Multifunctionality through Embedding Patterned Nanostructures in High-Performance Composites.

Despite being a pillar of high-performance materials in industry, manufacturing carbon fiber composites with simultaneously enhanced multifunctionality and structural properties has remained elusive due to the lack of practical bottom-up approaches with control over nanoscale interactions. Guided by the droplet's internal currents and amphiphilicity of nanomaterials, herein, a programmable spray coating is introduced for the deposition of multiple nanomaterials with tailorable patterns in composite.  It is shown that such patterns regulate the formation of interfaces, damage containment, and electrical-thermal conductivity of the composites, which is absent in conventional manufacturing that primarily rely on incorporating nanomaterials to achieve specific functionalities. Molecular dynamics simulations show that increasing the hydrophilicity of the hybrid nanomaterials, which is synchronous with shifting patterns from disk to ring, improves the interactions between the carbon surfaces and epoxy at the interfaces,manifested in enhanced interlaminar and flexural performance. Transitioning from ring to disk creates a larger interconnected network  leading to improved thermal and electrical properties without penalty in mechanical properties. This novel approach introduces a new design , where the mechanical and multifunctional performance is controlled by the shape of the deposited patterns, thus eliminating the trade-off between properties that are considered paradoxical in today's manufacturing of hierarchical composites.

Fundamentals of Crystalline Evolution and Properties of Carbon Nanotube-Reinforced Polyether Ether Ketone Nanocomposites in Fused Filament Fabrication.

As fused filament fabrication (FFF) continues to gain popularity, many studies are turning to nanomaterials or optimization of printing parameters to improve the materials' properties; however, many overlook how materials formulation and additive manufacturing (AM) processes cooperatively engineer the evolution of properties across length scales. Evaluating the in-process evolution of the nanocomposite using AM will provide a fundamental understanding of the material's microstructure, which can be tailored to create unique characteristics in functionality and performance. In this study, the crystallinity behavior of polyetheretherketone (PEEK) was studied in the presence of carbon nanotubes (CNTs) as a nucleation aid for improved crystallization during FFF processing. Using various characterization techniques and molecular dynamics simulations, it was discovered that the crystallization behavior of extruded filaments is very different from that of 3D printed roads. Additionally, the printed material exhibited cold crystallization, and the CNT addition increased the crystallization of printed roads, which were amorphous without CNT addition. Tensile strength and modulus were increased by as much as 42 and 51%, respectively, due to higher crystallinity during printing. Detailed knowledge on the morphology of PEEK-CNT used in FFF allows gaining a fundamental understanding of the morphological evolution occurring during the AM process that in turn enables formulating materials for the AM process to achieve tailored mechanical and functional properties, such as crystallinity or conductivity.

Aqueous Dispersion of Carbon Nanomaterials with Cellulose Nanocrystals: An Investigation of Molecular Interactions.

Dispersing carbon nanomaterials in solvents is effective in transferring their significant mechanical and functional properties to polymers and nanocomposites. However, poor dispersion of carbon nanomaterials impedes exploiting their full potential in nanocomposites. Cellulose nanocrystals (CNCs) are promising for dispersing and stabilizing pristine carbon nanotubes (pCNTs) and graphene nanoplatelets (pGnP) in protic media without functionalization. Here, the underlying mechanisms at the molecular level are investigated between CNC and pCNT/pGnP that stabilize their dispersion in polar solvents. Based on the spectroscopy and microscopy characterization of CNCpCNT/pGnP and density functional theory (DFT) calculations, an additional intermolecular mechanism is proposed between CNC and pCNT/pGnP that forms carbonoxygen covalent bonds between hydroxyl end groups of CNCs and the defected sites of pCNTs/pGnPs preventing re-agglomeration in polar solvents. This work's findings indicate that the CNC-assisted process enables new capabilities in harnessing nanostructures at the molecular level and tailoring the performance of nanocomposites at higher length scales.

ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement.

Pharmacophore modeling is an important step in computer-aided drug design for identifying interaction points between the receptor and ligand complex. Pharmacophore-based models can be used for de novo drug design, lead identification, and optimization in virtual screening as well as for multi-target drug design. There is a need to develop a user-friendly interface to filter the pharmacophore points resulting from multiple ligand conformations. Here, we present ELIXIR-A, a Python-based pharmacophore refinement tool, to help refine the pharmacophores between multiple ligands from multiple receptors. Furthermore, the output can be easily used in virtual pharmacophore-based screening platforms, thereby contributing to the development of drug discovery.

