Mass amplifying probe for sensitive fluorescence anisotropy detection of small molecules in complex biological samples

Fluorescence anisotropy (FA) is a reliable and excellent choice for fluorescence sensing. One of the key factors influencing the FA value for any molecule is the molar mass of the molecule being measured. As a result, the FA method with functional nucleic acid aptamers has been limited to macromolecules such as proteins and is generally not applicable for the analysis of small molecules because their molecular masses are relatively too small to produce observable FA value changes. We report here a molecular mass amplifying strategy to construct anisotropy aptamer probes for small molecules. The probe is designed in such a way that only when a target molecule binds to the probe does it activate its binding ability to an anisotropy amplifier (a high molecular mass molecule such as protein), thus significantly increasing the molecular mass and FA value of the probe/target complex. Specifically, a mass amplifying probe (MAP) consists of a targeting aptamer domain against a target molecule and molecular mass amplifying aptamer domain for the amplifier protein. The probe is initially rendered inactive by a small blocking strand partially complementary to both target aptamer and amplifier protein aptamer so that the mass amplifying aptamer domain would not bind to the amplifier protein unless the probe has been activated by the target. In this way, we prepared two probes that constitute a target (ATP and cocaine respectively) aptamer, a thrombin (as the mass amplifier) aptamer, and a fluorophore. Both probes worked well against their corresponding small molecule targets, and the detection limits for ATP and cocaine were 0.5 μM and 0.8 μM, respectively. More importantly, because FA is less affected by environmental interferences, ATP in cell media and cocaine in urine were directly detected without any tedious sample pretreatment. Our results established that our molecular mass amplifying strategy can be used to design aptamer probes for rapid, sensitive, and selective detection of small molecules by means of FA in complex biological samples.     

A life cycle inventory of carbon dioxide as a solvent and additive for industry and in products

Life cycle inventories of four industrial carbon dioxide production processes are reported. The inventory data were calculated using design‐based methodology. Energy consumptions and critical emissions of the four processes are compared. Quasi‐microscopic allocation was applied to processes with multiple products. The inventory data of this study are transparent and can be used in other life cycle studies. Copyright © 2007 Society of Chemical Industry     

Microalgal biomass as a fermentation feedstock for bioethanol production

BACKGROUND: The increasing cost of fossil fuels as well as the escalating social and industrial awareness of the environmental impacts associated with the use of fossil fuels has created the need for more sustainable fuel options. Bioethanol, produced from renewable biomass such as sugar and starch materials, is believed to be one of these options, and it is currently being harnessed extensively. However, the utilization of sugar and starch materials as feedstocks for bioethanol production creates a major competition with the food market in terms of land for cultivation, and this makes bioethanol from these sources economically less attractive. RESULT: This study explores the suitability of microalgae (Chlorococum sp.) as a substrate for bioethanol production via yeast (Saccharomyces bayanus) under different fermentation conditions. Results show a maximum ethanol concentration of 3.83 g L^?1 obtained from 10 g L^?1 of lipid‐extracted microalgae debris. CONCLUSION: This productivity level (～38% w/w), which is in keeping with that of current production systems endorses microalgae as a promising substrate for bioethanol production. Copyright © 2009 Society of Chemical Industry     

Analysis of computational EELS modelling results for MgO-based systems

The ab-initio density functional theory (DFT) code CASTEP was used to model oxygen K edges in various magnesium oxide systems. Firstly, for the bulk material the process of geometry optimisation was carried out. Predicted oxygen K edges were found for a single cell with experimental lattice parameters, and parameters obtained after geometry optimisation, both with single electron core-holes in place. After geometry optimisation, a different predicted result was obtained, although it was qualitatively similar to the result for experimental lattice parameters in some respects. For example, approximately the same sets of peaks are observed, though in different energy positions, and with different relative peak intensities within those sets. Ultimately for the single cell results the experimental lattice parameters generated the predicted result that was in the closest agreement with experiment. It was further observed that a large supercell result (based on the experimental lattice parameters, utilising a core-hole) led to a slightly improved comparison with experiment as compared to the corresponding single cell result, although the latter result, and indeed a ground state calculation also give reasonable agreement with experiment. To rationalise these observations it was necessary to investigate the density of states (DOS) for the MgO cell and its constituent atoms, and it was observed that the conduction bands were of predominantly magnesium character. Furthermore, the core-hole’s introduction had relatively little overall effect on the p DOS prediction for oxygen, though there is a significant localised change close to the Fermi level. This work also considers interface and surface results. The principal aim of the study was to explore the interface of Fe (0 0 1)/MgO (0 0 1), crucial in certain classes of magnetic tunnel junctions (MTJs), which have significant technological applications. An initial step was to consider a MgO (0 0 1) surface. It was verified that a surface could be constructed such that within that surface a theoretical result could be found that matched the bulk result. It was then valid to use this surface as part of an interface with iron. Theoretical results obtained at that interface compare well with experimental results from an epitaxially grown MTJ, and various conclusions are drawn with regard to the nature of the interface.     

Estimating distributed anatomical connectivity using fast marching methods and diffusion tensor imaging

A method is presented for determining paths of anatomical connection between regions of the brain using magnetic resonance diffusion tensor information. Level set theory, applied using fast marching methods, is used to generate three-dimensional time of arrival maps, from which connection paths between brain regions may be identified. The method is demonstrated in the normal brain and it is shown that major white matter tracts may be elucidated and that multiple connections and tract branching are allowed. Maps of connectivity between brain regions are also determined. Four options are described for estimating the degree of connectivity between regions.     

