Ultrasensitive colorimetric detection of protein by aptamer - Au nanoparticles conjugates based on a dot-blot assay

A simple, rapid and ultrasensitive colorimetric detection of protein using aptamer-Au nanoparticles (AuNPs) conjugates based on a dot-blot array has been developed, which was combined with the unique optical properties of AuNPs, enabling the visual detection of protein within minutes without any instrument.

Bifunctional magnetic-optical nanocomposites: Grafting lanthanide complex onto core-shell magnetic silica nanoarchitecture

Anew class of bifunctional architecture combining the useful functions of superparamagnetism and terbium complex luminescence into one material has been prepared via two main steps by a modified Stober method and the layer-by-layer (LbL) assembly technique. The obtained bifunctional nanocomposites exhibit superparamagnetic behavior, high fluorescence intensity, and color purity. The architecture has been characterized by field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), UV-vis absorption and emission spectroscopy, X-ray diffraction, and superconducting quantum interference device (SQUID) magnetometry.

Colliding and Moving Bose-Einstein Condensates: Studies of superfluidity and optical tweezers for condensate transport

In this thesis, two different sets of experiments are described. The first is an exploration of the microscopic superfluidity of dilute gaseous Bose- Einstein condensates. The second set of experiments were performed using transported condensates in a new BEC apparatus. Superfluidity was probed by moving impurities through a trapped condensate. The impurities were created using an optical Raman transition, which transferred a small fraction of the atoms into an untrapped hyperfine state. A dramatic reduction in the collisions between the moving impurities and the condensate was observed when the velocity of the impurities was close to the speed of sound of the condensate. This reduction was attributed to the superfluid properties of a BEC. In addition, we observed an increase in the collisional density as the number of impurity atoms increased. This enhancement is an indication of bosonic stimulation by the occupied final states. This stimulation was observed both at small and large velocities relative to the speed of sound. A theoretical calculation of the effect of finite temperature indicated that collision rate should be enhanced at small velocities due to thermal excitations. However, in the current experiments we were insensitive to this effect. Finally, the factor of two between the collisional rate between indistinguishable and distinguishable atoms was confirmed. A new BEC apparatus that can transport condensates using optical tweezers was constructed. Condensates containing 10-15 million sodium atoms were produced in 20 s using conventional BEC production techniques. These condensates were then transferred into an optical trap that was translated from the ‘production chamber’ into a separate vacuum chamber: the ‘science chamber’. Typically, we transferred 2-3 million condensed atoms in less than 2 s. This transport technique avoids optical and mechanical constrainsts of conventional condensate experiments and allows for the possibility of novel experiments. In the first experiments using transported BEC, we loaded condensed atoms from the optical tweezers into both macroscopic and miniaturized magnetic traps. Using microfabricated wires on a silicon chip, we observed excitation-less propagation of a BEC in a magnetic waveguide. The condensates fragmented when brought very close to the wire surface indicating that imperfections in the fabrication process might limit future experiments. Finally, we generated a continuous BEC source by periodically replenishing a condensate held in an optical reservoir trap using fresh condensates delivered using optical tweezers. More than a million condensed atoms were always present in the continuous source, raising the possibility of realizing a truly continuous atom lase.

