Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Crosstalks between integrin alpha 5 and IGF2/IGFBP2 signalling trigger human bone marrow-derived mesenchymal stromal osteogenic differentiation

<p>Abstract</p> <p>Background</p> <p>The potential of mesenchymal stromal cells (MSCs) to differentiate into functional bone forming cells provides an important tool for bone regeneration. The identification of factors that trigger osteoblast differentiation in MSCs is therefore critical to promote the osteogenic potential of human MSCs. In this study, we used microarray analysis to identify signalling molecules that promote osteogenic differentiation in human bone marrow stroma derived MSCs.</p> <p>Results</p> <p>Microarray analysis and validation experiments showed that the expression of IGF2 and IGFBP2 was increased together with integrin alpha5 (ITGA5) during dexamethasone-induced osteoblast differentiation in human MSCs. This effect was functional since we found that IGF2 and IGFBP2 enhanced the expression of osteoblast phenotypic markers and <it>in vitro </it>osteogenic capacity of hMSCs. Interestingly, we showed that downregulation of endogenous ITGA5 using specific shRNA decreased IGF2 and IGFBP2 expression in hMSCs. Conversely, ITGA5 overexpression upregulated IGF2 and IGFBP2 expression in hMSCs, which indicates tight crosstalks between these molecules. Consistent with this concept, activation of endogenous ITGA5 using a specific antibody that primes the integrin, or a peptide that specifically activates ITGA5 increased IGF2 and IGFBP2 expression in hMSCs. Finally, we showed that pharmacological inhibition of FAK/ERK1/2-MAPKs or PI3K signalling pathways that are enhanced by ITGA5 activation, blunted IGF2 and IGFBP2 expression in hMSCs.</p> <p>Conclusion</p> <p>The results show that ITGA5 is a key mediator of IGF2 and IGFBP2 expression that promotes osteoblast differentiation in human MSCs, and reveal that crosstalks between ITGA5 and IGF2/IGFBP2 signalling are important mechanisms that trigger osteogenic differentiation in human bone marrow derived mesenchymal stromal cells.</p

Tents, Chairs, Tacos, Kites, and Rods: Shapes and Plasmonic Properties of Singly Twinned Magnesium Nanoparticles

Nanostructures of some metals can sustain light-driven electron oscillations called localized surface plasmon resonances, or LSPRs, that give rise to absorption, scattering, and local electric field enhancement. Their resonant frequency is dictated by the nanoparticle (NP) shape and size, fueling much research geared toward discovery and control of new structures. LSPR properties also depend on composition; traditional, rare, and expensive noble metals (Ag, Au) are increasingly eclipsed by earth-abundant alternatives, with Mg being an exciting candidate capable of sustaining resonances across the ultraviolet, visible, and near-infrared spectral ranges. Here, we report numerical predictions and experimental verifications of a set of shapes based on Mg NPs displaying various twinning patterns including (101̅1), (101̅2), (101̅3), and (112̅1), that create tent-, chair-, taco-, and kite-shaped NPs, respectively. These are strikingly different from what is obtained for typical plasmonic metals because Mg crystallizes in a hexagonal close packed structure, as opposed to the cubic Al, Cu, Ag, and Au. A numerical survey of the optical response of the various structures, as well as the effect of size and aspect ratio, reveals their rich array of resonances, which are supported by single-particle optical scattering experiments. Further, corresponding numerical and experimental studies of the near-field plasmon distribution via scanning transmission electron microscopy electron-energy loss spectroscopy unravels a mode nature and distribution that are unlike those of either hexagonal plates or cylindrical rods. These NPs, made from earth-abundant Mg, provide interesting ways to control light at the nanoscale across the ultraviolet, visible, and near-infrared spectral ranges

To sink, swim, twin, or nucleate: A critical appraisal of crystal aggregation processes

Abstract Crystal aggregates in igneous rocks have been variously ascribed to growth processes (e.g., twinning, heterogeneous nucleation, epitaxial growth, dendritic growth), or dynamical processes (e.g., synneusis, accumulation during settling). We tested these hypotheses by quantifying the relative orientation of adjacent crystals using electron backscatter diffraction. Both olivine aggregates from Kīlauea volcano (Hawaiʻi, USA) and chromite aggregates from the Bushveld Complex (South Africa) show diverse attachment geometries inconsistent with growth processes. Near-random attachments in chromite aggregates are consistent with accumulation by settling of individual crystals. Attachment geometries and prominent geochemical differences across grain boundaries in olivine aggregates are indicative of synneusis.</jats:p

