John S Beattie

The University of Edinburgh, Edinburgh, Scotland, United Kingdom

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Publications (23)61.76 Total impact

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    ABSTRACT: Electrodeposition of platinum metal from a chloride-based platinum electroplating bath at 35 °C onto high quality titanium nitride electrodes produced by standard microfabrication techniques has been demonstrated and characterised using electrochemical methods and scanning electron microscopy. When using a relatively simple two potential step electroplating procedure, it is possible to produce good quality deposits which are both adherent and metallic in appearance, without the need for electrode pre-treatment. Cyclic voltammetric analysis of these electrodeposited Pt/TiN films in dilute sulfuric acid yields voltammograms with features characteristic of bulk polycrystalline platinum electrodes. Voltammetry in potassium ferricyanide yields reversible voltammograms, indicating the good electrical conductivity of and connectivity between the deposited Pt and the TiN substrate and hence the absence of any significant resistive surface titanium dioxide or oxynitride film. This process is compatible with the production of platinum array electrodes, which can be integrated with silicon based microelectronic circuitry to produce array based sensors and biosensors.
    No preview · Article · Jun 2013 · Electrochemistry Communications
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    ABSTRACT: DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.
    No preview · Article · Oct 2009 · The Analyst
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    ABSTRACT: All donor blood samples must be tested pretransfusion to determine the donor blood type. Standard testing protocols require that assays be performed for important bloodborne pathogens such as hepatitis C, syphilis, hepatitis B, and human immunodeficiency virus. We have demonstrated proof of the concept that a protein microarray can type whole blood and detect antibody to significant pathogens simultaneously from the same donor blood sample. The data collected demonstrate the ability of the array to accurately type blood samples while also detecting the presence of antibodies against both human immunodeficiency virus and hepatitis C virus. In conclusion, we have successfully developed a platform capable of typing human whole blood samples, while at the same time testing for the presence of antibodies specific for human immunodeficiency virus/hepatitis C virus. The major benefits of this system are its amenability to expansion with additional assays, for example, rhesus typing and syphilis and/or hepatitis B virus detection, and also the adaptability of the assay to higher-throughput analysis, currently 16 individual samples per slide, but readily expandable to a 96-well format.
    No preview · Article · Aug 2008 · Analytical Biochemistry
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    ABSTRACT: The molecular conformation of a synthetic branched, 4-way DNA Holliday junction (HJ) was electrochemically switched between the open and closed (stacked) conformers. Switching was achieved by electrochemically induced quantitative release of Mg(2+) ions from the oxidised poly(N-methylpyrrole) film (PPy), which contained polyacrylate as an immobile counter anion and Mg(2+) ions as charge compensating mobile cations. This increase in the Mg(2+) concentration screened the electrostatic repulsion between the widely separated arms in the open HJ configuration, inducing switching to the closed conformation. Upon electrochemical reduction of PPy, entrapment of Mg(2+) ions back into the PPy film induced the reverse HJ switching from the closed to open state. The conformational transition was monitored using fluorescence resonance energy transfer (FRET) between donor and acceptor dyes each located at the terminus of one of the arms. The demonstrated electrochemical control of the conformation of the used probe-target HJ complex, previously reported as a highly sequence specific nanodevice for detecting of unlabelled target [Buck, A.H., Campbell, C.J., Dickinson, P., Mountford, C.P., Stoquert, H.C., Terry, J.G., Evans, S.A.G., Keane, L., Su, T.J., Mount, A.R., Walton, A.J., Beattie, J.S., Crain, J., Ghazal, P., 2007. Anal. Chem., 79, 4724-4728], allows the development of electronically addressable DNA nanodevices and label-free gene detection assays.
