Natalie Kostesha

Blueshift of the surface plasmon resonance in silver nanoparticles studied with EELS

Abstract We study the surface plasmon (SP) resonance energy of isolated spherical Ag nanoparticles dispersed on a silicon nitride substrate in the diameter range 3.5–26 nm with monochromated electron energy-loss spectroscopy. A significant blueshift of the SP resonance energy of 0.5 eV is measured when the particle size decreases from 26 down to 3.5 nm. We interpret the observed blueshift using three models for a metallic sphere embedded in homogeneous background material: a classical Drude model with a homogeneous electron density profile in the metal, a semiclassical model corrected for an inhomogeneous electron density associated with quantum confinement, and a semiclassical nonlocal hydrodynamic description of the electron density. We find that the latter two models provide a qualitative explanation for the observed blueshift, but the theoretical predictions show smaller blueshifts than observed experimentally.

Magnetic domain wall conduits for single cell applications

The ability to trap, manipulate and release single cells on a surface is important both for fundamental studies of cellular processes and for the development of novel lab-on-chip miniaturized tools for biological and medical applications. In this paper we demonstrate how magnetic domain walls generated in micro- and nano-structures fabricated on a chip surface can be used to handle single yeast cells labeled with magnetic beads. In detail, first we show that the proposed approach maintains the microorganism viable, as proven by monitoring the division of labeled yeast cells trapped by domain walls over 16 hours. Moreover, we demonstrate the controlled transport and release of individual yeast cells via displacement and annihilation of individual domain walls in micro- and nano-sized magnetic structures. These results pave the way to the implementation of magnetic devices based on domain walls technology in lab-on-chip systems devoted to accurate individual cell trapping and manipulation.

Bioelectrochemical probing of intracellular redox processes in living yeast cells-application of redox polymer wiring in a microfluidic environment

AbstractConventionally, microbial bioelectrochemical assays have been conducted using immobilized cells on an electrode that is placed in an electrochemical batch cell. In this paper, we describe a developed microfluidic platform with integrated microelectrode arrays for automated bioelectrochemical assays utilizing a new double mediator system to map redox metabolism and screen for genetic modifications in Saccharomyces cerevisiae cells. The function of this new double mediator system based on menadione and osmium redox polymer (PVI-Os) is demonstrated. “Wiring” of S. cerevisiae cells using PVI-Os shows a significant improvement of bioelectrochemical monitoring in a microfluidic environment and functions as an effective immobilization matrix for cells that are not strongly adherent. The function of the developed microfluidic platform is demonstrated using two strains of S. cerevisiae, ENY.WA and its deletion mutant EBY44, which lacks the enzyme phosphoglucose isomerase. The cellular responses to introduced glucose and fructose were recorded for the two S. cerevisiae strains, and the obtained results are compared with previously published work when using an electrochemical batch cell, indicating that microfluidic bioelectrochemical assays employing the menadione–PVI-Os double mediator system provides an effective means to conduct automated microbial assays. FigureMicrofluidic platform for bioelectrochemical assays using osmium redox polymer “wired” living yeast cells

Electrochemical probing of in vivo 5-hydroxymethyl furfural reduction in Saccharomyces cerevisiae.

In this work, mediated amperometry was used to evaluate whether differences in intracellular nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) level could be observed between a genetically modified Saccharomyces cerevisiae strain, engineered for NADPH dependent 5-hydroxymethyl-2-furaldehyde (HMF) reduction, and its control strain. Cells overexpressing the alcohol dehydrogenase 6 gene (ADH6 strain) and cells carrying the corresponding control plasmid (control strain) were each immobilized on Au-microelectrodes. The real-time dynamics of NAD(P)H availability in the two strains, preincubated with HMF, was probed using the menadione-ferricyanide double mediator system. A lower intracellular NADPH level as the consequence of more effective HMF reduction was observed for the ADH6 strain both with and without added glucose, which increases the overall cellular NADPH level. The mediated amperometric signal during real-time monitoring of the concentration dependent HMF reduction in living cells could be translated into the cellular enzyme kinetic parameters: K(M,cell)(app), V(MAX), k(cat,cell), and k(cat,cell)/K)M,cell)(app). The results indicated that the overexpression of the ADH6 gene gave a 68% decrease in K(M,cell)(app) and 42% increase in V(MAX), resulting in a 4-fold increase in k(cat,cell)/K(M,cell)(app). These results demonstrate that the mediated amperometric method is useful for monitoring the short-term dynamics of NAD(P)H variations and determining cellular enzyme kinetic parameters in S. cerevisiae cells.

Probing the redox metabolism in the strictly anaerobic, extremely thermophilic, hydrogen-producing Caldicellulosiruptor saccharolyticus using amperometry.