Quality assessment of surgical disc samples discriminates human annulus fibrosus and nucleus pulposus on tissue and molecular level

A discrimination of the highly specialised annulus fibrosus (AF) and nucleus pulposus (NP) cells in the mature human intervertebral disc (IVD) is thus far still not possible in a reliable way. The aim of this study was to identify molecular markers that distinguish AF and NP cells in human disc tissue using microarray analysis as a screening tool. AF and NP samples were obtained from 28 cervical discs. First, all samples underwent quality sorting using two novel scoring systems for small-sized disc tissue samples including macroscopic, haptic and histological evaluation. Subsequently, samples with clear disc characteristics of either AF or NP that were free from impurities of foreign tissue (IVD score) and with low signs of disc degeneration on cellular level (DD score) were selected for GeneChip analysis (HGU1332P). The 11 AF and 9 NP samples showed distinctly different genome-wide transcriptomes. The majority of differentially expressed genes (DEGs) could be specifically assigned to the AF, whereas no DEG was exclusively expressed in the NP. Nevertheless, we identified 11 novel marker genes that clearly distinguished AF and NP, as confirmed by quantitative gene expression analysis. The novel established scoring systems and molecular markers showed the identity of AF and NP in disc starting material and are thus of great importance in the quality assurance of cell-based therapeutics in regenerative treatment of disc degeneration

Therapies with CCL25 require controlled release via microparticles to avoid strong inflammatory reactions

Background: Chemokine therapy with C-C motif chemokine ligand 25 (CCL25) is currently under investigation as a promising approach to treat articular cartilage degeneration. We developed a delayed release mechanism based on Poly (lactic-co-glycolic acid) (PLGA) microparticle encapsulation for intraarticular injections to ensure prolonged release of therapeutic dosages. However, CCL25 plays an important role in immune cell regulation and inflammatory processes like T-cell homing and chronic tissue inflammation. Therefore, the potential of CCL25 to activate immune cells must be assessed more thoroughly before further translation into clinical practice. The aim of this study was to evaluate the reaction of different immune cell subsets upon stimulation with different dosages of CCL25 in comparison to CCL25 released from PLGA particles. Results: Immune cell subsets were treated for up to 5 days with CCL25 and subsequently analyzed regarding their cytokine secretion, surface marker expression, polarization, and migratory behavior. The CCL25 receptor C-C chemokine receptor type 9 (CCR9) was expressed to a different extent on all immune cell subsets. Direct stimulation of peripheral blood mononuclear cells (PBMCs) with high dosages of CCL25 resulted in strong increases in the secretion of monocyte chemoattractant protein-1 (MCP-1), interleukin-8 (IL-8), interleukin-1 beta (IL-1 beta), tumor-necrosis-factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma), upregulation of human leukocyte antigen-DR (HLA-DR) on monocytes and CD4(+) T-cells, as well as immune cell migration along a CCL25 gradient. Immune cell stimulation with the supernatants from CCL25 loaded PLGA microparticles caused moderate increases in MCP-1, IL-8, and IL-1 beta levels, but no changes in surface marker expression or migration. Both CCL25-loaded and unloaded PLGA microparticles induced an increase in IL-8 and MCP-1 release in PBMCs and macrophages, and a slight shift of the surface marker profile towards the direction of M2-macrophage polarization. Conclusions: While supernatants of CCL25 loaded PLGA microparticles did not provoke strong inflammatory reactions, direct stimulation with CCL25 shows the critical potential to induce global inflammatory activation of human leukocytes at certain concentrations. These findings underline the importance of a safe and reliable release system in a therapeutic setup. Failure of the delivery system could result in strong local and systemic inflammatory reactions that could potentially negate the benefits of chemokine therapy

Voting procedures and parliamentary representation in the European Parliament

Parliamentary representation is a fluid concept. Yet, while the behaviour of elected representatives during roll call votes has been widely analysed, we know little about how parliamentarians act when their individual voting choices are not made public. This paper explores the relationship between voting procedures and the likelihood that Members of the European Parliament prioritise the interests of their EP party group versus the interests of their national party. Using an original survey, I find that MEPs are more likely to prioritise the interests of their national party over those of their EP party group when voting by show of hands or electronically, as opposed to by roll call. Moreover, this voting procedure effect is particularly salient among MEPs elected from 2004/07 accession countries