    Full-text · Article · Jun 2008 · Biosensors & Bioelectronics
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    ABSTRACT: This paper investigates the properties of a simple DNA-based nanodevice capable of detecting single base mutations in unlabeled nucleic acid target sequences. Detection is achieved by a two-stage process combining first complementary-base hybridization of a target and then a conformational change as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cruciform construct (similar to a Holliday junction) is formed which can adopt open and closed junction conformations. Switching between these forms occurs by junction folding in the presence of divalent ions. It has been shown from the steady-state fluorescence of judiciously labeled constructs that there are differences between the fluorescence resonance energy transfer (FRET) efficiencies of closed forms, dependent on the target sequence near the branch point, where the arms of the cruciform cross. This difference in FRET efficiency is attributed to structural variations between these folded junctions with their different branch point sequences arising from the single base mutations. This provides a robust means for the discrimination of single nucleotide mismatches in a specific region of the target. In this paper, these structural differences are analyzed by fitting observed time-resolved donor fluorescence decay data to a Gaussian distribution of donor-acceptor separations. This shows the closest mean separation (approximately 40 A) for the perfectly matched case, whereas larger separations (up to 50 A) are found for the single point mutations. These differences therefore indicate a structural basis for the observed FRET differences in the closed configuration which underpins the operation of these devices as biosensors capable of resolving single base mutations.
    No preview · Article · Mar 2008 · The Journal of Physical Chemistry B
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    ABSTRACT: All donor blood samples must be tested pre-transfusion to determine the blood type of donor erythrocytes, based on the ABO typing system. Current methods of testing are well characterised, but require a number of processing steps prior to analysis. In addition, standard testing protocols require additional assays such as hepatitis C and HIV testing be performed separately. We describe and evaluate a protein microarray platform for ABO blood typing that has the potential to be a simple reliable high throughput method, with the added capability for the integration of other important pre-transfusion tests. Sixty seven donor blood samples were incubated on microarrays printed with multiple spotted replicates of blood type antigen specific antibodies. We utilised a hold-out cross validation approach, combined with Receiver Operator Characteristic (ROC) curves to define thresholds within which a sample could be defined as being of a particular blood type. The threshold values from the ROC curve analysis demonstrated an excellent ability to accurately separate samples based on ABO blood type. The results obtained when the thresholds from the training sets were applied to test sets were also very encouraging, with misclassified samples being present in only 2 of the training sets and a mean classification error of 4.28%. When the mean thresholds were applied to the 67 donor samples, 95.5% were correctly blood typed (64 of 67 samples). We have demonstrated the ability of our protein microarray platform to successfully and accurately type human whole blood samples. We believe that this flexible platform provides a strong basis for an integrated approach for combined blood typing and pathogen testing in human whole blood.
    No preview · Article · Feb 2008 · Journal of Immunoassay and Immunochemistry
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    ABSTRACT: We present a new type of DNA switch, based on the Holliday junction, that uses a combination of binding and conformational switching to enable specific label-free detection of DNA and RNA. We show that a single RNA oligonucleotide species can be detected in a complex mixture of extracted cellular RNA and demonstrate that by exploiting different aspects of the switch characteristics we can achieve 30-fold discrimination between single-nucleotide mismatches in a DNA oligonucleotide.
    No preview · Article · Jul 2007 · Analytical Chemistry
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    ABSTRACT: Zn was electrochemically deposited onto square TiN electrodes with edge dimensions of 490 μm and 40 μm. These were fabricated by standard microfabrication techniques, which provide an extremely reproducible electrode for experimentation. Reliable constant-potential electrodeposition of Zn on the TiN was performed at −1.2 V, just below the Zn/Zn2+ redox potential. At more negative potentials, the hydrogen evolution reaction on TiN interfered with bulk metal electrodeposition, resulting in poor quality Zn films. A two-step plating procedure was shown to be most efficient for electrochemical deposition of Zn, with Zn nucleation on the TiN substrate at high cathodic overpotential during the first step and a second step of bulk metal growth on the nucleated layer at low cathodic overpotential. These results were most consistent with 3D progressive nucleation of Zn on the TiN surface. Using this procedure, deposits of Zn on 490 μm TiN electrodes were uniform. In contrast, Zn deposits on 40 μm electrodes formed high-surface area and volume surface structures resulting from preferential growth at the electrode corners due to enhanced hemispherical diffusion at these sites. This should enable the formation of high surface area, high current density Zn anodes on biocompatible TiN microelectrodes, which could find application as improved microanodes for implantable miniature power supplies, e.g., implantable glucose sensors and internal cardioverter defibrillators.