Highly Efficient Rubrene–Graphene Charge‐Transfer Interfaces as Phototransistors in the Visible Regime

Atomically thin materials such as graphene are uniquely responsive to charge transfer from adjacent materials, making them ideal charge‐transport layers in phototransistor devices. Effective implementation of organic semiconductors as a photoactive layer would open up a multitude of applications in biomimetic circuitry and ultra‐broadband imaging but polycrystalline and amorphous thin films have shown inferior performance compared to inorganic semiconductors. Here, the long‐range order in rubrene single crystals is utilized to engineer organic‐semiconductor–graphene phototransistors surpassing previously reported photogating efficiencies by one order of magnitude. Phototransistors based upon these interfaces are spectrally selective to visible wavelengths and, through photoconductive gain mechanisms, achieve responsivity as large as 10⁷ A W^?1 and a detectivity of 9 × 10¹¹ Jones at room temperature. These findings point toward implementing low‐cost, flexible materials for amplified imaging at ultralow light levels.     

Dispersion analysis and computational efficiency of elastic lattice methods for seismic wave propagation

Discrete particle methods or elastic lattice methods represent a 3D elastic solid by a series of interconnected springs arranged on a regular lattice. Generally, these methods only consider nearest neighbour interactions, i.e. they are first-order in space. These interconnected springs interacted through a force term (Hooke's Law for an elastic body), which when viewed on a macroscopic scale provide a numerical solution for the elastodynamic wave equations. Along with solving the elastodynamic wave equations these schemes are capable of simulating elastic static deformation. However, as these methods rely on nearest neighbour interactions they suffer from more pronounced numerical dispersion than traditional continuum methods. By including a new force term, the numerical dispersion can be reduced while keeping the flexibility of the nearest neighbour interaction rule. We present results of simulations where the additional force term reduces the numerical dispersion and increases the accuracy of the elastic lattice method solution. The computational efficiency and parallel scaling of this method on multiple processors is compared with a finite-difference solution to assess the computational cost of using this approach for simulating seismic wave propagation. We also show the applicability of this method to modelling seismic propagation in a complex Earth model.     

Easy adaptation of protein structure to sequence

An investigation into the conservation of coarse, medium andfine grain structural properties has been performed over a dataset of 175 protein tertiary structures in 34 different families,each characterized by a common core fold and a library of conservedsites formed for each family. It is shown that, while the conservationof coarse and medium grain properties correlates to the structuraldeviation between the proteins, fine grain properties are poorlyconserved except in functional sites. This flexibility in finegrain properties suggests that folding can be viewed as an optimizationprocess whereby side chains have freedom to position themselvesas best as possible given environmental conformationa] constraintsand that given a basic framework, the local structure is ableto adapt easily to sequence variation. The conserved cores ofthe 34 families are used to estimate a minimal core size of35% of the fold, consistent with buried residue considerations.Finally, conservation in side chain l torsion angles is combinedwith structural deviation, sequence deviation and resolutionto suggest a set of example structure pairs suitable for testingautomatic homology modelling programs     

Malware and steganography in hard disk firmware

The hard disk drive remains the most commonly used form of storage media in both commercial and domestic computer systems. These drives can contain a vast range of data both of personal value and commercial significance. This paper focuses on two key areas; the potential for the drive operation to be impacted by malicious software and the possibility for the drive firmware to be manipulated to enable a form of steganography. Hard drive firmware is required for the correct operation of the disk drive in particular for dealing with errors arising due to natural wear as the drive ages. Where an area of the drive becomes unreliable due to wear and tear, the disk firmware which monitors the reliability of data access will copy the data from the failing area to a specially designated reserved area. The firmware remaps this data shift so the old data area and the original copy of the data are no longer accessible by the computer operating system. There are now a small number of commercially available devices, intended for data recovery, which can be used to modify the hard drive firmware components. This functionality can be used to conceal code on the disk drive, either as a form of steganography or to potentially include malicious code with the intention to infect or damage software or possibly system hardware. This paper discusses the potential problem generated by firmware being manipulated for malicious purposes.     

3D Printed Tooling for Injection Molded Microfluidics

Microfluidics have been used for several decades to conduct a wide range of research in chemistry and the life sciences. The reduced dimensions of these devices give them advantages over classical analysis techniques such as increased sensitivity, shorter analysis times, and lower reagent consumption. However, current manufacturing processes for microfluidic chips either limit them to materials with unwanted properties, or are not cost-effective for rapid-prototyping approaches. Here the authors show that inlays for injection moulding can be 3D printed, thus reducing the skills, cost, and time required for tool fabrication. They demonstrate the importance of orientation of the part during 3D printing so that features as small as 100 × 200 µm can be printed. They also demonstrate that the 3D printed inlay is durable enough to fabricate at least 500 parts. Furthermore, devices can be designed, manufactured, and tested within one working day. Finally, as demonstrators they design and mould a microfluidic chip to house a plasmonic biosensor as well as a device to house liver organoids showing how such chips can be used in organ-on-a-chip applications. This new fabrication technique bridges the gap between small production and industrial scale manufacturing, while making microfluidics cheaper, and more widely accessible.