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Objective: \ud Fibroblast-like synoviocytes (FLS) play a pivotal role in rheumatoid arthritis (RA) by contributing to synovial inflammation and progressive joint damage. An imprinted epigenetic state is associated with the FLS aggressive phenotype. We identified CASP8 (encoding for caspase-8) as a differentially marked gene and evaluated its pathogenic role in RA FLSs.\ud \ud Methods: \ud RA FLS lines were obtained from synovial tissues at arthroplasty and used at passage 5-8. Caspase-8 was silenced using small interfering RNA, and its effect was determined in cell adhesion, migration and invasion assays. Quantitative reverse transcription PCR and western blot were used to assess gene and protein expression, respectively. A caspase-8 selective inhibitor was used determine the role of enzymatic activity on FLS migration and invasion. Caspase-8 isoform transcripts and epigenetic marks in FLSs were analyzed in FLS public databases. Crystal structures of caspase-8B and G were determined.\ud \ud Results: \ud Caspase-8 deficiency in RA FLSs reduced cell adhesion, migration, and invasion independent of its catalytic activity. Epigenetic and transcriptomic analyses of RA FLSs revealed that a specific caspase-8 isoform, variant G, is the dominant isoform expressed (~80% of total caspase-8) and induced by PDGF. The crystal structures of caspase-8 variant G and B were identical except for a unique unstructured 59 amino acid N-terminal domain in variant G. Selective knockdown of caspase-8G was solely responsible for the effects of caspase-8 on calpain activity and cell invasion in FLS.\ud \ud Conclusion: \ud Blocking caspase-8 variant G could decrease cell invasion in diseases like RA without the potential deleterious effects of nonspecific caspase-8 inhibition.

Genome wide association studies have revealed >150 loci associated with schizophrenia risk1–4, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements5,6. However, no study so far has profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects or the effect of antipsychotic treatment on such epigenetic marks. Here we show the first comprehensive epigenomic characterization of the frontal cortex of 29 individuals with schizophrenia and 29 matched controls, including histone modifications associated with active promoters and enhancers H3K4me3 and H3K27ac along with RNA expression in neuronal and glial nuclei. Schizophrenia subjects exhibited thousands of cell type-specific epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, RGS4 and HTR2A. Comparing untreated and treated schizophrenia subjects with controls, our findings provide entirely new insights into differentially modified genes associated with unexpected pathways that are potential markers of antipsychotic treatment. Additionally, we show that the effect of age on the epigenomic landscape is more pronounced in frontal cortex samples of antipsychotic-treated schizophrenia subjects. Together, our data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark the impact of age and antipsychotic treatment on chromatin organization.

Directed evolution is a powerful approach for engineering proteins with enhanced affinity or specificity for a ligand of interest but typically requires many rounds of screening/library mutagenesis to obtain mutants with desired properties. Furthermore, mutant libraries generally only cover a small fraction of the available sequence space. Here, for the first time, we use ordinal regression to model protein sequence data generated through successive rounds of sorting and amplification of a protein-ligand system. We show that the ordinal regression model trained on only two sorts successfully predicts chromodomain CBX1 mutants that would have stronger binding affinity with the H3K9me3 peptide. Furthermore, we can extract the predictive features using contextual regression, a method to interpret nonlinear models, which successfully guides identification of strong binders not even present in the original library. We have demonstrated the power of this approach by experimentally confirming that we were able to achieve the same improvement in binding affinity previously achieved through a more laborious directed evolution process. This study presents an approach that reduces the number of rounds of selection required to isolate strong binders and facilitates the identification of strong binders not present in the original library.

Phosphate-based bioactive glasses (PBGs) dissolve harmlessly in the body with a dissolution rate which depends sensitively on composition. This makes them proposed vectors for e.g. drug delivery, or other applications where an active component needs to be delivered at a therapeutically appropriate rate. Molecular dynamics (MD) simulations provide atomic-level structural information about PBG compositions. We review recent work to show that MD is an excellent tool to unravel the connections between the PBG glass composition, its atomic structure, and its dissolution rate, which can help to optimise PBGs for specific medical applications.

Classical molecular dynamics (MD) simulations were used to study the structural changes in the surfaces of biocompatible phosphate glasses with compositions (P2O5)0.45(CaO)x(Na2O)0.55−x (x=30, 35, 40) to evaluate their effect on the solubility of the material. Direct comparison of the data for the three compositions highlighted the critical role that an enhancement in Na+ concentration plays in the hydrolysis of the material, which is responsible for the release of network components into solution. The calculations also confirm that the most soluble material is (P2O5)0.45(CaO)0.30(Na2O)0.25, has the lowest calcium coordination number, thereby causing fewer cross links to phosphate chains.