Mechanisms of Immunomodulation and Cytoprotection Conferred to Pancreatic Islet by Human Amniotic Epithelial Cells.

Inhibiting pro-inflammatory cytokine activity can reverse inflammation mediated dysfunction of islet grafts. Human amniotic epithelial cells (hAECs) possess regenerative, immunomodulatory and anti-inflammatory properties. We hypothesized that hAECs could protect islets from cellular damage induced by pro-inflammatory cytokines. To verify our hypothesis, hAEC monocultures, rat islets (RI), or RI-hAEC co-cultures where exposed to a pro-inflammatory cytokine cocktail (Interferon γ: IFN-γ, Tumor necrosis factor α: TNF-α and Interleukin-1ß: IL-1ß). The secretion of anti-inflammatory cytokines and gene expression changes in hAECs and viability and function of RI were evaluated. The expression of non-classical Major Histocompatibility Complex (MHC) class I molecules by hAECs cultured with various IFN-γ concentrations were assessed. Exposure to the pro-inflammatory cocktail significantly increased the secretion of the anti-inflammatory cytokines IL6, IL10 and G-CSF by hAECs, which was confirmed by upregulation of IL6, and IL10 gene expression. HLA-G, HLA-E and PDL-1 gene expression was also increased. This correlated with an upregulation of STAT1, STAT3 and NF-κB1gene expression levels. RI co-cultured with hAECs maintained normal function after cytokine exposure compared to RI cultured alone, and showed significantly lower apoptosis rate. Our results show that exposure to pro-inflammatory cytokines stimulates secretion of anti-inflammatory and immunomodulatory factors by hAECs through the JAK1/2 - STAT1/3 and the NF-κB1 pathways, which in turn protects islets against inflammation-induced damages. Integrating hAECs in islet transplants appears as a valuable strategy to achieve to inhibit inflammation mediated islet damage, prolong islet survival, improve their engraftment and achieve local immune protection allowing reducing systemic immunosuppressive regimens. This study focuses on the cytoprotective effect of isolated hAECs on islets exposed to pro-inflammatory cytokines in vitro. Exposure to pro-inflammatory cytokines stimulated secretion of anti-inflammatory and immunomodulatory factors by hAECs putatively through the JAK1/2 - STAT1/3 and the NF-κB1 pathways. This had protective effect on islets against inflammation-induced damages. Taken together our results indicate that incorporating hAECs in islet transplants could be a valuable strategy to inhibit inflammation mediated islet damage, prolong islet survival, improve their engraftment and achieve local immune protection allowing to reduce systemic immunosuppressive regimens.

Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis.

From the combined perspective of biologists, microscope instrumentation developers, imaging core facility scientists, and high performance computing experts, we discuss the challenges faced when selecting imaging and analysis tools in the field of light-sheet microscopy. Our goal is to provide a contextual framework of basic computing concepts that cell and developmental biologists can refer to when mapping the peculiarities of different light-sheet data to specific existing computing environments and image analysis pipelines. We provide our perspective on efficient processes for tool selection and review current hardware and software commonly used in light-sheet image analysis, as well as discuss what ideal tools for the future may look like.

Quantum Chemical Modeling of the Effects of Hydrated Lime (Calcium Hydroxide) as a Filler in Bituminous Materials.

Hydrated lime is widely used as a mineral filler to improve several properties of bituminous materials such as reducing the susceptibility of the composite to moisture-induced damage. Although experimental evidence supports the efficacy of using hydrated lime as a mineral filler, the molecular scale mechanism of reactivity of hydrated lime within the bitumen to reduce moisture damage is not understood. This is important when considering the durability of structural applications of bituminous materials such as asphalt concrete pavements subjected to both environmental and loading extremes. In this study, the interaction between hydrated lime and the key molecular building blocks of bitumen is modeled using density functional theory and compared against analogues of other common fillers such as calcite and quartz. Free energies of dissociation (ΔG dissoc) are calculated, and the nature of the bonds is characterized with contour maps of the Laplacian of the electron density. Hydrated lime is capable of reacting with specific functional groups in bitumen moieties and developing strong, water-resistant complexes. Among the functional groups investigated, carboxylic acids are the preferential reaction sites between hydrated lime and the bitumen moieties. Values as high as ΔG dissoc = +49.42 kcal/mol are reported for hydrated lime with water as the surrounding solvent. In contrast, analogues of calcite (ΔG dissoc = +15.84 kcal/mol) and quartz (ΔG dissoc = +4.76 kcal/mol) are unable to chemically react as strongly as hydrated lime in the presence of water. Contour maps of the Laplacian of the electron density indicate that the bonds between hydrated lime and model asphalt moieties are of an ionic nature. The atomistic modeling results correlate with thermodynamic calculations derived from experimental constants and are consistent with infrared spectrometric data.

