Creating aptamers and their use in resisitive pulse sensors

Resistive pulse sensors, RPS, are allowing the transport mechanism of molecules, proteins and even nanoparticles to be characterized as they traverse small channels. Here we present our recent advancement of the technique identifying key experimental designs for potential POC assays. The first assay utilized superparamagnetic beads, if the surfaces of the beads are modified with an aptamer, the frequency of beads (translocations/minute) through the pore can be related to the concentration of specific proteins in the solution. Herein, we have demonstrated the successful use of TRPS to observe the binding of two proteins, to their specific aptamers simultaneously. We then adapt the measurement strategy and demonstrate that the translocation times of particles can be used to infer the zeta potential to measure the change in zeta potential of DNA modified particles. By measuring the translocation times of DNA modified nanoparticles as a function of packing density, length, structure, and hybridisation time, we observe a clear difference in zeta potential using both mean values, and population distributions as a function of the DNA structure. Finally we present the first comparison between assays that use resistive pulses or rectification ratios on a tunable pore platform

Tunable nanopores: Resistive pulses and current rectification

Tunable nanopores: Resistive pulses and current rectificatio

Tunable resistive pulse sensing: potential applications in nanomedicine

An accurate characterization of nanomaterials used in clinical diagnosis and therapeutics is of paramount importance to realize the full potential of nanotechnology in medicine and to avoid unexpected and potentially harmful toxic effects due to these materials. A number of technical modalities are currently in use to study the physical, chemical and biological properties of nanomaterials but they all have advantages and disadvantages. In this review, we discuss the potential of a relative newcomer, tunable resistive pulse sensing, for the characterization of nanomaterials and its applications in nanodiagnostics

Effect of breastfeeding on gastrointestinal infection in infants: A targeted maximum likelihood approach for clustered longitudinal data

The PROmotion of Breastfeeding Intervention Trial (PROBIT) cluster-randomized a program encouraging breastfeeding to new mothers in hospital centers. The original studies indicated that this intervention successfully increased duration of breastfeeding and lowered rates of gastrointestinal tract infections in newborns. Additional scientific and popular interest lies in determining the causal effect of longer breastfeeding on gastrointestinal infection. In this study, we estimate the expected infection count under various lengths of breastfeeding in order to estimate the effect of breastfeeding duration on infection. Due to the presence of baseline and time-dependent confounding, specialized "causal" estimation methods are required. We demonstrate the double-robust method of Targeted Maximum Likelihood Estimation (TMLE) in the context of this application and review some related methods and the adjustments required to account for clustering. We compare TMLE (implemented both parametrically and using a data-adaptive algorithm) to other causal methods for this example. In addition, we conduct a simulation study to determine (1) the effectiveness of controlling for clustering indicators when cluster-specific confounders are unmeasured and (2) the importance of using data-adaptive TMLE.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS727 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Multiplexed, label-free detection of biomarkers using aptamers and Tunable Resistive Pulse Sensing (AptaTRPS).

Diagnostics that are capable of detecting multiple biomarkers are improving the accuracy and efficiency of bioassays. In previous work we have demonstrated the potential of an aptamer-based sensor (aptasensor) utilising Tunable Resistive Pulse Sensing (TRPS). Here, we have advanced the technique identifying key experimental designs for potential POC assays. The assay utilised superparamagnetic beads, and using TRPS monitored their translocations through a pore. If the surfaces of the beads are modified with an aptamer, the frequency of beads (translocations/min) through the pore can be related to the concentration of specific proteins in the solution. Herein, we have demonstrated the successful use of TRPS to observe the binding of two proteins, to their specific aptamers simultaneously. We describe a series of experiments illustrating key factors which we believe are integral to bead-based assays and demonstrate a general method for a multiplexed assay. In summary, we have explored the effects of beads size, concentration, potential bias, pH and aptamer affinity to enhance the sensitivity and practically of a TRPS aptasensor. The method utilises the fact the binding of the aptamer to the protein results in a change in charge density on the bead surface, the isoelectric point of the protein then dominates the mobility of the beads, creating a multiplexed assay termed AptaTRPS. By alteration of the applied potential to the instrument it is possible to produce a positive signal in a simple multiplexed assay

Chemotherapeutic Drug Design: An Efficient Synthesis of 4-Substituted Alpha-Methylene-Gamma-Lactones

Sesquiterpene lactones are plant-derived compounds that have been shown to possess significant activity against inflammation and cancer. Comparative studies of sesquiterpene lactone structure and tumor cytotoxicity indicate that the presence of an α-methylene-γ-lactone moiety is necessary for bioactivity. This observation has led to the hypothesis that simple compounds containing this pharmacophore may also exhibit similar anti-cancer properties. To test this theory, an efficient synthesis of 4-substituted α-methylene-γ-lactone has been developed. The model compound in this study, α-methylene-γ-dodecalactone, has been prepared from commercially available 1-decene in six steps. The synthesis features a nucleophilic epoxide ring-opening reaction followed by an intramolecular cyclization to prepare a key lactone intermediate. The described sequence should provide access to a large number of 4-substituted α-methylene-γ-lactone analogues that can be used to better understand the role alkyl substituents play in the bioactivity of this class of compounds