Chromatin looping plays a pivotal role in gene expression and other biological processes through bringing distal regulatory elements into spatial proximity. The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in three-dimensional (3D) space. Previously, identification of DBP cooperation has been limited to those binding to neighbouring regions in the proximal linear genome (1D cooperation). Here we present the first study that integrates protein ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs. We develop a new network model that allows identification of cooperation between multiple DBPs and reveals cell-type-specific and -independent regulations. Using this framework, we retrieve many known and previously unknown 3D-cooperations between DBPs in chromosomal loops that may be a key factor in influencing the 3D organization of chromatin., The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in 3D space. Here, Zhang et al. present an algorithm integrating ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs.

We have used classical molecular dynamics simulations to characterise the structure of three compositions of silver-containing phosphate glasses with 45mol% P2O5, 30mol% CaO, and varying amounts of Na2O and Ag2O. These compositions all have the same network connectivity, allowing us to highlight two other structural features which will affect the glass dissolution. Firstly, the number of different phosphate chains bonded to each modifier atom was computed and it was observed that silver and sodium bind to roughly the same number of phosphate chains, despite the differences in their local environments. Secondly, the clustering of modifier cations was characterised and shown to be enhanced at low concentrations of sodium and silver, but not to exist for calcium.

Classical molecular dynamics (MD) simulations were used to study the effects of water on the structural relaxation of the surfaces of bio-active phosphate-based glasses with compositions (P2O5)0.45(CaO)x(Na2O)0.55-x (x = 0.30, 0.35 and 0.40). Direct comparison of the data for the three compositions showed that surfaces with x = 0.30 experienced the highest calcium diffusion, as well as highest sodium concentration at the glass/water interface, confirming these systems as the most soluble of the three compositions studied. Our results also show the importance of surface hydroxylation in the simulation of these types of bio-glasses, which causes differential relaxation of the surfaces, leading to changes in network polymerization that modulate the diffusion of water and modifiers into and out of the glasses, with direct impact on dissolution.

Epigenetics contributes to the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS), including histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3), open chromatin, RNA expression and whole-genome DNA methylation. To address complex multidimensional relationship and reveal epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells and are associated with active enhancers and promoters and specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington’s Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets., Fibroblast-like synoviocytes (FLS) in the intimal layer of the synovium can become invasive and destroy cartilage in patients with rheumatoid arthritis (RA). Here the authors integrate a variety of epigenomic data to map the epigenome of FLS in RA and identify potential therapeutic targets.

First-principles and classical molecular dynamics simulations of undoped and silver-doped phosphate-based glasses with 50 mol% P2O5, 0-20 mol% Ag2O, and varying amounts of Na2O and CaO have been carried out. Ag occupies a distorted local coordination with a mean Ag-O bond length of 2.5 Å and an ill-defined first coordination shell. This environment is shown to be distorted octahedral/trigonal bipyramidal. Ag-O coordination numbers of 5.42 and 5.54-5.71 are calculated for first-principles and classical methodologies respectively. A disproportionation in the medium-range phosphorus Q(n) distribution is explicitly displayed upon silver-doping via CaO substitution, approximating 2Q(2)→Q(1) + Q(3), but not on silver-doping via Na2O substitution. An accompanying increase in FWHM of the phosphorus to bridging oxygen partial pair-correlation function is strong evidence for a bulk structural mechanism associated with decreased dissolution rates with increased silver content. Experimentally, Ag2O ↔ Na2O substitution is known to decrease dissolution and we show this to be a result of Ag's local bonding.

Bioactive phosphate-based glasses (PBGs) have several possible biomedical applications because of the chemical reactions they undergo with their surroundings when implanted into the body. The dissolution rate of PBGs in physiological conditions is a crucial parameter for these applications, to ensure, e.g., delivery of drugs or nutrients to the body at the correct rate. While it has been well-known that increasing the CaO content of these glasses at the expense of Na2O slows the dissolution rate, this paper provides an atomistic explanation of this for the first time. In this work, molecular dynamics simulations of five ternary P2O5-CaO-Na2O glasses reveal the structural properties at the atomic level that enhance the durability of PBGs as more Ca is added: (i) Ca binds together more fragments of the phosphate glass network than Na, (ii) Ca binds together more PO4 tetrahedra than Na, and (iii) Ca has a lower concentration of intratetrahedral phosphate bonding than Na. This behavior is rooted in the calcium ion's higher charge and field strength. These results open the path to precise control and optimization of the PBG dissolution rate for specific biomedical applications.

Motivation: MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency. Availability and implementation: The program is available at http://wanglab.ucsd.edu/MIEC-SVM. Contact: wei-wang@ucsd.edu Supplementary information : Supplementary data available at Bioinformatics online.