Photonic integrated circuits for the generation of coherent optical signals

The demand for optical bandwidth continues to increase year on year and is being driven primarily by entertainment services and video streaming to the home. Current photonic systems are coping with this demand by increasing data rates through faster modulation techniques, spectrally efficient transmission systems and by increasing the number of modulated optical channels per fibre strand. Such photonic systems are large and power hungry due to the high number of discrete components required in their operation. Photonic integration offers excellent potential for combining otherwise discrete system components together on a single device to provide robust, power efficient and cost effective solutions. In particular, the design of optical modulators has been an area of immense interest in recent times. Not only has research been aimed at developing modulators with faster data rates, but there has also a push towards making modulators as compact as possible. Mach-Zehnder modulators (MZM) have proven to be highly successful in many optical communication applications. However, due to the relatively weak electro-optic effect on which they are based, they remain large with typical device lengths of 4 to 7 mm while requiring a travelling wave structure for high-speed operation. Nested MZMs have been extensively used in the generation of advanced modulation formats, where multi-symbol transmission can be used to increase data rates at a given modulation frequency. Such nested structures have high losses and require both complex fabrication and packaging. In recent times, it has been shown that Electro-absorption modulators (EAMs) can be used in a specific arrangement to generate Quadrature Phase Shift Keying (QPSK) modulation. EAM based QPSK modulators have increased potential for integration and can be made significantly more compact than MZM based modulators. Such modulator designs suffer from losses in excess of 40 dB, which limits their use in practical applications. The work in this thesis has focused on how these losses can be reduced by using photonic integration. In particular, the integration of multiple lasers with the modulator structure was considered as an excellent means of reducing fibre coupling losses while maximising the optical power on chip. A significant difficultly when using multiple integrated lasers in such an arrangement was to ensure coherence between the integrated lasers. The work investigated in this thesis demonstrates for the first time how optical injection locking between discrete lasers on a single photonic integrated circuit (PIC) can be used in the generation of coherent optical signals. This was done by first considering the monolithic integration of lasers and optical couplers to form an on chip optical power splitter, before then examining the behaviour of a mutually coupled system of integrated lasers. By operating the system in a highly asymmetric coupling regime, a stable phase locking region was found between the integrated lasers. It was then shown that in this stable phase locked region the optical outputs of each laser were coherent with each other and phase locked to a common master laser.

Control of the orientational order and nonlinear optical response of the "push-pull" chromophore RuPZn via specific incorporation into densely packed monolayer ensembles of an amphiphilic four-helix bundle peptide: characterization of the peptide-chromophore complexes.

"Push-pull" chromophores based on extended pi-electron systems have been designed to exhibit exceptionally large molecular hyperpolarizabilities. We have engineered an amphiphilic four-helix bundle peptide to vectorially incorporate such hyperpolarizable chromophores having a metalloporphyrin moiety, with high specificity into the interior core of the bundle. The amphiphilic exterior of the bundle facilitates the formation of densely packed monolayer ensembles of the vectorially oriented peptide-chromophore complexes at the liquid-gas interface. Chemical specificity designed into the ends of the bundle facilitates the subsequent covalent attachment of these monolayer ensembles onto the surface of an inorganic substrate. In this article, we describe the structural characterization of these monolayer ensembles at each stage of their fabrication for one such peptide-chromophore complex designated as AP0-RuPZn. In the accompanying article, we describe the characterization of their macroscopic nonlinear optical properties.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

Thermal, mechanical and optical modelling of VCSEL packaging

Hybrid OECB (Opto-Electrical Circuit Boards) are expected to make a significant impact in the telecomm switches arena within the next five years, creating optical backplanes with high speed point-to-point optical interconnects. OECB's incorporate short range optical interconnects, and are based on VCSEL (Vertical Cavity Surface Emitting Diode) and PD (Photo Diode) pairs, connected to each other via embedded waveguides in the OECB. The VCSEL device is flip-chip assembled onto an organic substrate with embedded optical waveguides. The performance of the VCSEL device is governed by the thermal, mechanical and optical characteristics of this assembly. During operation, the VCSEL device will heat up and the thermal change together with the CTE mismatch in the materials, will result in potential misalignment between the VCSEL apertures and the waveguide openings in the substrate. Any degree of misalignment will affect the optical performance of the package. This paper will present results from a highly coupled modelling analysis involving thermal, mechanical and optical models. The paper will also present results from an optimisation analysis based on Design of Experiments (DOE).

Review of the technology and reliability issues arising as optical interconnects migrate onto the circuit board

