Ultrasensitive impedimetric lectin based biosensor for glycoproteins containing sialic acid

We report on an ultrasensitive label-free lectin-based impedimetric biosensor for the determination of the sialylated glycoproteins fetuin and asialofetuin. A sialic acid binding agglutinin from Sambucus nigra I was covalently immobilised on a mixed self-assembled monolayer (SAM) consisting of 11-mercaptoundecanoic acid and 6-mercaptohexanol. Poly(vinyl alcohol) was used as a blocking agent. The sensor layer was characterised by atomic force microscopy, electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy. The biosensor exhibits a linear range that spans 7 orders of magnitude for both glycoproteins, with a detection limit as low as 0.33 fM for fetuin and 0.54 fM for asialofetuin. We also show, by making control experiments with oxidised asialofetuin, that the biosensor is capable of quantitatively detecting changes in the fraction of sialic acid on glycoproteins. We conclude that this work lays a solid foundation for future applications of such a biosensor in terms of the diagnosis of diseases such as chronic inflammatory rheumatoid arthritis, genetic disorders and cancer, all of which are associated with aberrant glycosylation of protein biomarkers.

Mercerized cellulose biocomposites: a study of influence of mercerization on cellulose supramolecular structure, water retention value and tensile properties

In this study the effect of the mercerization degree on the water retention value (WRV) and tensile properties of compression molded sulphite dissolving pulp was evaluated. The pulp was treated with 9, 10, or 11 % aqueous NaOH solution for 1 h before compression molding. To study the time dependence of mercerization the pulp was treated with 12 wt% aqueous NaOH for 1, 6 or 48 h. The cellulose I and II contents of the biocomposites were determined by solid state cross polarization/magic angle spinning carbon 13 nuclear magnetic resonance (CP/MAS ¹³C NMR) spectroscopy. By spectral fitting of the C6 and C1 region the cellulose I and II content, respectively, could be determined. Mercerization decreased the total crystallinity (sum of cellulose I and cellulose II content) and it was not possible to convert all cellulose I to cellulose II in the NaOH range investigated. Neither increased the conversion significantly with 12 wt% NaOH at longer treatment times. The slowdown of the cellulose I conversion was suggested as being the result from the formation of cellulose II as a consequence of coalescence of anti-parallel surfaces of neighboring fibrils (Blackwell et al. in Tappi 61:71–72, 1978; Revol and Goring in J Appl Polym Sci 26:1275–1282, 1981; Okano and Sarko in J Appl Polym Sci 30:325–332, 1985). Compression molding of the partially mercerized dissolving pulps yielded biocomposites with tensile properties that could be correlated to the decrease in cellulose I content in the pulps. Mercerization introduces cellulose II and disordered cellulose and lowered the total crystallinity reflected as higher water sensitivity (higher WRV values) and poorer stiffness of the mercerized biocomposites.     

Challenges for impedimetric affinity sensors targeting protein detection

The review provides articles discussing big challenges behind successful design of impedimetric biosensors and the way such challenges were/could be addressed for highly sensitive affinity detection of proteins. In particular, the effect of gold etching by chloride ions or by CN^? ions (released from the redox probe [Fe(CN)₆]^3-/4-), the effect of ionic strength of the assay buffer; the effect of initial interfacial properties (capacitance) and the effect of the high analyte:bioreceptor ratio on electrochemical impedance spectroscopy–based biosensing are discussed. The review provides also short discussion related to other factors, which can significantly affect operational performance of electrochemical impedance spectroscopy–based biosensing including novel conductive interfaces, small bioreceptors, strategies for improved selectivity (nonbiofouling interfaces) and sensitivity (use of nanoparticles).     

Design and synthesis of two epoxide derivatives from 3-ethynylaniline

For several years ago, several epoxide derivatives have been prepared using different methods; however, some protocols use reagents which could be expensive and require specials conditions. The aim of this investigation was to prepare two new epoxide-derivatives from 3-ethynylaniline using some reactions such as oximation, acetylation, 2 + 2 addition, functionalized chloroamides, and epoxidation via Darzens reaction. The chemical characteristics of epoxide derivatives were determinate through a spectroscopic and spectrometric analysis. In conclusion, it is noteworthy that the reactions used in this study do not involve expensive reagents or special conditions for the synthesis of epoxide derivatives.     

On‐Surface Synthesis and Characterization of Triply Fused Porphyrin–Graphene Nanoribbon Hybrids

On‐surface synthesis offers a versatile approach to prepare novel carbon‐based nanostructures that cannot be obtained by conventional solution chemistry. Graphene nanoribbons (GNRs) have potential for a variety of applications. A key issue for their application in molecular electronics is in the fine‐tuning of their electronic properties through structural modifications, such as heteroatom doping or the incorporation of non‐benzenoid rings. In this context, the covalent fusion of GNRs and porphyrins (Pors) is a highly appealing strategy. Herein we present the selective on‐surface synthesis of a Por–GNR hybrid, which consists of two Pors connected by a short GNR segment. The atomically precise structure of the Por–GNR hybrid has been characterized by bond‐resolved scanning tunneling microscopy (STM) and noncontact atomic force microscopy (nc‐AFM). The electronic properties have been investigated by scanning tunneling spectroscopy (STS), in combination with DFT calculations, which reveals a low electronic gap of 0.4 eV.     

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Alkyloxycarbonyl group migration in furanosides

A migration of methyloxycarbonyl group from secondary to primary hydroxyl was observed in furanosides (ribosides and xylosides) under usual desilylation conditions using tetrabutylammonium fluoride. The migration was studied further on several alkyloxycarbonyl furanosides under either basic or acidic conditions. As follows from ¹³C labelling experiments and product distribution, the migration in xylosides, proceeds intramolecularly via six-membered cyclic carbonate, whereas in ribosides, the migration is intermolecular. Acidic conditions prevented the migration in ribosides whereas the migration in xylosides was circumvented under neutral conditions.     

On linear-fractional relations and images of angular operators

For plus-operators in a Banach indefinite space, we consider a linear-fractional relation. The classes of operators with the empty domain of definition for such a relation are described. The sufficient (and necessary, in some meaning) conditions for the chain rule to be valid are given.     

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms.