Deciphering structure-activity relationships in a series of Tat/TAR inhibitors

A series of pentameric “Polyamide Amino Acids” (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC₅₀ ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.     

4 in 1: Antibody‐free protocol for isolating the main hepatic cells from healthy and cirrhotic single rat livers

Liver cells isolated from pre‐clinical models are essential tools for studying liver (patho)physiology, and also for screening new therapeutic options. We aimed at developing a new antibody‐free isolation method able to obtain the four main hepatic cell types (hepatocytes, liver sinusoidal endothelial cells [LSEC], hepatic macrophages [HMΦ] and hepatic stellate cells [HSC]) from a single rat liver. Control and cirrhotic (CCl₄ and TAA) rat livers (n = 6) were perfused, digested with collagenase and mechanically disaggregated obtaining a multicellular suspension. Hepatocytes were purified by low revolution centrifugations while non‐parenchymal cells were subjected to differential centrifugation. Two different fractions were obtained: HSC and mixed LSEC + HMΦ. Further LSEC and HMΦ enrichment was achieved by selective adherence time to collagen‐coated substrates. Isolated cells showed high viability (80%‐95%) and purity (>95%) and were characterized as functional: hepatocytes synthetized albumin and urea, LSEC maintained endocytic capacity and in vivo fenestrae distribution, HMΦ increased expression of inflammatory markers in response to LPS and HSC were activated upon in vitro culture. The 4 in 1 protocol allows the simultaneous isolation of highly pure and functional hepatic cell sub‐populations from control or cirrhotic single livers without antibody selection.     

Inverse Optical Cavity Design for Ultrabroadband Light Absorption Beyond the Conventional Limit in Low‐Bandgap Nonfullerene Acceptor–Based Solar Cells

In the subwavelength regime, several nanophotonic configurations have been proposed to overcome the conventional light trapping or light absorption enhancement limit in solar cells also known as the Yablonovitch limit. It has been recently suggested that establishing such limit should rely on computational inverse electromagnetic design instead of the traditional approach combining intuition and a priori known physical effect. In the present work, by applying an inverse full wave vector electromagnetic computational approach, a 1D nanostructured optical cavity with a new resonance configuration is designed that provides an ultrabroadband (≈450 nm) light absorption enhancement when applied to a 107 nm thick active layer organic solar cell based on a low‐bandgap (1.32 eV) nonfullerene acceptor. It is demonstrated computationally and experimentally that the absorption enhancement provided by such a cavity surpasses the conventional limit resulting from an ergodic optical geometry by a 7% average over a 450 nm band and by more than 20% in the NIR. In such a cavity configuration the solar cells exhibit a maximum power conversion efficiency above 14%, corresponding to the highest ever measured for devices based on the specific nonfullerene acceptor used.     

Comprehensive structure-activity-relationship of azaindoles as highly potent FLT3 inhibitors

Acute myeloid leukemia (AML) is characterized by fast progression and low survival rates, in which Fms-like tyrosine kinase 3 (FLT3) receptor mutations have been identified as a driver mutation in cancer progression in a subgroup of AML patients. Clinical trials have shown emergence of drug resistant mutants, emphasizing the ongoing need for new chemical matter to enable the treatment of this disease. Here, we present the discovery and topological structure-activity relationship (SAR) study of analogs of isoquinolinesulfonamide H-89, a well-known PKA inhibitor, as FLT3 inhibitors. Surprisingly, we found that the SAR was not consistent with the observed binding mode of H-89 in PKA. Matched molecular pair analysis resulted in the identification of highly active sub-nanomolar azaindoles as novel FLT3-inhibitors. Structure based modelling using the FLT3 crystal structure suggested an alternative, flipped binding orientation of the new inhibitors.     