Bio-Engineering of Pre-Vascularized Islet Organoids for the Treatment of Type 1 Diabetes.

Lack of rapid revascularization and inflammatory attacks at the site of transplantation contribute to impaired islet engraftment and suboptimal metabolic control after clinical islet transplantation. In order to overcome these limitations and enhance engraftment and revascularization, we have generated and transplanted pre-vascularized insulin-secreting organoids composed of rat islet cells, human amniotic epithelial cells (hAECs), and human umbilical vein endothelial cells (HUVECs). Our study demonstrates that pre-vascularized islet organoids exhibit enhanced in vitro function compared to native islets, and, most importantly, better engraftment and improved vascularization in vivo in a murine model. This is mainly due to cross-talk between hAECs, HUVECs and islet cells, mediated by the upregulation of genes promoting angiogenesis (vegf-a) and ß cell function (glp-1r, pdx1). The possibility of adding a selected source of endothelial cells for the neo-vascularization of insulin-scereting grafts may also allow implementation of ß cell replacement therapies in more favourable transplantation sites than the liver.

Author Correction: Insulin-producing organoids engineered from islet and amniotic epithelial cells to treat diabetes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Engineering of Primary Pancreatic Islet Cell Spheroids for Three-dimensional Culture or Transplantation: A Methodological Comparative Study.

Three-dimensional (3D) cell culture by engineering spheroids has gained increasing attention in recent years because of the potential advantages of such systems over conventional two-dimensional (2D) tissue culture. Benefits include the ability of 3D to provide a more physiologically relevant environment, for the generation of uniform, size-controlled spheroids with organ-like microarchitecture and morphology. In recent years, different techniques have been described for the generation of cellular spheroids. Here, we have compared the efficiency of four different methods of islet cell aggregation. Rat pancreatic islets were dissociated into single cells before reaggregation. Spheroids were generated either by (i) self-aggregation in nonadherent petri dishes, (ii) in 3D hanging drop culture, (iii) in agarose microwell plates or (iv) using the Sphericalplate 5D™. Generated spheroids consisted of 250 cells, except for the self-aggregation method, where the number of cells per spheroid cannot be controlled. Cell function and morphology were assessed by glucose stimulated insulin secretion (GSIS) test and histology, respectively. The quantity of material, labor intensity, and time necessary for spheroid production were compared between the different techniques. Results were also compared with native islets. Native islets and self-aggregated spheroids showed an important heterogeneity in terms of size and shape and were larger than spheroids generated with the other methods. Spheroids generated in hanging drops, in the Sphericalplate 5D™, and in agarose microwell plates were homogeneous, with well-defined round shape and a mean diameter of 90 µm. GSIS results showed improved insulin secretion in response to glucose in comparison with native islets and self-aggregated spheroids. Spheroids can be generated using different techniques and each of them present advantages and inconveniences. For islet cell aggregation, we recommend, based on our results, to use the hanging drop technique, the agarose microwell plates, or the Sphericalplate 5D™ depending on the experiments, the latter being the only option available for large-scale spheroids production.

Hydrogel Synthesis and Stabilization via Tetrazine Click-Induced Secondary Interactions.

The discovery of tetrazine click-induced secondary interactions is reported as a promising new tool for polymeric biomaterial synthesis. This phenomenon is first demonstrated as a tool for poly(ethylene glycol) (PEG) hydrogel assembly via purely non-covalent interactions and is shown to yield robust gels with storage moduli one to two orders of magnitude higher than other non-covalent crosslinking methods. In addition, tetrazine click-induced secondary interactions also enhance the properties of covalently crosslinked hydrogels. A head-to-head comparison of PEG hydrogels crosslinked with tetrazine-norbornene and thiol-norbornene click chemistry reveals an approximately sixfold increase in storage modulus and unprecedented resistance to hydrolytic degradation in tetrazine click-crosslinked gels without substantial differences in gel fraction. Molecular dynamic simulations attribute these differences to the presence of secondary interactions between the tetrazine-norbornene cycloaddition products, which are absent in the thiol-norbornene crosslinked gels.