    Full-text · Article · Feb 2007 · Electrochemistry Communications
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    ABSTRACT: A Holliday junction (HJ) consists of four DNA double helices, with a branch point discontinuity at the intersection of the component strands. At low ionic strength, the HJ adopts an open conformation, with four widely spaced arms, primarily due to strong electrostatic repulsion between the phosphate groups on the backbones. At high ionic strength, screening of this repulsion induces a switch to a more compact (closed) junction conformation. Fluorescent labelling with dyes placed on the HJ arms allows this conformational switch to be detected optically using fluorescence resonance energy transfer (FRET), producing a sensitive fluorescent output of the switch state. This paper presents a systematic and quantitative survey of the switch characteristics of such a labelled HJ. A short HJ (arm length 8 bp) is shown to be prone to dissociation at low switching ion concentration, whereas an HJ of arm length 12 bp is shown to be stable over all switching ion concentrations studied. The switching characteristics of this HJ have been systematically and quantitatively studied for a variety of switching ions, by measuring the required ion concentration, the sharpness of the switching transition and the fluorescent output intensity of the open and closed states. This stable HJ is shown to have favourable switch characteristics for a number of inorganic switching ions, making it a promising candidate for use in nanoscale biomolecular switch devices.
    Full-text · Article · Jan 2007 · Biophysical Chemistry
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    ABSTRACT: This work reports how the use of a standard integrated circuit (IC) fabrication process can improve the potential of silicon nitride layers as substrates for microarray technology. It has been shown that chemical mechanical polishing (CMP) substantially improves the fluorescent intensity of positive control gene and test gene microarray spots on both low-pressure chemical vapor deposition (LPCVD) and plasma-enhanced chemical vapor deposition (PECVD) silicon nitride films, while maintaining a low fluorescent background. This results in the improved discrimination of low expressing genes. The results for the PECVD silicon nitride, which has been previously reported as unsuitable for microarray spotting, are particularly significant for future devices that hope to incorporate microelectronic control and analysis circuitry, due to the film's use as a final passivating layer.
    No preview · Article · Jan 2007 · Langmuir
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    ABSTRACT: Conformational transitions in a 4-way DNA junction when titrated with ionic solutions are studied using time-resolved fluorescence resonance energy transfer. Parameters characterising the transition in terms of critical ion concentration (c1/2) and the Hill coefficient for ion binding are obtained by fitting a simple two-state model using steady-state spectra. Data obtained from a fluorescence lifetime plate reader and analysed by fitting a single exponential to donor fluorescence lifetime decays are shown to be in good agreement with the parameters obtained from steady-state measurements. Fluorescence lifetimes, however, offer advantages, particularly in being independent of fluorophore concentration, output intensity, inhomogeneity in the excitation source and output wavelength. We demonstrate preliminary FRET-FLIM images of DNA junction solutions obtained using a picosecond gated CCD which are in agreement with results from a fluorescence lifetime plate reader. The results suggest that time-resolved FRET-FLIM is sensitive to subtle structural changes and may be useful in assays based on 4-way DNA junctions.
    Full-text · Article · Dec 2006 · Journal of Fluorescence
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    G R Grimes · T Q Wen · M Mewissen · R M Baxter · S Moodie · J S Beattie · P Ghazal
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    ABSTRACT: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. AVAILABILITY: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/.