Capsular arabinomannans from Mycobacterium avium with morphotype-specific structural differences but identical biological activity

The capsules of two colony morphotypes of Mycobacterium avium strain 2151 were investigated, i.e. the virulent smooth-transparent (SmT1) and the nonvirulent smooth-opaque (SmO) types. From both morphotypes we separated a nonacylated arabinomannan (AM) from an acylated polysaccharide fraction by affinity chromatography, of which the AMs were structurally characterized. The AMs from the virulent morphotype, in contrast to that from the nonvirulent form, possessed a larger mannan chain and a shorter arabinan chain. Incubation of murine bone marrow-derived macrophages and human dendritic cells showed that the acylated polysaccharide fractions were potent inducers of tumor necrosis factor-alpha, interleukin-12, and interleukin-10 compared with nonacylated AMs, which led to only a marginal cytokine release. Further in vitro experiments showed that both the acylated polysaccharide fractions and the nonacylated AMs were able to induce in vitro anti-tumor cytotoxicity of human peripheral blood mononuclear cells. Thus, morphotype-specific structural differences in the capsular AMs of M. avium do not correlate with biological activity; however, their acylation is a prerequisite for effective stimulation of murine macrophages and human dendritic cells.     

Using unmanned aerial vehicle‐based multispectral,RGB and thermal imagery for phenotyping of forest genetic trials: A case study in Pinus halepensis

The assessment of genetic differentiation in functional traits is fundamental towards understanding the adaptive characteristics of forest species. While traditional phenotyping techniques are costly and time‐consuming, remote sensing data derived from cameras mounted on unmanned aerial vehicles (UAVs) provide potentially valid high‐throughput information for assessing morphophysiological differences among tree populations. In this work, we test for genetic variation in vegetation indices (VIs) and canopy temperature among populations of Pinus halepensis as proxies for canopy architecture, leaf area, photosynthetic pigments, photosynthetic efficiency and water use. The interpopulation associations between vegetation properties and above‐ground growth (stem volume) were also assessed. Three flights (July 2016, November 2016 and May 2017) were performed in a genetic trial consisting of 56 populations covering a large part of the species range. Multispectral (visible and near infrared wavelengths), RGB (red, green, blue) and thermal images were used to estimate canopy temperature and vegetation cover (VC) and derive several VIs. Differences among populations emerged consistently across flights for VC and VIs related to leaf area, indicating genetic divergence in crown architecture. Population differences in indices related to photosynthetic pigments emerged only in May 2017 and were probably related to a contrasting phenology of needle development. Conversely, the low population differentiation for the same indices in July 2016 and November 2016 suggested weak interpopulation variation in the photosynthetic machinery of mature needles of P. halepensis. Population differences in canopy temperature found in July 2016 were indicative of variation in stomatal regulation under drought stress. Stem volume correlated with indices related to leaf area (positively) and with canopy temperature (negatively), indicating a strong influence of canopy properties and stomatal conductance on above‐ground growth at the population level. Specifically, a combination of VIs and canopy temperature accounted for about 60% of population variability in stem volume of adult trees. This is the first study to propose UAV remote sensing as an effective tool for screening genetic variation in morphophysiological traits of adult forest trees.     

Direct and indirect impacts of wildfire on faunal communities of Mediterranean temporary ponds

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Preliminary studies of the 2D crystallization of Omp1 of Serratia marcescens: observation by atomic force microscopy in native membranes environment and reconstituted in proteolipid sheets

In this work the porin Omp1 of Serratia marcescens was expressed in a porin deficient mutant (Escherichia coli UH302) and its functionality studied following the accumulation of ciprofloxacin in bacteria. The protein was extracted, purified and reconstituted in proteoliposomes of different composition (lipopolysaccharide (LPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)). Maximum extraction of the detergent was achieved applying different steps of dialysis and centrifugation. Proteolipid sheets with different composition were spread onto mica and observed by atomic force microscopy. Two-dimensional crystal of Omp1 was not observed in any case due to low resolution achieved. Judging from the images features POPC is the most suitable phospholipid to enhance 2D lattice formation for Omp1.