A simple and inexpensive method for evaluation of in vitro cell adhesion on screws

Only a limited number of techniques are available for assessing the effect of different coating materials on cell adherence to screws. In this study, we describe a simple and inexpensive method for evaluation of cell adhesion on irregular surfaces such as the surgical or implant screws. For this purpose, we prepared semi-submerged screws in the petri dishes using agar. Using BSA- or HA-coated screws, we tested whether BSA or HA could improve cell adherence when used as coating materials. Agar-coated screws were used as internal control. Then the “ratio of cell adherence” was calculated by subtracting the reference RCA value obtained from the agar coated screws (internal control). When compared to that of the non-coated screws both the HA- and BSA-coating improved cell adherence on the screws by 2.34 and 2.72 fold respectively. Similarly, MTT assay data revealed that the metabolic capacities of cells on HA- or BSA-coated screws were improved by 2.36 and 2.86 fold respectively. These findings suggest that this protocol can be used for comparing the ability of cells to attach on irregular surfaces such as dental or orthopedic screws and assessing their viability.     

SURF’s UP! — Protein classification by surface comparisons

Large-scale genome sequencing and structural genomics projects generate numerous sequences and structures for 'hypothetical' proteins without functional characterizations. Detection of homology to experimentally characterized proteins can provide functional clues, but the accuracy of homology-based predictions is limited by the paucity of tools for quantitative comparison of diverging residues responsible for the functional divergence. SURF'S UP! is a web server for analysis of functional relationships in protein families, as inferred from protein surface maps comparison according to the algorithm. It assigns a numerical score to the similarity between patterns of physicochemical features(charge, hydrophobicity) on compared protein surfaces. It allows recognizing clusters of proteins that have similar surfaces, hence presumably similar functions. The server takes as an input a set of protein coordinates and returns files with "spherical coordinates" of proteins in a PDB format and their graphical presentation, a matrix with values of mutual similarities between the surfaces, and the unrooted tree that represents the clustering of similar surfaces, calculated by the neighbor-joining method. SURF'S UP! facilitates the comparative analysis of physicochemical features of the surface, which are the key determinants of the protein function. By concentrating on coarse surface features, SURF'S UP! can work with models obtained from comparative modelling. Although it is designed to analyse the conservation among homologs, it can also be used to compare surfaces of non-homologous proteins with different three-dimensional folds, as long as a functionally meaningful structural superposition is supplied by the user. Another valuable characteristic of our method is the lack of initial assumptions about the functional features to be compared. SURF'S UP! is freely available for academic researchers at http://asia.genesilico.pl/surfs_up/.     

Capture of genomic DNA on glass microscope slides

It is well known that DNA strands bind to silica surfaces in the presence of high concentrations of chaotropic salts. We developed simple methods to evaluate binding and recovery of DNA on flat glass microscope slides and compared their properties with commercially available silica "spin columns". Surprisingly, genomic DNA was recovered efficiently from untreated glass slides. Binding and elution times from glass slides were optimized in experiments with DNA samples of various sizes and defined buffers. Average DNA recovery from 500 ng of input genomic DNA varied from 25 to 53% for the glass slide protocol. Yields were comparable to those of spin columns. Human serum albumin and plasma components decreased DNA binding to glass several-fold in a concentration-dependent manner. These results support the concept of using flat glass slides as DNA purification surfaces in microfluidic devices for PCR sample preparation.     

Wang–Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins

Generic features associated with the adsorption of proteins on solid surfaces are reviewed within the framework of the hydrophobic-polar (HP) lattice protein model. The thermodynamic behaviour and structural properties of various HP protein sequences interacting with attractive surfaces have been studied using extensive Wang–Landau sampling with different types of surfaces, each of which attracts either: all monomers, only hydrophobic (H) monomers or only polar (P) monomers, respectively. Consequently, different types of folding behaviour occur for varied surface strengths. Analysis of the combined patterns of various structural observables, e.g. the derivatives of the number of interaction contacts, together with the specific heat, leads to the identification of fundamental categories of folding and transition hierarchies. We also inferred a connection between the transition categories and the relative surface strengths, i.e. the ratios of the surface attractive strengths to the intra-chain attraction among H monomers. Thus, we believe that the folding hierarchies and identification scheme are generic for different HP sequences interacting with attractive surfaces, regardless of the chain length, sequence or surface attraction.     

Structural analysis of wheat wax (Triticum aestivum, c.v. ‘Naturastar’ L.): from the molecular level to three dimensional crystals

In order to elucidate the self assembly process of plant epicuticular waxes, and the molecular arrangement within the crystals, re-crystallisation of wax platelets was studied on biological and non-biological surfaces. Wax platelets were extracted from the leaf blades of wheat (Triticum aestivum L., c.v. ‘Naturastar’, Poaceae). Waxes were analysed by gas chromatography (GC) and mass spectrometry (MS). Octacosan-1-ol was found to be the most abundant chemical component of the wax mixture (66 m%) and also the determining compound for the shape of the wax platelets. The electron diffraction pattern showed that both the wax mixture and pure octacosan-1-ol are crystalline. The re-crystallisation of the natural wax mixture and the pure octacosan-1-ol were studied by scanning tunnelling microscopy (STM), atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Crystallisation of wheat waxes and pure octacosano-1-ol on the non polar highly ordered pyrolytic graphite (HOPG) led to the formation of platelet structures similar to those found on the plant surface. In contrast, irregular wax morphologies and flat lying plates were formed on glass, silicon, salt crystals (NaCl) and mica surfaces. Movement of wheat wax through isolated Convallaria majalis cuticles led to typical wax platelets of wheat, arranged in the complex patterns typical for C. majalis. STM of pure octacosan-1-ol monolayers on HOPG showed that the arrangement of the molecules strictly followed the hexagonal structure of the substrate crystal. Re-crystallisation of wheat waxes on non-polar crystalline HOPG substrate showed that technical surfaces could be used to generate microstructured, biomimetic surfaces. AFM and SEM studies proved that a template effect of the substrate determined the orientation of the re-grown crystals. These effects of the structure and polarity of the substrate on the morphology of the epicuticular waxes are relevant for understanding interactions between biological as well as technical surfaces and waxes.     

