How Do Cells Make Decisions: Engineering Micro- and Nanoenvironments for Cell Migration

Cell migration contributes to cancer metastasis and involves cell adhesion to the extracellular matrix (ECM), force generation through the cell's cytoskeletal, and finally cell detachment. Both adhesive cues from the ECM and soluble cues from neighbouring cells and tissue trigger intracellular signalling pathways that are essential for cell migration. While the machinery of many signalling pathways is relatively well understood, how hierarchies of different and conflicting signals are established is a new area of cellular cancer research. We examine the recent advances in microfabrication, microfluidics, and nanotechnology that can be utilized to engineer micro- and nanoscaled cellular environments. Controlling both adhesive and soluble cues for migration may allow us to decipher how cells become motile, choose the direction for migration, and how oncogenic transformations influences these decision-making processes

Light Activated Electrochemistry: Light Intensity and pH Dependence on Electrochemical Performance of Anthraquinone Derivatized Silicon

We seek to understand how the thermodynamics and kinetics of anthraquinone-containing self-assembled monolayer on silicon electrodes are affected by two key experimental variables: the intensity of the light assisting the anthraquinone/anthrahydroquinone redox process and the local solution environment. The substrates are chemically passivated poorly doped p-type silicon electrodes. The study presents a strategy for the selective modulation of either the anodic or the cathodic process occurring at the interface. Cyclic voltammetry studies showed that unlike for a proton-coupled electron transfer process performed at metallic electrodes, for the redox reaction of the anthraquinone unit on a silicon electrode it becomes possible to (i) selectively facilitate only the oxidation process by increasing the electrolyte pH or (ii) at a given pH value to increase the illumination intensity to anodically shift the onset of the reduction step only but leave the oxidation process thermodynamic unchanged. A model concerning the proton coupled electron transfer mechanism was proposed, where the electron transfer is the rate-determining step for the anthraquinone reduction while a deprotonation step is the rate-determining event for the anthrahydroquinone oxidation on poorly doped illuminated p-type silicon

Proximity extension of circular DNA aptamers with real-time protein detection

Multivalent circular aptamers or ‘captamers’ have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the ‘proximity extension’ assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer–thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier

Light-Activated Electrochemistry for the Two-Dimensional Interrogation of Electroactive Regions on a Monolithic Surface with Dramatically Improved Spatial Resolution

The concept of light-activated electrochemistry (LAE) was recently presented where faradaic electrochemistry could be spatially resolved on a monolithic silicon electrode by illuminating the specific region with light. A major implication from the previous study using illumination from the nonsolution side, or backside, is that the spatial resolution is limited by the finite thickness of silicon wafer. To overcome this restriction, and enable the further application of LAE, in combination with optical imaging for example, herein the spatial resolution of LAE using topside illumination (illumination from the solution side) is explored. The applied potential and irradiated light intensity are found to have significant effects on the spatial resolution. A spatial resolution of ~30 µm was achieved with optimal parameters, which is a 20 times improvement compared with the previously reported backside illumination design, demonstrating the potential application of the strategy including microarray patterning of silicon or for single cell analysis

A novel route to copper(ii) detection using \u27click\u27 chemistry-induced aggregation of gold nanoparticles

A simple colorimetric method for the detection of copper ions in water is described. This method is based on the \u27click\u27 copper(i)-catalyzed azide-alkyne cycloaddition reaction and its use in promoting the aggregation of azide-tagged gold nanoparticles by a dialkyne cross-linker is described. Nanoparticle cross-linking, evidenced as a colour change, is used for the detection of copper ions. The lowest detected concentration by the naked eye was 1.8 μM, with the response linear with log(concentration) between 1.8-200 μM. The selectivity relative to other potentially interfering ions was evaluated

Algorithms for Big Data: Graphs and PageRank

This work consists of a study of a set of techniques and strategies related with algorithm's design, whose purpose is the resolution of problems on massive data sets, in an efficient way. This field is known as Algorithms for Big Data. In particular, this work has studied the Streaming Algorithms, which represents the basis of the data structures of sublinear order $o(n)$ in space, known as Sketches. In addition, it has deepened in the study of problems applied to Graphs on the Semi-Streaming model. Next, the PageRank algorithm was analyzed as a concrete case study. Finally, the development of a library for the resolution of graph problems, implemented on the top of the intensive mathematical computation platform known as TensorFlow has been started.Comment: in Spanish, 143 pages, final degree project (bachelor's thesis

Electroconductive Hydrogel Based on Functional Poly(Ethylenedioxy Thiophene).

Poly(ethylene dioxythiophene) with functional pendant groups bearing double bonds is synthesized and employed for the fabrication of electroactive hydrogels with advantageous characteristics: covalently cross-linked porous 3D scaffolds with notable swelling ratio, appropriate mechanical properties, electroactivity in physiological conditions, and suitability for proliferation and differentiation of C2C12 cells. This is a new approach for the fabrication of conductive engineered constructs

Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation

Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation

Cellobiose Dehydrogenase Aryl Diazonium Modified Single Walled Carbon Nanotubes: Enhanced Direct Electron Transfer through a Positively Charged Surface

One of the challenges in the field of biosensors and biofuel cells is to establish a highly efficient electron transfer rate between the active site of redox enzymes and electrodes to fully access the catalytic potential of the biocatalyst and achieve high current densities. We report on very efficient direct electron transfer (DET) between cellobiose dehydrogenase (CDH) from Phanerochaete sordida (PsCDH) and surface modified single walled carbon nanotubes (SWCNT). Sonicated SWCNTs were adsorbed on the top of glassy carbon electrodes and modified with aryl diazonium salts generated in situ from p-aminobenzoic acid and p-phenylenediamine, thus featuring at acidic pH (3.5 and 4.5) negative or positive surface charges. After adsorption of PsCDH, both electrode types showed excellent long-term stability and very efficient DET. The modified electrode presenting p-aminophenyl groups produced a DET current density of 500,mu A cm(-2) at 200 mV vs normal hydrogen reference electrode (NHE) in a 5 mM lactose solution buffered at pH 3.5. This is the highest reported DET value so far using a CDH modified electrode and comes close to electrodes using mediated electron transfer. Moreover, the onset of the electrocatalytic current for lactose oxidation started at 70 mV vs NHE, a potential which is 50 mV lower compared to when unmodified SWCNTs were used. This effect potentially reduces the interference by oxidizable matrix components in biosensors and increases the open circuit potential in biofuel cells. The stability of the electrode was greatly increased compared with unmodified but cross-linked SWCNTs electrodes and lost only 15% of the initial current after 50 h of constant potential scanning