An amber obligate active site-directed ligand evolution technique for phage display.

Although noncanonical amino acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two decades ago, their application for use in drug discovery has been limited due to inherent library bias towards sense-containing phages. Here, we report a technique based on superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias that has hindered incorporation of ncAAs into phage libraries. We then take advantage of this technique for development of active site-directed ligand evolution of peptides, where the ncAA serves as an anchor to direct the binding of its peptides to the target's active site. To demonstrate this, phage-displayed peptide libraries are developed that contain a genetically encoded butyryl lysine and are subsequently used to select for ligands that bind SIRT2. These ligands are then modified to develop low nanomolar inhibitors of SIRT2.

Shielding islets with human amniotic epithelial cells enhances islet engraftment and revascularization in a murine diabetes model.

Hypoxia is a major cause of considerable islet loss during the early posttransplant period. Here, we investigate whether shielding islets with human amniotic epithelial cells (hAECs), which possess anti-inflammatory and regenerative properties, improves islet engraftment and survival. Shielded islets were generated on agarose microwells by mixing rat islets (RIs) or human islets (HI) and hAECs (100 hAECs/IEQ). Islet secretory function and viability were assessed after culture in hypoxia (1% O2 ) or normoxia (21% O2 ) in vitro. In vivo function was evaluated after transplant under the kidney capsule of diabetic immunodeficient mice. Graft morphology and vascularization were evaluated by immunohistochemistry. Both shielded RIs and HIs show higher viability and increased glucose-stimulated insulin secretion after exposure to hypoxia in vitro compared with control islets. Transplant of shielded islets results in considerably earlier normoglycemia and vascularization, an enhanced glucose tolerance, and a higher ß cell mass. Our results show that hAECs have a clear cytoprotective effect against hypoxic damages in vitro. This strategy improves ß cell mass engraftment and islet revascularization, leading to an improved capacity of islets to reverse hyperglycemia, and could be rapidly applicable in the clinical situation seeing that the modification to HIs are minor.

The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.

Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site.

Metal-Templated, Tight Loop Conformation of a Cys-X-Cys Biomimetic Assembles a Dimanganese Complex.

With the goal of generating anionic analogues to MN2 S2 ⋅Mn(CO)3 Br we introduced metallodithiolate ligands, MN2 S22- prepared from the Cys-X-Cys biomimetic, ema4- ligand (ema=N,N'-ethylenebis(mercaptoacetamide); M=NiII , [VIV ≡O]2+ and FeIII ) to Mn(CO)5 Br. An unexpected, remarkably stable dimanganese product, (H2 N2 (CH2 C=O(µ-S))2 )[Mn(CO)3 ]2 resulted from loss of M originally residing in the N2 S24- pocket, replaced by protonation at the amido nitrogens, generating H2 ema2- . Accordingly, the ema ligand has switched its coordination mode from an N2 S24- cavity holding a single metal, to a binucleating H2 ema2- with bridging sulfurs and carboxamide oxygens within Mn-µ-S-CH2 -C-O, 5-membered rings. In situ metal-templating by zinc ions gives quantitative yields of the Mn2 product. By computational studies we compared the conformations of "linear" ema4- to ema4- frozen in the "tight-loop" around single metals, and to the "looser" fold possible for H2 ema2- that is the optimal arrangement for binucleation. XRD molecular structures show extensive H-bonding at the amido-nitrogen protons in the solid state.

Insulin-producing organoids engineered from islet and amniotic epithelial cells to treat diabetes.

Maintaining long-term euglycemia after intraportal islet transplantation is hampered by the considerable islet loss in the peri-transplant period attributed to inflammation, ischemia and poor angiogenesis. Here, we show that viable and functional islet organoids can be successfully generated from dissociated islet cells (ICs) and human amniotic epithelial cells (hAECs). Incorporation of hAECs into islet organoids markedly enhances engraftment, viability and graft function in a mouse type 1 diabetes model. Our results demonstrate that the integration of hAECs into islet cell organoids has great potential in the development of cell-based therapies for type 1 diabetes. Engineering of functional mini-organs using this strategy will allow the exploration of more favorable implantation sites, and can be expanded to unlimited (stem-cell-derived or xenogeneic) sources of insulin-producing cells.

