their natal cloud and focus on the transition from the HII region to the atomic PDR (crossing the ionisation front (IF)), and the subsequent transition to the molecular PDR (crossing the dissociation front (DF)). We use high-resolution near-IR integral field spectroscopic data from NIRSpec on JWST to observe the Orion Bar PDR as part of the PDRs4All JWST Early Release Science Program. The NIRSpec data reveal a forest of lines including, but not limited to, HeI, HI, and CI recombination lines, ionic lines, OI and NI fluorescence lines, Aromatic Infrared Bands (AIBs including aromatic CH, aliphatic CH, and their CD counterparts), CO2 ice, pure rotational and ro-vibrational lines from H2, and ro-vibrational lines HD, CO, and CH+, most of them detected for the first time towards a PDR. Their spatial distribution resolves the H and He ionisation structure in the Huygens region, gives insight into the geometry of the Bar, and confirms the large-scale stratification of PDRs. We observe numerous smaller scale structures whose typical size decreases with distance from Ori C and IR lines from CI, if solely arising from radiative recombination and cascade, reveal very high gas temperatures consistent with the hot irradiated surface of small-scale dense clumps deep inside the PDR. The H2 lines reveal multiple, prominent filaments which exhibit different characteristics. This leaves the impression of a "terraced" transition from the predominantly atomic surface region to the CO-rich molecular zone deeper in. This study showcases the discovery space created by JWST to further our understanding of the impact radiation from young stars has on their natal molecular cloud and proto-planetary disk, which touches on star- and planet formation as well as galaxy evolution.Comment: 52 pages, 30 figures, submitted to A&

PDRs4All II: JWST's NIR and MIR imaging view of the Orion Nebula

The JWST has captured the most detailed and sharpest infrared images ever taken of the inner region of the Orion Nebula, the nearest massive star formation region, and a prototypical highly irradiated dense photo-dissociation region (PDR). We investigate the fundamental interaction of far-ultraviolet photons with molecular clouds. The transitions across the ionization front (IF), dissociation front (DF), and the molecular cloud are studied at high-angular resolution. These transitions are relevant to understanding the effects of radiative feedback from massive stars and the dominant physical and chemical processes that lead to the IR emission that JWST will detect in many Galactic and extragalactic environments. Due to the proximity of the Orion Nebula and the unprecedented angular resolution of JWST, these data reveal that the molecular cloud borders are hyper structured at small angular scales of 0.1-1" (0.0002-0.002 pc or 40-400 au at 414 pc). A diverse set of features are observed such as ridges, waves, globules and photoevaporated protoplanetary disks. At the PDR atomic to molecular transition, several bright features are detected that are associated with the highly irradiated surroundings of the dense molecular condensations and embedded young star. Toward the Orion Bar PDR, a highly sculpted interface is detected with sharp edges and density increases near the IF and DF. This was predicted by previous modeling studies, but the fronts were unresolved in most tracers. A complex, structured, and folded DF surface was traced by the H2 lines. This dataset was used to revisit the commonly adopted 2D PDR structure of the Orion Bar. JWST provides us with a complete view of the PDR, all the way from the PDR edge to the substructured dense region, and this allowed us to determine, in detail, where the emission of the atomic and molecular lines, aromatic bands, and dust originate

A far-ultraviolet-driven photoevaporation flow observed in a protoplanetary disk

Most low-mass stars form in stellar clusters that also contain massive stars, which are sources of far-ultraviolet (FUV) radiation. Theoretical models predict that this FUV radiation produces photo-dissociation regions (PDRs) on the surfaces of protoplanetary disks around low-mass stars, impacting planet formation within the disks. We report JWST and Atacama Large Millimetere Array observations of a FUV-irradiated protoplanetary disk in the Orion Nebula. Emission lines are detected from the PDR; modelling their kinematics and excitation allows us to constrain the physical conditions within the gas. We quantify the mass-loss rate induced by the FUV irradiation, finding it is sufficient to remove gas from the disk in less than a million years. This is rapid enough to affect giant planet formation in the disk

Ateliers genre et queer : un compte-rendu

Nous revenons sur les ateliers « Ce que le genre fait à l’histoire de l’art » et « Pour une histoire de l’art queer », ces deux ateliers ont pris place dans le cadre du congrès Rotondes organisé par l’IHNA les 21 et 22 octobre 2021. Le premier a été animé par Eva Belgherbi (École du Louvre - Université de Poitiers), Justine Bohbote (élève conservatrice du patrimoine) et Julie Botte (Université Sorbonne Nouvelle - Paris 3). Le second est animé par Marion Cazaux (Université de Pau et des Pays d..

Queer : entre esthétique et politique

Carnet hypothèses du collectif ARQhttps://arqueer.hypotheses.org/39

Rosa Bonheur : une lesbienne au placard ?

MHKZOhttps://mhkzo.com/portfolio/article-rosa-bonheur-une-lesbienne-au-placard

Le travestissement comme imposture du genre ?

International audienc