Fibronectin adsorption on tantalum: the influence of nanoroughness

The complex mechanisms of protein adsorption at the solid-liquid interface is of great importance in many research areas, including protein purification, biocompatibility of medical implants, biosensing, and biofouling. The protein adsorption process depends crucially on both the nanoscale chemistry and topography of the interface. Here, we investigate the adsorption of the cell-binding protein fibronectin on flat and nanometer scale rough tantalum oxide surfaces using ellipsometry and quartz crystal microbalance with dissipation (QCM-D). On the flat tantalum oxide surfaces, the interfacial protein spreading causes an increase in the rigidity and a decrease in the thickness of the adsorbed fibronectin layer with decreasing bulk protein concentration. For the tantalum oxide surfaces with well-controlled, stochastic nanometer scale roughness, similar concentration effects are observed for the rigidity of the fibronectin layer and saturated fibronectin uptake. However, we find that the nanorough tantalum oxide surfaces promote additional protein conformational changes, an effect especially apparent from the QCM-D signals, interpreted as an additional stiffening of the formed fibronectin layers.     

A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis

The benefits of defining common spot boundaries when several gels from 2-DE are compared and analyzed have lately been stressed by both commercial software producers and users of this software. Though the importance of common spot boundaries is clearly stated, few reports exist that target this issue explicitly. In this study a method for defining common spots boundaries is developed, called the spot density method. The method consists of the following steps: segmentation and spot identification on each individual gel, transferring the spot-center coordinates for all gels onto a single new gel, collecting spot centers clustered together in the new gel and finally assigning pixels and new spot boundaries based on the spots in each cluster. The method is compared to a synthetic gel approach, and validated by visual inspection of three representative areas in the gels. The gel images need to be aligned prior to segmentation and spot identification, but the method can be used regardless of the choice of segmentation procedure. This makes the method an easy extension to existing methods for spot identification and matching. Conclusions based on the visual inspection are that the spot density method identifies partly overlapping spots and low-intensity spots better than the synthetic gel approach.     

Improved DNA fragment length estimation in capillary electrophoresis

In CE the charged DNA strands are fractionated according to fragment lengths as they migrate through the capillary, since shorter DNA fragments pass through the sieving matrix faster. Multiplexed internal size standards are used to estimate the size of unknown DNA fragments. In the literature there are statements about migration abnormalities for the 250 and 340 bp fragments in the GeneScan-500 (GS500) internal size standards. Such anomalous migration of size standards could obviously introduce errors in the estimation of unknown fragments. Therefore, a number of analysis programs simply exclude some of these fragments. In the present work we first evaluate the effect of excluding each of the fragments in the internal size standards used in CE. Next, a method which is based on estimating the true values of the anomalous fragments is presented. The results obtained by the new method indicate a significant improvement compared to results obtained when one (or both) of the anomalous fragments in GS500 is (are) excluded or included when estimating the size of unknown DNA fragments. In the higher-molecular-weight region, the average error is reduced from 1.91 bp in ABI GeneMapper (excluding 250 bp) to 0.15 bp in the new method (using the estimated values for 250 and 340 bp). In the lower-molecular-weight region, excluding both fragments will improve the results by an average of 0.74 bp compared to ABI GeneMapper.     

Fibronectin adsorption on gold, Ti-, and Ta-oxide investigated by QCM-D and RSA modelling

The adsorption of fibronectin on gold, Ti-, and Ta-oxide surfaces is investigated by means of the quartz crystal microbalance with dissipation (QCM-D) technique. The surface chemistry (gold, Ti-, and Ta-oxide) is found to influence the frequency shift observed during adsorption of the fibronectin layer with the magnitude being Delta f Au>Delta f Ti-oxide approximately Delta f Ta-oxide. Corresponding variations in the dissipation change normalised to frequency change (Delta D/Delta f) for the layer are observed. The QCM-D data are further analyzed by the random sequential adsorption (RSA) model, and adsorption rate parameter ka and footprint (a) determined, which supported the trend seen in the Delta f and Delta D/Delta f values. The value of ka found by the RSA modelling of the QCM-D resonance frequency data is found to match the ratio between the mass measured by QCM-D and the mass reported by optical techniques in literature. We conclude that comparison of the adsorption rate parameter (ka) obtained by RSA modelling of the QCM-D data with ka values obtained from RSA modelling of data obtained using optical techniques can be a route to determine the degree of hydration of the adsorbed protein layer.     