Light has the greatest information carrying potential of all the perceivable interconnect mediums; consequently, optical fiber interconnects rapidly replaced copper in telecommunications networks, providing bandwidth capacity far in excess of its predecessors. As a result the modern telecommunications infrastructure has evolved into a global mesh of optical networks with VCSEL’s (Vertical Cavity Surface Emitting Lasers) dominating the short-link markets, predominately due to their low-cost. This cost benefit of VCSELs has allowed optical interconnects to again replace bandwidth limited copper as bottlenecks appear on VSR (Very Short Reach) interconnects between co-located equipment inside the CO (Central-Office). Spurred by the successful deployment in the VSR domain and in response to both intra-board backplane applications and inter-board requirements to extend the bandwidth between IC’s (Integrated Circuits), current research is migrating optical links toward board level USR (Ultra Short Reach) interconnects. Whilst reconfigurable Free Space Optical Interconnect (FSOI) are an option, they are complicated by precise line-of-sight alignment conditions hence benefits exist in developing guided wave technologies, which have been classified into three generations. First and second generation technologies are based upon optical fibers and are both capable of providing a suitable platform for intra-board applications. However, to allow component assembly, an integral requirement for inter-board applications, 3rd generation Opto-Electrical Circuit Boards (OECB’s) containing embedded waveguides are desirable. Currently, the greatest challenge preventing the deployment of OECB’s is achieving the out-of-plane coupling to SMT devices. With the most suitable low-cost platform being to integrate the optics into the OECB manufacturing process, several research avenues are being explored although none to date have demonstrated sufficient coupling performance. Once in place, the OECB assemblies will generate new reliability issues such as assembly configurations, manufacturing tolerances, and hermetic requirements that will also require development before total off-chip photonic interconnection can truly be achieved

A rapid optical immunoassay for the screening of T-2 and HT-2 toxin in cereals and maize-based baby food

A rapid surface plasmon resonance (SPR) screening assay has been developed for the combined detection of T-2 and HT-2 toxins in naturally contaminated cereals using a sensor chip coated with an HT-2 toxin derivative and a monoclonal antibody. The antibody raised against HT-2 displayed high cross-reactivity with T-2 toxin while there was no cross-reaction observed with other commonly occurring trichothecenes. A simple extraction procedure using 40% methanol was applied to baby food, breakfast cereal, and wheat samples prior to biosensor analysis. Limits of detection (LOD) for each matrix were determined as 25 mu g kg(-1) for baby food and breakfast cereal and 26 mu g kg(-1) for wheat. Intra-assay precision (n = 6) was calculated for each matrix. The results were expressed as the relative standard deviation and determined as 2.8% (100 mu g kg(-1)) and 1.8% (200 mu g kg(-1)) in breakfast cereal, 4.6% (50 mu g kg(-1)) and 3.6% (100 mu g kg(-1)) in wheat and 0.97% (25 mu g kg(-1)) and 6.3% (50 mu g kg(-1)) in baby food. Between run precision (n = 3) performed at the same levels yielded relative standard deviations of 6.7% and 3.9% for breakfast cereals, 3.3% and 1.6% for wheat and 6.8% and 0.08% for baby food, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Protein surface recognition using geometrically pure Ru(II) tris(bipyridine) derivatives

This manuscript illustrates that the geometric arrangement of protein-binding groups around a ruthenium(II) core leads to dramatic differences in cytochrome c (cyt c) binding highlighting that it is possible to define synthetic receptors with shape complementarity to protein surfaces.

Detection of streptomycin residues in whole milk using an optical immunobiosensor

The development of an assay for the detection of streptomycin residues in pasteurized whole milk using an optical biosensor (Biacore) is reported. Streptomycin-adipic hydrazide coupled to bovine thyroglobulin was used to produce a sheep polyclonal antibody. The antibody displayed excellent cross-reactivity with dihydrostreptomycin (106%). There was no significant cross-reaction with other aminoglycosides or common antibiotics. Streptomycin was also immobilized onto a CM5 sensor chip to provide a stable, reusable surface. The developed assay permitted the direct analysis of whole milk samples (similar to3.5% fat) without prior centrifugation and defatting. Results were available in 5 min. The limit of detection of the assay was determined as 4.1 ng/mL, well below the European maximum residue limit (MRL) of 200 ng/mL. Repeatability (or coefficient of variation) between runs was determined as 3.5% (100 ng/mL; 0.5 x MRL), 5.7% (200 ng/mL; MRL), and 7.6% (400 ng/mL; 2 x MRL).

Programmable image processing chip

A new high performance, programmable image processing chip targeted at video and HDTV applications is described. This was initially developed for image small object recognition but has much broader functional application including 1D and 2D FIR filtering as well as neural network computation. The core of the circuit is made up of an array of twenty one multiplication-accumulation cells based on systolic architecture. Devices can be cascaded to increase the order of the filter both vertically and horizontally. The chip has been fabricated in a 0.6 µ, low power CMOS technology and operates on 10 bit input data at over 54 Megasamples per second. The introduction gives some background to the chip design and highlights that there are few other comparable devices. Section 2 gives a brief introduction to small object detection. The chip architecture and the chip design will be described in detail in the later sections.

