The NTD Nanoscope: potential applications and implementations

<p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.</p> <p>Results</p> <p>The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.</p> <p>Conclusions</p> <p>SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.</p

Recent Advances on Iron Oxide Magnetic Nanoparticles as Sorbents of Organic Pollutants in Water and Wastewater Treatment

The constant growth in population worldwide over the past decades continues to put forward the need to provide access to safe, clean water to meet human needs. There is a need for cost-effective technologies for water and wastewater treatment that can meet the global demands and the rigorous water quality standards and at the same maximizing pollutant efficiency removal. Current remediation technologies have failed in keeping up with these factors without becoming cost-prohibitive. Most recently, nanotechnology has been sought as the best alternative to increase access to water supplies by remediating those already contaminated and offering ways to access unconventional sources. The use of iron oxide magnetic nanoparticles as nanoadsorbents has led way to a new class of magnetic separation strategies for water treatment. This review focuses on highlighting some of the most recent advances in core-shell iron oxide magnetic nanoparticles and nanocomposites containing iron oxide nanoparticles currently being developed for water and wastewater treatment of organic pollutants. We discuss the novelty of these novel materials and the insight gained from their advances that can help develop cost-effective reusable technologies for scale-up and commercial use

Highly Thiolated Poly (Beta-Amino Ester) Nanoparticles for Acute Redox Applications

Disulfides are used extensively in reversible cross-linking because of the ease of reduction into click-reactive thiols. However, the free-radical scavenging properties upon reduction are often under-considered. The free thiols produced upon reduction of this disulfide material mimic the cellular reducing chemistry (glutathione) that serves as a buffer against acute oxidative stress. A nanoparticle formulation producing biologically relevant concentrations of thiols may not only provide ample chemical conjugation sites, but potentially be useful against severe acute oxidative stress exposure, such as in targeted radioprotection. In this work, we describe the synthesis and characterization of highly thiolated poly (β-amino ester) (PBAE) nanoparticles formed from the reduction of bulk disulfide cross-linked PBAE hydrogels. Degradation-tunable PBAE hydrogels were initially synthesized containing up to 26 wt % cystamine, which were reduced into soluble thiolated oligomers and formulated into nanoparticles upon single emulsion. These thiolated nanoparticles were size-stable in phosphate buffered saline consisting of up to 11.0 ± 1.1 mM (3.7 ± 0.3 mmol thiol/g, n = 3 M ± SD), which is an antioxidant concentration within the order of magnitude of cellular glutathione (1–10 mM)

Development of Novel \u3cem\u3eN\u3c/em\u3e-isopropylacrylamide (NIPAAm) Based Hydrogels with Varying Content of Chrysin Multiacrylate

A series of novel temperature responsive hydrogels were synthesized by free radical polymerization with varying content of chrysin multiacrylate (ChryMA). The goal was to study the impact of this novel polyphenolic-based multiacrylate on the properties of N-isopropylacrylamide (NIPAAm) hydrogels. The temperature responsive behavior of the copolymerized gels was characterized by swelling studies, and their lower critical solution temperature (LCST) was characterized through differential scanning calorimetry (DSC). It was shown that the incorporation of ChryMA decreased the swelling ratios of the hydrogels and shifted their LCSTs to a lower temperature. Gels with different ChryMA content showed different levels of response to temperature change. Higher content gels had a broader phase transition and smaller temperature response, which could be attributed to the increased hydrophobicity being introduced by the ChryMA

Mechanism Design in Social Networks

This paper studies an auction design problem for a seller to sell a commodity in a social network, where each individual (the seller or a buyer) can only communicate with her neighbors. The challenge to the seller is to design a mechanism to incentivize the buyers, who are aware of the auction, to further propagate the information to their neighbors so that more buyers will participate in the auction and hence, the seller will be able to make a higher revenue. We propose a novel auction mechanism, called information diffusion mechanism (IDM), which incentivizes the buyers to not only truthfully report their valuations on the commodity to the seller, but also further propagate the auction information to all their neighbors. In comparison, the direct extension of the well-known Vickrey-Clarke-Groves (VCG) mechanism in social networks can also incentivize the information diffusion, but it will decrease the seller's revenue or even lead to a deficit sometimes. The formalization of the problem has not yet been addressed in the literature of mechanism design and our solution is very significant in the presence of large-scale online social networks.Comment: In The Thirty-First AAAI Conference on Artificial Intelligence, San Francisco, US, 04-09 Feb 201

Convection in nanofluids with a particle-concentration-dependent thermal conductivity

Thermal convection in nanofluids is investigated by means of a continuum model for binary-fluid mixtures, with a thermal conductivity depending on the local concentration of colloidal particles. The applied temperature difference between the upper and the lower boundary leads via the Soret effect to a variation of the colloid concentration and therefore to a spatially varying heat conductivity. An increasing difference between the heat conductivity of the mixture near the colder and the warmer boundary results in a shift of the onset of convection to higher values of the Rayleigh number for positive values of the separation ratio psi>0 and to smaller values in the range psi<0. Beyond some critical difference of the thermal conductivity between the two boundaries, we find an oscillatory onset of convection not only for psi<0, but also within a finite range of psi>0. This range can be extended by increasing the difference in the thermal conductivity and it is bounded by two codimension-2 bifurcations.Comment: 13 pages, 11 figures; submitted to Physical Review

Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

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Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

<p>Abstract</p> <p>Background</p> <p>The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector.</p> <p>Results</p> <p>We present evidence that different forms of channel blockade can be associated with the same antibody, we associate these different blockades with different orientations of "capture" of an antibody in the detector's nanometer-scale channel. We directly detect the presence of antibodies via reductions in channel current. Changes to blockade patterns upon addition of antigen suggest indirect detection of antibody/antigen binding. Similarly, DNA-hairpin anchored antibodies have been studied, where the DNA linkage is to the carboxy-terminus at the base of the antibody's Fc region, with significantly fewer types of (lengthy) capture blockades than was observed for free (un-bound) IgG antibody. The introduction of chaotropic agents and its effects on protein-protein interactions have also been observed.</p> <p>Conclusion</p> <p>Nanopore-based approaches may eventually provide a direct analysis of the complex conformational "negotiations" that occur upon binding between proteins.</p