Changes in the redox metabolism in the anaerobic, extremely thermophilic, hydrogen-forming bacterium Caldicellulosiruptor saccharolyticus were probed for the first time in vivo using mediated amperometry with ferricyanide as a thermotolerant external mediator. Clear differences in the intracellular electron flow were observed when cells were supplied with different carbon sources. A higher electrochemical response was detected when cells were supplied with xylose than with sucrose or glucose. Moreover, using the mediated electrochemical method, it was possible to detect differences in the electron flow between cells harvested in the exponential and stationary growth phases. The electron flow of C. saccharolyticus was dependent on the NADH- and reduced ferredoxin generation flux and the competitive behavior of cytosolic and membrane-associated oxidoreductases. Sodium oxamate was used to inhibit the NADH-dependent lactate dehydrogenase, upon which more NADH was directed to membrane-associated enzymes for ferricyanide reduction, leading to a higher electrochemical signal. The method is noninvasive and the results presented here demonstrate that this method can be used to accurately detect changes in the intracellular electron flow and to probe redox enzyme properties of a strictly anaerobic thermophile in vivo.

Data representation and feature selection for colorimetric sensor arrays used as explosives detectors

Within the framework of the strategic research project Xsense at the Technical University of Denmark, we are developing a colorimetric sensor array which can be useful for detection of explosives like DNT, TNT, HMX, RDX and TATP and identification of volatile organic compounds in the presence of water vapor in air. In order to analyze colorimetric sensors with statistical methods, the sensory output must be put into numerical form suitable for analysis. We present new ways of extracting features from a colorimetric sensor and determine the quality and robustness of these features using machine learning classifiers. Sensors, and in particular explosive sensors, must not only be able to classify explosives, they must also be able to measure the certainty of the classifier regarding the decision it has made. This means there is a need for classifiers that not only give a decision, but also give a posterior probability about the decision. We will compare K-nearest neighbor, artificial neural networks and sparse logistic regression for colorimetric sensor data analysis. Using the sparse solutions we perform feature selection and feature ranking and compare to Gram-Schmidt orthogonalization.

Xsense: a miniaturised multi-sensor platform for explosives detection

Realizing that no one sensing principle is perfect we set out to combine four fundamentally different sensing principles into one device. The reasoning is that each sensor will complement the others and provide redundancy under various environmental conditions. As each sensor can be fabricated using microfabrication the inherent advantages associated with MEMS technologies such as low fabrication costs and small device size allows us to integrate the four sensors into one portable device at a low cost.

Optimization of an immunoassay of 2,6-dichlorobenzamide (BAM) and development of regenerative surfaces by immunosorbent modification with newly synthesised BAM hapten library.

Dichlobenil is an extensively used herbicide worldwide which is transformed to the mobile 2,6-dichlorobenzamide (BAM) in soil. BAM has been found in many European groundwater resources that are exploited for drinking water. Currently, immunoassay based monitoring technique (plate based ELISA) is being employed to quantitatively detect BAM in water samples. In this work, as a starting step of developing immunoassay based on-site monitoring systems for pesticide analysis, the heterogeneous BAM immunoassay is optimised in terms of surface (polymer) regeneration. We have synthesised a small library of BAM haptens which are slightly different in chemical structures, immobilised them on surfaces and compared the affinity constants of the monoclonal antibody HYB 273 towards them. By using ELISA technology, we also have checked the regeneration potentials of the haptens, correlated these results to the affinity constants and found that BAM hapten with an intermediate affinity has better regeneration potential.

Feature extraction using distribution representation for colorimetric sensor arrays used as explosives detectors

We present a colorimetric sensor array which is able to detect explosives such as DNT, TNT, HMX, RDX and TATP and identifying volatile organic compounds in the presence of water vapor in air. To analyze colorimetric sensors with statistical methods, a suitable representation of sensory readings is required. We present a new approach of extracting features from a colorimetric sensor array based on a color distribution representation. For each sensor in the array, we construct a K-nearest neighbor classifier based on the Hellinger distances between color distribution of a test compound and the color distribution of all the training compounds. The performance of this set of classifiers are benchmarked against a set of K-nearest neighbor classifiers that is based on traditional feature representation (e.g., mean or global mode). The suggested approach of using the entire distribution outperforms the traditional approaches which use a single feature.

Xsense: using nanotechnology to combine detection methods for high sensitivity handheld explosives detectors

In an effort to produce a handheld explosives sensor the Xsense project has been initiated at the Technical University of Denmark in collaboration with a number of partners. Using micro- and nano technological approaches it will be attempted to integrate four detection principles into a single device. At the end of the project, the consortium aims at having delivered a sensor platform consisting of four independent detector principles capable of detecting concentrations of TNT at sub parts-per-billion (ppb) concentrations and with a false positive rate less than 1 parts-per-thousand. The specificity, sensitivity and reliability are ensured by the use of clever data processing , surface functionalisation and nanostructured sensors and sensor surfaces.