Production of a broad specificity antibody for the development and validation of an optical SPR screening method for free and intracellular microcystins and nodularin in cyanobacteria cultures

A highly sensitive broad specificity monoclonal antibody was produced and characterised for microcystin detection through the development of a rapid surface plasmon resonance (SPR) optical biosensor based immunoassay. The antibody displayed the following cross-reactivity: MC-LR 100%; MC-RR 108%; MC-YR 68%; MC-LA 69%; MC-LW 71%; MC-LF 68%; and Nodularin 94%. Microcystin-LR was covalently attached to a CM5 chip and with the monoclonal antibody was employed in a competitive 4min injection assay to detect total microcystins in water samples below the WHO recommended limit (1µg/L). A 'total microcystin' level was determined by measuring free and intracellular concentrations in cyanobacterial culture samples as this toxin is an endotoxin. Glass bead beating was used to lyse the cells as a rapid extraction procedure. This method was validated according to European Commission Decision 96/23/EC criteria. The method was proven to measure intracellular microcystin levels, the main source of the toxin, which often goes undetected by other analytical procedures and is advantageous in that it can be used for the monitoring of blooms to provide an early warning of toxicity. It was shown to be repeatable and reproducible, with recoveries from spiked samples ranging from 74 to 123%, and had % CVs below 10% for intra-assay analysis and 15% for inter-assay analysis. The detection capability of the assay was calculated as 0.5ng/mL for extracellular toxins and 0.05ng/mL for intracellular microcystins. A comparison of the SPR method with LC-MS/MS was achieved by testing six Microcystis aeruginosa cultures and this study yielded a correlation R(2) value of 0.9989.

Targeting translocator protein (18 kDa) (TSPO) dampens pro-inflammatory microglia reactivity in the retina and protects from degeneration

BACKGROUND: Reactive microglia are commonly seen in retinal degenerative diseases, and neurotoxic microglia responses can contribute to photoreceptor cell death. We and others have previously shown that translocator protein (18 kDa) (TSPO) is highly induced in retinal degenerations and that the selective TSPO ligand XBD173 (AC-5216, emapunil) exerts strong anti-inflammatory effects on microglia in vitro and ex vivo. Here, we investigated whether targeting TSPO with XBD173 has immuno-modulatory and neuroprotective functions in two mouse models of acute retinal degeneration using bright white light exposure.

METHODS: BALB/cJ and Cx3cr1 (GFP/+) mice received intraperitoneal injections of 10 mg/kg XBD173 or vehicle for five consecutive days, starting 1 day prior to exposure to either 15,000 lux white light for 1 h or 50,000 lux focal light for 10 min, respectively. The effects of XBD173 treatment on microglia and Müller cell reactivity were analyzed by immuno-stainings of retinal sections and flat mounts, fluorescence-activated cell sorting (FACS) analysis, and mRNA expression of microglia markers using quantitative real-time PCR (qRT-PCR). Optical coherence tomography (OCT), terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) stainings, and morphometric analyses were used to quantify the extent of retinal degeneration and photoreceptor apoptosis.

RESULTS: Four days after the mice were challenged with bright white light, a large number of amoeboid-shaped alerted microglia appeared in the degenerating outer retina, which was nearly completely prevented by treatment with XBD173. This treatment also down-regulated the expression of TSPO protein in microglia but did not change the TSPO levels in the retinal pigment epithelium (RPE). RT-PCR analysis showed that the microglia/macrophage markers Cd68 and activated microglia/macrophage whey acidic protein (Amwap) as well as the pro-inflammatory genes Ccl2 and Il6 were reduced after XBD173 treatment. Light-induced degeneration of the outer retina was nearly fully blocked by XBD173 treatment. We further confirmed these findings in an independent mouse model of focal light damage. Retinas of animals receiving XBD173 therapy displayed significantly more ramified non-reactive microglia and more viable arrestin-positive cone photoreceptors than vehicle controls.

CONCLUSIONS: Targeting TSPO with XBD173 effectively counter-regulates microgliosis and ameliorates light-induced retinal damage, highlighting a new pharmacological concept for the treatment of retinal degenerations.