Anti-VEGFR2 therapy delays growth of preclinical pediatric tumor models and enhances anti-tumor activity of chemotherapy.

Vascular endothelial growth factor receptor 2 (VEGFR2) is an attractive therapeutic target in solid malignancies due to its central role in tumor angiogenesis. Ramucirumab (Cyramza®, LY3009806) is a human monoclonal antibody specific for VEGFR2 approved for several adult indications and currently in a phase 1 clinical trial for pediatric patients with solid tumors (NCT02564198). Here, we evaluated ramucirumab in vitro and the anti-murine VEGFR2 antibody DC101 in vivo with or without chemotherapy across a range of pediatric cancer models. Ramucirumab abrogated in vitro endothelial cord formation driven by cancer cell lines representing multiple pediatric histologies; this response was independent of the origin of the tumor cell-line. Several pediatric cancer mouse models responded to single agent DC101-mediated VEGFR2 inhibition with tumor growth delay. Preclinical stable disease and partial xenograft regressions were observed in mouse models of Ewing's sarcoma, synovial sarcoma, neuroblastoma, and desmoplastic small round cell tumor treated with DC101 and cytotoxic chemotherapy. In contrast, DC101 treatment in osteosarcoma models had limited efficacy alone or in combination with chemotherapeutics. Our data indicate differential efficacy of targeting the VEGFR2 pathway in pediatric models and support the continued evaluation of VEGFR2 inhibition in combination with cytotoxic chemotherapy in multiple pediatric indications.

Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis.

An active segment of the research community designing small molecules ("minimalist mimics" of peptide fragments) to interfere with protein-protein interactions have based their studies on an implicit hypothesis. Here we refer to this as the Secondary Structure Hypothesis, that might be defined as, "If a small molecule can orient amino acid side-chains in directions that resemble side-chains of the parent secondary structure at the interface, then that small molecule is a candidate to perturb the protein-protein interaction". Rigorous tests of this hypothesis require co-crystallization of minimalist mimics with protein receptors, and comparison of the bound conformations with the interface secondary structures they were designed to resemble. Unfortunately, to the best of our knowledge, there is no such analysis in the literature, and it is unlikely that enough examples will emerge in the near future to test the hypothesis. Research described here was designed to challenge this hypothesis from a different perspective. In a previous study, preferred conformations of a series of novel minimalist mimics were simulated then systematically overlaid on >240 000 crystallographically characterized protein-protein interfaces. Select data from that overlay procedure revealed chemotypes that overlay side chains on various PPI interfaces with a relatively high frequency of occurrence. The first aim of this work was to determine if good secondary structure mimics overlay frequently on PPI interfaces. The second aim of this work was to determine if overlays of preferred conformers at interface regions involve secondary structures. Thus situations where these conformations overlaid extremely well on PPI interfaces were analyzed to determine if secondary structures featured the PPI regions where these molecules overlaid in the previous study. Combining conclusions from these two studies enabled us to formulate a hypothesis that is complementary to the Secondary Structure Hypothesis, but, unlike this, is supported by abundant data. We call this the Interface Mimicry Hypothesis.

Design criteria for minimalist mimics of protein-protein interface segments.

Small molecules that can interrupt or inhibit protein-protein interactions (PPIs) are valuable as probes in chemical biology and medicinal chemistry, but they are also notoriously difficult to develop. Design of non-peptidic small molecules that mimic amino acid side-chain interactions in PPIs ("minimalist mimics") is seen as a way to fast track discovery of PPI inhibitors. However, there has been little comment on general design criteria for minimalist mimics, even though such guidelines could steer construction of libraries to screen against multiple PPI targets. We hypothesized insight into general design criteria for minimalist mimics could be gained by comparing preferred conformations of typical minimalist mimic designs against side-chain orientations on a huge number of PPI interfaces. That thought led to this work which features nine minimalist mimic designs: one from the literature, and eight new "hypothetical" ones conceived by us. Simulated preferred conformers of these were systematically aligned with >240 000 PPI interfaces from the Protein Data Bank. Conclusions from those analyses did indeed reveal various design considerations that are discussed here. Surprisingly, this study also showed one of the minimalist mimic designs aligned on PPI interface segments more than 15 times more frequently than any other in the series (according to uniform standards described herein); reasons for this are also discussed.