Click functionalization of methacrylate-based hydrogels and their cellular response

Methacrylate-based hydrogels, such as homo- and copolymers of 2-hydroxyethyl methacrylate (HEMA), have demonstrated significant potential for use in biomedical applications. However, many of these hydrogels tend to resist cell attachment and growth at their surfaces, which can be detrimental for certain applications. In this article, glycidyl methacrylate (GMA) was copolymerized with HEMA to generate gels functionalized with epoxide groups. The epoxides were then functionalized by two sequential click reactions, namely, nucleophilic ring opening of epoxides with sodium azide and then coupling of small molecules and peptides via Huisgen's copper catalyzed 1,3-dipolar cycloaddition of azides with alkynes. Using this strategy it was possible to control the degree of functionalization by controlling the feed ratio of monomers during polymerization. In vitro cell culture of human retinal pigment epithelial cell line (ARPE-19) with the hydrogels showed improved cell adhesion, growth and proliferation for hydrogels that were functionalized with a peptide containing the RGD sequence. In addition, the cell attachment progressively decreased with increasing densities of the RGD containing peptide. In summary, a facile methodology has been presented that gives rise to hydrogels with controlled degrees of functionality, such that the cell response is directly related to the levels and nature of that functionality.

Secondary structure element alignment kernel method for prediction of protein structural classes

In this paper, we aim at predicting protein structural classes for low-homology data sets based on predicted secondary structures. We propose a new and simple kernel method, named as SSEAKSVM, to predict protein structural classes. The secondary structures of all protein sequences are obtained by using the tool PSIPRED and then a linear kernel on the basis of secondary structure element alignment scores is constructed for training a support vector machine classifier without parameter adjusting. Our method SSEAKSVM was evaluated on two low-homology datasets 25PDB and 1189 with sequence homology being 25% and 40%, respectively. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies on these two data sets are 86.3% and 84.5%, respectively, which are higher than those obtained by other existing methods. Especially, our method achieves higher accuracies (88.1% and 88.5%) for differentiating the α + β class and the α/β class compared to other methods. This suggests that our method is valuable to predict protein structural classes particularly for low-homology protein sequences. The source code of the method in this paper can be downloaded at http://math.xtu.edu.cn/myphp/math/research/source/SSEAK_source_code.rar.

Structure matters: Adoption of structured classification Approach in the context of cognitive presence classification

Within online learning communities, receiving timely and meaningful insights into the quality of learning activities is an important part of an effective educational experience. Commonly adopted methods – such as the Community of Inquiry framework – rely on manual coding of online discussion transcripts, which is a costly and time consuming process. There are several efforts underway to enable the automated classification of online discussion messages using supervised machine learning, which would enable the real-time analysis of interactions occurring within online learning communities. This paper investigates the importance of incorporating features that utilise the structure of on-line discussions for the classification of "cognitive presence" – the central dimension of the Community of Inquiry framework focusing on the quality of students' critical thinking within online learning communities. We implemented a Conditional Random Field classification solution, which incorporates structural features that may be useful in increasing classification performance over other implementations. Our approach leads to an improvement in classification accuracy of 5.8% over current existing techniques when tested on the same dataset, with a precision and recall of 0.630 and 0.504 respectively.

A germline polymorphism of thymine DNA glycosylase induces genomic instability and cellular transformation

Thymine DNA glycosylase (TDG) functions in base excision repair, a DNA repair pathway that acts in a lesion-specific manner to correct individual damaged or altered bases. TDG preferentially catalyzes the removal of thymine and uracil paired with guanine, and is also active on 5-fluorouracil (5-FU) paired with adenine or guanine. The rs4135113 single nucleotide polymorphism (SNP) of TDG is found in 10% of the global population. This coding SNP results in the alteration of Gly199 to Ser. Gly199 is part of a loop responsible for stabilizing the flipped abasic nucleotide in the active site pocket. Biochemical analyses indicate that G199S exhibits tighter binding to both its substrate and abasic product. The persistent accumulation of abasic sites in cells expressing G199S leads to the induction of double-strand breaks (DSBs). Cells expressing the G199S variant also activate a DNA damage response. When expressed in cells, G199S induces genomic instability and cellular transformation. Together, these results suggest that individuals harboring the G199S variant may have increased risk for developing cancer.

Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula × P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).