UV light-assisted mineralisation and biodetoxification of Ponceau S with hydroxyl and sulfate radicals

The present study reports simultaneous mineralisation and biodetoxification of Ponceau S (3-hydroxy-4-(2-sulfo-4-[4-sulfophenylazo]phenylazo)-2,7-naphthalenedisulfonic acid sodium salt), an azo dye, by UV light assisted oxidation with hydroxyl and sulfate radicals. Metal ion catalysts used in the work were: Fe²⁺ and Ag⁺, and the oxidants used were: hydrogen peroxide and S₂O₈^2?. Strategies adopted to make the processes environmentally benign and economically viable by achieving maximum mineralisation in the shortest possible time are described. Mineralisation efficiency (Em) of various systems was found to follow the order: E_m(Fe²⁺/H₂O₂/UV) > E_m(Fe²⁺/S₂O₈^2?/UV) > E_m(Ag⁺/H₂O₂/UV) ≈ E_m(Ag⁺/S₂O₈^2?/UV). Thus, Fe²⁺ and HP are the most suitable metal ion catalyst and oxidant respectively, showing higher efficiency at pH 3 followed by that at pH 6.6. It is possible to enhance the Fe²⁺/H₂O₂/UV process electrical energy efficiency by maintaining the concentration of Fe at either 0.05 mM or 0.03 mM and that of the oxidant at 2.5 mM. The bioassay study revealed that the Fe²⁺/S₂O₈^2?/UV process biodetoxification efficiency is higher at pH 3 (93.7 %) followed by that at pH 6.6 (80.1 %) at the concentration of Fe ²⁺ and S₂O₈^2? of 0.03 mM and 2.5 mM, respectively. Thus, not only the concentration of Fe²⁺, but also the nature of the oxidant and pH play an important role in the biodetoxification process and S₂O₈^2? possesses higher biodetoxification efficiency than H₂O₂.     

Single‐Molecule Fluorescence Detection of a Synthetic Heparan Sulfate Disaccharide

The first single‐molecule fluorescence detection of a structurally‐defined synthetic carbohydrate is reported: a heparan sulfate (HS) disaccharide fragment labeled with Alexa488. Single molecules have been measured whilst freely diffusing in solution and controlled encapsulation in surface‐tethered lipid vesicles has allowed extended observations of carbohydrate molecules down to the single‐molecule level. The diverse and dynamic nature of HS–protein interactions means that new tools to investigate pure HS fragments at the molecular level would significantly enhance our understanding of HS. This work is a proof‐of‐principle demonstration of the feasibility of single‐molecule studies of synthetic carbohydrates which offers a new approach to the study of pure glycosaminoglycan (GAG) fragments.     

The inconsistency in adsorption properties and powder XRD data of MOF-5 is rationalized by framework interpenetration and the presence of organic and inorganic species in the nanocavities

MOF-5 is the archetype metal-organic framework and has been subjected to numerous studies the past few years. The focal point of this report is the pitfalls related to the MOF-5 phase identification based on powder XRD data. A broad set of conditions and procedures have been reported for MOF-5 synthesis. These variations have led to materials with substantially different adsorption properties (specific surface areas in the range 700 to 3400 m(2)/g). The relatively low weight loss observed for some as synthesized samples upon solvent removal is also indicative of a low pore volume. Regrettably, these materials have all been described as MOF-5 without any further comments. Furthermore, the reported powder XRD patterns hint at structural differences: The variations in surface area are accompanied by peak splitting phenomena and rather pronounced changes in the relative peak intensities in the powder XRD patterns. In this work, we use single-crystal XRD to investigate structural differences between low and high surface area MOF-5. The low surface area MOF-5 sample had two different classes of crystals. For the dominant phase, Zn(OH)2 species partly occupied the cavities. The presence of Zn species makes the hosting cavity and possibly also adjacent cavities inaccessible and thus efficiently reduces the pore volume of the material. Furthermore, the minor phase consisted of doubly interpenetrated MOF-5 networks, which lowers the adsorption capacity. The presence of Zn species and lattice interpenetration changes the symmetry from cubic to trigonal and explains the peak splitting observed in the powder XRD patterns. Pore-filling effects from the Zn species (and partly the solvent molecules) are also responsible for the pronounced variations in powder XRD peak intensities. This latter conclusion is particularly useful for predicting the adsorption properties of a MOF-5-type material from powder XRD.     

Synthesis of functionalized, unsymmetrical 1,3,4,6-tetrasubstituted 2,5-diketopiperazines

A general and efficient method for the synthesis of unsymmetrical 1,3,4,6-tetrasubstituted 2,5-diketo- piperazines (DKPs) is described. Cyclization of N-amide alkylated dipeptide methyl esters, followed by alkylation, furnished the corresponding tetrasubstituted DKPs in good overall yields. The influence of steric hindrance in the alkylation reactions appeared to be of lesser importance as long as reactive alkylating agents were used. Furthermore, we have demonstrated the use of tetrasubstituted DKPs as a scaffold for further chemical manipulations to produce novel DKPs with desired properties.     

Structural Tracking of a Bimolecular Reaction in Solution by Time‐Resolved X‐Ray Scattering

Molecular movies : Time‐resolved X‐ray scattering provides direct structural information on an electronically excited complex while it is formed in the bimolecular reaction between excited octahydrogen[tetrakis‐μ‐diphosphito‐1κP:2κP′‐diplatinate](4‐) (PtPOP*) and thallium ions. In the exciplex one thallium(I) and two platinum(II) ions are found to be collinear.

     

Identification and characterization of endonuclein binding proteins: evidence of modulatory effects on signal transduction and chaperone activity

Background  

We have previously identified endonuclein as a cell cycle regulated WD-repeat protein that is up-regulated in adenocarcinoma of the pancreas. Now, we aim to investigate its biomedical functions.