    Preview · Article · Sep 2006 · Bioinformatics
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    ABSTRACT: Microarrays promise great advances in areas of diagnostic testing where there is a need to perform multiple assays in parallel. In the short term, protein microarrays have a greater potential to impact diagnostics than DNA arrays due to their potential for direct sample measurements. Here, we report an antibody microarray technique for selectively recognizing glycan and peptide motifs on the surface of red blood cells. We present results demonstrating the optimization and efficacy of the microarray approach as a highly sensitive and specific microscale multiplex assay for blood typing. We also show that our microarray can be used to screen red blood cell surface antigens using whole blood in a label-free detection mode. Finally, our results indicate this method has potential for broader applications in biochip medicine.
    No preview · Article · Apr 2006 · Analytical Chemistry
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    Full-text · Article · Jan 2006
  • J Beattie · L Jordan · B Algozzine
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    ABSTRACT: This invaluable resource offers teachers in elementary and secondary schools a deeper understanding of "what works" when teaching students with disabilities in general education classrooms.
    No preview · Book · Jan 2006
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    ABSTRACT: The Holliday junction (HJ) structure, consisting of four DNA double helices with a central branch point, is capable of switching between conformational states upon ion binding. The HJ nanoswitch described here comprises a long, dual labeled cloverleaf oligonucleotide and a short, unlabeled oligonucleotide. Fluorescent labeling with donor and acceptor dyes placed on the HJ arms of the cloverleaf strand allows the ion induced conformational switch to be detected optically using fluorescence resonance energy transfer (FRET). The influence of donor and acceptor dye location on the detection of conformational switching has been investigated using two distinct HJ structures. In addition, the effect of increasing HJ arm length in order to increase donor and acceptor dye separation has been evaluated. We report that a preferential HJ nanoswitch structure can be determined, capable of efficient detection of ion induced conformational switching
    No preview · Conference Paper · Jan 2006
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    ABSTRACT: First Page of the Article
    No preview · Conference Paper · Feb 2005
  • J.S. Beattie · J. Fleck
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    ABSTRACT: Understanding strategy in small high technology companies presents a paradox. In an environment of uncertain technologies and dynamic markets taking the time and resources to develop a formal strategy seems futile, yet a strategic perspective is vital in small companies with lit tit margin for error. Strategy in this context seems both impossible and essential. This study focuses on how small high-tech companies strategically manage their technology -arguably then' most important asset. Most relevant high-tech theoretical prescriptions are based on a large company perspective; advice for strategic technology management in small companies is sparse and overly focussed on 'technology planning'. Rather than simply equating strategy with planning, multiple perspectives can be used to explain strategic technology management in small high-tech firms. A model of strategy is presented which views practice in small high tech firms from different viewpoints: strategy as rational planning, as incremental learning and as imagined vision, all within a social context. This holistic view provides a coherent description of actual high-tech strategy practice, via an analytic model that helps practitioners understand the complex nature of their strategic management, and in turn learn and improve.
    No preview · Conference Paper · Feb 2005
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    ABSTRACT: Macrophages play an integral role in the host immune system, bridging innate and adaptive immunity. As such, they are finely attuned to extracellular and intracellular stimuli and respond by rapidly initiating multiple signalling cascades with diverse effector functions. The macrophage cell is therefore an experimentally and clinically amenable biological system for the mapping of biological pathways. The goal of the macrophage expression atlas is to systematically investigate the pathway biology and interaction network of macrophages challenged with a variety of insults, in particular via infection and activation with key inflammatory mediators. As an important first step towards this we present a single searchable database resource containing high-throughput macrophage gene expression studies. The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for gene expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX-MEA follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the searching of expression data from different microarray experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the research community. GPX-MEA is the first example of a quality scored gene expression database focussed on a macrophage cellular system that allows efficient identification of transcriptional patterns. The resource will provide novel insights into the phenotypic response of macrophages to a variety of benign, inflammatory, and pathogen insults. GPX-MEA is available through the GPX website at http://www.gti.ed.ac.uk/GPX.
    Full-text · Article · Feb 2005 · BMC Genomics

  • No preview · Conference Paper · Jan 2004