城市不同下垫面的降雨径流污染

当点源污染被有效控制后,面源污染成为城市水质恶化的主要原因之一。屋面和路面等不透水面以及绿地是城市的3种主要下垫面形式。当暴雨产生时,各种下垫面特别是屋面和路面上汇聚大量污染物质产生径流,对城市生态环境造成严重的污染。以文教区为例,对屋面、路面、草坪的径流水质进行了监测,指标包括pH、悬浮固体(SS)、化学需氧量(COD)、总氮(TN)、总磷(TP)和生化需氧量(BOD5)等。比较分析发现,3种下垫面类型的径流水质均较差,COD、TN、TP、BOD5平均浓度超过地表水环境质量Ⅴ级标准。COD、TN和TP浓度与SS含量之间相关性较好,相关系数可达0.85以上。径流中污染物浓度受多个因素的影响,其中降雨量和降雨强度是两个重要因素,雨强越大,雨水对城市下垫面的冲刷就越强;在相同的污染物累积量条件下,降雨量越大,径流中污染物浓度越低。     

Effects of substrate structure on speed and acceleration capacity in climbing geckos

We studied the effects of substrate structure on locomotor performance in a climbing gecko, Hemidactylus garnoti . We quantified three performance traits (acceleration capacity, instantaneous speed, and final speed) on three substrates: (i) smooth wood, (ii) a cloth surface, and (iii) a wire mesh. While acceleration capacity and instantaneous speed were highest on the wooden surface, final speed did not differ significantly among substrates. Using scanning electron microscopy (SEM) pictures, we estimated that 98% of the wooden surface is available for adhesion by the setae on the toepads, while this percentage is much lower for the mesh and cloth (41 and 37%, respectively). We suggest that when a gecko climbs up a gap-filled substrate, such as the wire mesh or cloth, adhesion will only happen between part of the toepad and the substrate, resulting in a diminished acceleration capacity. The higher acceleration capacity on the wooden substrate and the fact that the geckos tend to slip less often on this particular surface, may explain the difference in instantaneous speed. As for final speed, geckos might achieve similar final speeds on all three substrates by employing different locomotor strategies. Our results suggest that microhabitat use in nature might have a profound effect on locomotor performance and survival for climbing lizards such as geckos.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 385–393.     

Effect of zinc on gene expression in osteoblastic MC3T3-E1 cells: enhancement of Runx2, OPG, and regucalcin mRNA expressions

Activation of fibroblast growth factor receptors (FGFRs) requires the formation of a ternary complex between fibroblast growth factors (FGFs), FGFRs, and heparan sulfate proteoglycans, which are all located on the cell surface and the basement membrane (BM)/extracellular matrix (ECM). Heparan sulfate proteoglycans appear to stabilize FGFs by inhibiting the rapid degradation of FGFs normally observed in solution. Because of the pivotal role of FGFs in proliferative and developmental pathways, a number of recent studies have attempted to engineer microenvironments to stabilize growth factors for use in applications in tissue culture and regenerative medicine. In this communication, we demonstrate that covalent linkage of FGF-2 to nanofibrillar surfaces (defined as covalently bound FGF-2) composed of a network of polyamide nanofibers resulted in the maintenance of the biological efficacy of FGF-2 when stored dry for at least 6 months at 25°C or 4°C. Moreover, covalently bound FGF-2 was more potent than FGF-2 in solution when measured in cellular assays of proliferation and viability using a variety of cell types. Covalently bound FGF-2 also strongly activated FGFR, extracellular signal-regulated kinase (ERK1/2), and c-fos. Hence cell-signaling molecules can be incorporated into a synthetic nanofibrillar surface, providing a novel means to enhance their stability and biological activity.     

Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment

Numerous methods are available for use as part of a virtual screening strategy but, as yet, no single method is able to guarantee both a level of confidence comparable to experimental screening and a level of computing efficiency that could drastically cut the costs of early phase drug discovery campaigns. Here, we present VSM-G (virtual screening manager for computational grids), a virtual screening platform that combines several structure-based drug design tools. VSM-G aims to be as user-friendly as possible while retaining enough flexibility to accommodate other in silico techniques as they are developed. In order to illustrate VSM-G concepts, we present a proof-of-concept study of a fast geometrical matching method based on spherical harmonics expansions surfaces. This technique is implemented in VSM-G as the first module of a multiple-step sequence tailored for high-throughput experiments. We show that, using this protocol, notable enrichment of the input molecular database can be achieved against a specific target, here the liver-X nuclear receptor. The benefits, limitations and applicability of the VSM-G approach are discussed. Possible improvements of both the geometrical matching technique and its implementation within VSM-G are suggested. Figure Basic principle of the virtual screening funnel process.