Removal of organic content from diesel exhaust particles alters cellular responses of primary human bronchial epithelial cells cultured at an air-liquid interface

Background Exposure to air pollutants, including diesel particulate matter, has been linked to adverse respiratory health effects. Inhaled diesel particulate matter contains adsorbed organic compounds. It is not clear whether the adsorbed organics or the residual components are more deleterious to airway cells. Using a physiologically relevant model, we investigated the role of diesel organic content on mediating cellular responses of primary human bronchial epithelial cells (HBECs) cultured at an air-liquid interface (ALI). Methods Primary HBECs were cultured and differentiated at ALI for at least 28 days. To determine which component is most harmful, we compared primary HBEC responses elicited by residual (with organics removed) diesel emissions (DE) to those elicited by neat (unmodified) DE for 30 and 60 minutes at ALI, with cigarette smoke condensate (CSC) as the positive control, and filtered air as negative control. Cell viability (WST-1 cell proliferation assay), inflammation (TNF-α, IL-6 and IL-8 ELISA) and changes in gene expression (qRT-PCR for HO-1, CYP1A1, TNF-α and IL-8 mRNA) were measured. Results Immunofluorescence and cytological staining confirmed the mucociliary phenotype of primary HBECs differentiated at ALI. Neat DE caused a comparable reduction in cell viability at 30 or 60 min exposures, whereas residual DE caused a greater reduction at 60 min. When corrected for cell viability, cytokine protein secretion for TNF-α, IL-6 and IL-8 were maximal with residual DE at 60 min. mRNA expression for HO-1, CYP1A1, TNF-α and IL-8 was not significantly different between exposures. Conclusion This study provides new insights into epithelial cell responses to diesel emissions using a physiologically relevant aerosol exposure model. Both the organic content and residual components of diesel emissions play an important role in determining bronchial epithelial cell response in vitro. Future studies should be directed at testing potentially useful interventions against the adverse health effects of air pollution exposure.

Crystal structure of morpholin-4-ium cinnamate

In the anhydrous salt formed from the reaction of morpholine with cinnamic acid, C4H10NO+ C9H7O2-, the acid side chain in the trans-cinnamate anion is significantly rotated out of the benzene plane [C-C-C-C torsion angle = 158.54(17)deg. In the crystal, one of the the aminium H atoms is involved in a asymmetric three-centre cation-anion N-H...(O,O') R2/1(4) hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. The second aminium H atom forms an inter-species N-H...O(carboxyl) hydrogen bond, generating a one-dimensional chain structure extending along [100]. Chains are linked by C-H...O interactions forming a supramolecular layer parallel to (01-1).

Electronic structure studies and photocatalytic properties of cubic Bi1.5ZnNb1.5O7

The photocatalytic ability of cubic Bi1.5ZnNb1.5O7 (BZN) pyrochlore for the decolorization of an acid orange 7 (AO7) azo dye in aqueous solution under ultraviolet (UV) irradiation has been investigated for the first time. BZN catalyst powders prepared using low temperature sol-gel and higher temperature solid-state methods have been evaluated and their reaction rates have been compared.The experimental band gap energy has been estimated from the optical absorption edge and has been used as reference for theoretical calculations. The electronic band structure of BZN has been investigated using first-principles density functional theory (DFT) calculations for random, completely and partially ordered solid solutions of Zn cations in both the A and B sites of the pyrochlore structure.The nature of the orbitals in the valence band (VB) and the conduction band (CB) has been identified and the theoretical band gap energy has been discussed in terms of the DFT model approximations.

The equilibrium geometry and electronic structure of Bi nanolines on clean and hydrogenated Si(001) surfaces

The equilibrium geometry, electronic structure and energetic stability of Bi nanolines on clean and hydrogenated Si(001) surfaces have been examined by means of ab initio total energy calculations and scanning tunnelling microscopy. For the Bi nanolines on a clean Si surface the two most plausible structural models, the Miki or M model (Miki et al 1999 Phys. Rev. B 59 14868) and the Haiku or H model (Owen et al 2002 Phys. Rev. Lett. 88 226104), have been examined in detail. The results of the total energy calculations support the stability of the H model over the M model, in agreement with previous theoretical results. For Bi nanolines on the hydrogenated Si(001) surface, we find that an atomic configuration derived from the H model is also more stable than an atomic configuration derived from the M model. However, the energetically less stable (M) model exhibits better agreement with experimental measurements for equilibrium geometry. The electronic structures of the H and M models are very similar. Both models exhibit a semiconducting character, with the highest occupied Bi-derived bands lying at ~0.5 eV below the valence band maximum. Simulated and experimental STM images confirm that at a low negative bias the Bi lines exhibit an 'antiwire' property for both structural models.