Molecular dynamics simulations of phosphate-based glasses P(2)O(5)-CaO-Na(2)O have been carried out, using an interatomic force field that has been parameterized to reproduce the structural and mechanical properties of crystalline phosphorus pentoxide, o(')(P(2)O(5))(∞) orthorhombic phase. Polarization effects have been included through the shell-model potential and formal charges have been used to aid transferability. A modification to the DL_POLY code (version 2.20) was used to model the high temperature shell dynamics. Structural characterizations of three biomedically applicative molar compositions, (P(2)O(5))(0.45)(CaO)(x)(Na(2)O)(0.55-x) (x = 0.30, 0.35, and 0.40), have been undertaken. Good agreement with available experimental and ab initio data is obtained. The simulations show that, dependent on composition, the phosphorus atoms are primarily bonded to two or three oxygens that in turn bridge to neighbouring phosphorus atoms. Na(+) and Ca(2+) modifiers are found to occupy a pseudo-octahedral bonding environment with mean oxygen coordination numbers of 6.55 and 6.85, respectively, across all compositions studied.

Quantum mechanical calculations of single crystal phosphorus pentoxide (P(2)O(5)) have been conducted using the plane-wave ultrasoft pseudopotential technique based on the density functional theory (DFT), in the generalized gradient approximation, with dispersive correction (DFT-D). The implementation of the dispersive correction is shown to improve significantly the structural agreement with experiment, compared to standard plane-wave DFT. The second order elastic constants for the o'(P(2)O(5))(∞) and o(P(2)O(5)) orthorhombic phases were obtained from a polynomial fit to the calculated energy-strain relation. Both phases are shown to be highly elastically anisotropic due to structural features. Polycrystalline aggregate properties have been evaluated to give complete mechanical descriptions. Further investigation of the electronic band structure and density of states has been completed. Analysis of the complex chemical bonding has been carried out using Lowdin atomic charge and valence charge density data showing mixed ionic and covalent character in both phases.

The local and medium-range structural properties of phosphate-based melts and glasses have been characterized by means of first principles (density functional theory) and classical (shell-model) molecular dynamics simulations. The structure of glasses with biomedically active molecular compositions, (P2O5)0.45(CaO)x(Na2O)0.55−x (x = 0.30, 0.35 and 0.40), have been generated using first principles molecular dynamics simulations for the full melt-and-quench procedure and the changes in the structural properties as the 3000 K melt is cooled down to room temperature have been compared extensively with those of the final glasses. The melts are characterized by a significant fraction of threefold (P3c) and fivefold (P5c) phosphorus atoms, but structural defects rapidly decrease during the cooling phase and for temperatures lower than 1800 K the system is free of under- and over-coordinated species. The analysis of the structures of the glasses at 300 K shows a prevalence of the metaphosphate Q2 and pyrophosphate Q1 species, whereas the number of Q3 units, which constitute the three-dimensional phosphate network, significantly decreases with the increase of calcium content in the glass. The radial and angular distribution functions indicate that higher calcium concentration in the glass leads to an increase of the rigidity of the phosphate tetrahedral network, which has been explained in terms of the calcium's higher field strength compared to that of sodium. The structural characterization of the melts and glasses obtained from first principles simulations was used to assess and validate a recently developed interatomic shell-model forcefield for phosphate-based materials. For all three compositions, our potential model is in good agreement with the first principles data. In the glass network, the forcefield provides a very good description of the split between the shorter distances of phosphorus to non-bonded oxygen and the longer distances of the phosphorus to bonded oxygen; the phosphorus–phosphorus medium-range distribution; and the coordination environment around the Na and Ca glass modifiers. Moreover, the distribution of the Qn species in the melts and glasses is in excellent agreement with the values extracted from the first principles simulations. In contrast, simulations using standard rigid ion potentials do not provide a satisfactory description of the local short-range structure of phosphate-based glasses and are therefore less suitable to model this class of multicomponent amorphous system.

Phosphate-based bioactive glasses containing fluoride ions offer the potential of a biomaterial which combines the bioactive properties of the phosphate glass and the protection from dental caries by fluoride. We conduct accurate first-principles molecular dynamics simulations of two compositions of fluorinated phosphate-based glass to assess its suitability as a biomaterial. There is a substantial amount of F–P bonding and as a result the glass network will be structurally homogeneous on medium-range length scales, without the inhomogeneities which reduce the bioactivity of other fluorinated bioactive glasses. We observe a decrease in the network connectivity with increasing F content, caused by the replacement of bridging oxygen atoms by non-bridging fluorine atoms, but this decrease is small and can be opposed by an increase in the phosphate content. We conclude that the structural changes caused by the incorporation of fluoride into phosphate-based glasses will not adversely affect their bioactivity, suggesting that fluorinated phosphate glasses offer a superior alternative to their silicate-based counterparts.