Bismuth nanolines on Si(001) and their influence on mesoscopic surface structure

Experimental studies of Bi heteroepitaxy on Si(001) have recently uncovered a self-organised nanoline motif which has no detectable width dispersion. The Bi lines can be grown with an aspect ratio that is greater than 350 : 1. This paper describes a study of the nanoline geometry and electronic structure using a combination of scanning tunneling microscopy (STM) and ab initio theoretical methods. In particular, the effect that the lines have on Si(001) surface structure at large length scales, l > 100 nm, is studied. It has been found that Bi line growth on surfaces that have regularly spaced single height steps results in a 'preferred' domain orientation.

Substrate, molecular structure, and solvent effects in 2D self-assembly via hydrogen and halogen bonding

Recently, halogen···halogen interactions have been demonstrated to stabilize two-dimensional supramolecular assemblies at the liquid–solid interface. Here we study the effect of changing the halogen, and report on the 2D supramolecular structures obtained by the adsorption of 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) and 2,4,6-tris(4-iodophenyl)-1,3,5-triazine (TIPT) on both highly oriented pyrolytic graphite and the (111) facet of a gold single crystal. These molecular systems were investigated by combining room-temperature scanning tunneling microscopy in ambient conditions with density functional theory, and are compared to results reported in the literature for the similar molecules 1,3,5-tri(4-bromophenyl)benzene (TBPB) and 1,3,5-tri(4-iodophenyl)benzene (TIPB). We find that the substrate exerts a much stronger effect than the nature of the halogen atoms in the molecular building blocks. Our results indicate that the triazine core, which renders TBPT and TIPT stiff and planar, leads to stronger adsorption energies and hence structures that are different from those found for TBPB and TIPB. On the reconstructed Au(111) surface we find that the TBPT network is sensitive to the fcc- and hcp-stacked regions, indicating a significant substrate effect. This makes TBPT the first molecule reported to form a continuous monolayer at room temperature in which molecular packing is altered on the differently reconstructed regions of the Au(111) surface. Solvent-dependent polymorphs with solvent coadsorption were observed for TBPT on HOPG. This is the first example of a multicomponent self-assembled molecular networks involving the rare cyclic, hydrogen-bonded hexamer of carboxylic groups, R66(24) synthon.

With great structure comes great functionality: Understanding and emulating spider silk

The overarching aim of biomimetic approaches to materials synthesis is to mimic simultaneously the structure and function of a natural material, in such a way that these functional properties can be systematically tailored and optimized. In the case of synthetic spider silk fibers, to date functionalities have largely focused on mechanical properties. A rapidly expanding body of literature documents this work, building on the emerging knowledge of structure–function relationships in native spider silks, and the spinning processes used to create them. Here, we describe some of the benchmark achievements reported until now, with a focus on the last five years. Progress in protein synthesis, notably the expression on full-size spidroins, has driven substantial improvements in synthetic spider silk performance. Spinning technology, however, lags behind and is a major limiting factor in biomimetic production. We also discuss applications for synthetic silk that primarily capitalize on its nonmechanical attributes, and that exploit the remarkable range of structures that can be formed from a synthetic silk feedstock.

Synthesis, characterization, and electronic structure studies of cubic Bi1.5ZnTa1.5O7 for photocatalytic applications

Bi1.5ZnTa1.5O7 (BZT) has been synthesized using an alkoxide based sol-gel reaction route. The evolution of the phases produced from the alkoxide precursors and their properties have been characterized as function of temperature using a combination of thermogravimetric analysis (TGA) coupled with mass spectrometry (MS), infrared emission spectrometry (IES), X-ray diffraction (XRD), ultraviolet and visible (UV-Vis) spectroscopy, Raman spectroscopy, and N2 adsorption/desorption isotherms. The lowest sintering temperature (600∘C) to obtain phase pure BZT powders with high surface area (14.5m2/g) has been determined from the thermal decomposition and phase analyses.The photocatalytic activity of the BZT powders has been tested for the decolorization of organic azo-dye and found to be photoactive under UV irradiation.The electronic band structure of the BZT has been investigated using density functional theory (DFT) calculations to determine the band gap energy (3.12 eV) and to compare it with experimental band gap (3.02 eV at 800∘C) from optical absorptionmeasurements. An excellent match is obtained for an assumption of Zn cation substitutions at specifically ordered sites in the BZT structure.

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.