Abstract: Methods, devices, substrates, and systems are disclosed involving arrays of zero-mode waveguides having nanopores extending through the bases that form the bottoms of the zero-mode-waveguides. Electric fields across the nanopores are used to attach single biomolecules such as polymerase enzymes within each zero-mode-waveguide. Electric fields across the nanopores can also be used for the active loading of nucleic acid templates into enzymes attached within the zero mode waveguides.

Abstract: Spectroscopic filter arrays and methods for making spectroscopic filter arrays are provided. The arrays are formed using a dispersion of filter particles having selected moieties attached to the surface of the particles and a microarray having complementary moieties formed in an array on a substrate, such that each filter particle is attached to a selected region of the microarray. The moiety on the substrate may be RNA or DNA or other molecule. The substrate may be a surface of a photodetector array, a transparent plate that may be placed in registration with the photodetector or a stamp used to transfer the filter array to a photodetector array.

Abstract: A method an system is disclosed for characterizing DNA and/or RNA duplexes. The biosensing device comprises a heating element using a power and being suitable for providing thermal denaturation of target DNA and/or RNA bioparticles, a sample holder adapted for receiving a biocompatible substrate having a functionalized surface which is coated with probe DNA and/or RNA whereto target DNA and/or RNA duplexes can be attached, the sample holder further being adapted for exposing the biocompatible substrate at one side to the heating element, a first temperature sensing element for sensing a temperature at the side where the biocompatible substrate can be exposed to the heating element and a second temperature sensing element for sensing a temperature at the side opposite thereto with respect to the biocompatible substrate.

Abstract: A microfluidic device and method for enzymatic processing of ultra-long macromolecules is accomplished using a microfluidic device a reaction chamber with a first manifold, a second manifold, and a plurality of reaction channels. Each reaction channel extends from the first manifold to the second manifold. First inlet and outlet channels fill the reaction channels via the manifolds with one or more macromolecule containers suspended in a first carrier fluid. The first inlet and outlet channels are configured such that a flow is guided through the reaction channels, and an enzymatic reagent is fed to the reaction chamber essentially without displacing the macromolecule containers trapped in the reaction channels. The second set of inlets and outlets are configured such that a flow established from the second inlet to the second outlet is guided through at least one of the manifolds and bypasses the reaction channels.

Abstract: A full process control for use with a molecular assay and a method of determine the efficacy of the molecular assay. A full process control can include a fixed cell, and specifically can include a fixed vegetative cell. A method of determining the efficacy of a molecular assay can include providing an internal control, mixing the internal control with a sample, lysing the internal control and the sample, and detecting the lysis product. The full process control and/or the internal control can be Bacillus subtilis cells.

Abstract: Certain aspects of the present invention provide devices and methods for preparing oligonucleotides and for assembling nucleic acid molecules using microfluidic devices.

Abstract: Contemplated methods and devices comprise performing electrochemical sample analysis in a multiplexed electrochemical detector having reduced electrical cross-talk. The electrochemical detector includes electrodes that share a common lead from a plurality of leads. The sample, which may be a liquid sample, is introduced into one or more sample wells and a signal is applied to at least one of the electrodes. A response signal is measured while simultaneously applying a substantially fixed potential to each of a remainder of the plurality of leads.

Abstract: A biochip includes: a chamber that has a longitudinal direction; a holding unit that holds a liquid sample within a predetermined area of the chamber provided along the longitudinal direction, and releases the liquid sample from the predetermined area to an area inside the chamber by using a predetermined pressing force; and a pressed member that applies the predetermined pressing force to the liquid sample.

Abstract: The present application discloses a substrate that includes a molecular layer of regularly spaced size-controlled macromolecules comprising a polymer comprising branched and linear regions in which a plurality of termini on the branched region are bound to the substrate, and a terminus of the linear region is functionalized.

Abstract: The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalizing genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention.

Abstract: This invention relates to an assay device and a method for pretreating a specimen containing a biologically-relevant substance and then assaying the biologically-relevant substance. Biologically-relevant substances used in the assay method include microorganisms, cells, viruses, nucleic acids, polysaccharides, proteins (including antigens, antibodies, chromoproteins, and enzymes), peptides, nucleic acids, and small molecules. This pretreatment method removes contaminants from the biologically-relevant substances using supports such as magnetic particles, gels, resins, membranes, and solid-phased reagents. Therefore, in the assay method the following steps are generally carried out (i) a pretreatment step of treating a specimen using one or more first supports and then one or more second supports, and (ii) the assay step carried out after the pretreatment step. In particular, the pretreatment method reduces false positives and false negatives in the assay.

Abstract: The present patent application describes a cantilever for atomic force microscopy (AFM), which includes a cantilever body having a fixed end and a free end, the free end having a surface region being chemically modified by a dendron in which a plurality of termini of the branched region of the dendron are bound to the surface, and a terminus of the linear region of the dendron is functionalized.

Abstract: Embodiments of the present disclosure feature a filtration system comprising a filtration module for particle filtration and methods of using the device for the isolation of particles (e.g., viable cells). Advantageously, embodiments of the device provide for the high throughput filtration of large volumes of sample while preserving cell viability and providing high yields.

Abstract: A device and method for analyte detection is provided. In an embodiment, the device includes a multi-layer filter configured to receive a fluid-borne sample including at least one analyte in combination with one or more non-analyte components. The multi-layer filter includes a sample preparation layer configured to dissolve upon receiving a portion of the fluid-borne sample to produce a solution including at least a portion of the fluid-borne sample. The device also includes an analysis cartridge for determining a presence and/or a concentration of the analyte in the solution. The device may be configured as a wearable mask or as a part of a ventilation system. In some embodiments, the analyte is detected using a polymerase chain reaction and a detectable marker. The device and method may be used to quickly detect the presence of an analyte in real-time and on-location.

Abstract: This invention provides methods for pyrosequencing and compositions comprising 3?-O— modified deoxynucleoside triphosphates.

Abstract: This document provides methods and materials for detecting genetic and/or epigenetic elements. For example, methods and materials for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, methods and materials for detecting the amount of target nucleic acid containing a genetic or epigenetic element within a sample, kits for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, kits for detecting the amount of target nucleic acid containing a genetic or epigenetic element present within a sample, and methods for making such kits are provided.

Abstract: A sample of blood containing CTCs, or other cells of interest, is stained with fluorescent markers for image analysis and scanned to identify the presence and location within the cartridge of target cells or subcellular elements. A sample containing desired target cells or subcellular elements is then further processed, in part by photobleaching the sample, so that those same targets may be re-analyzed with additional biomarkers conjugated to the same or different fluorochromes using the same imaging criteria that were used for the initial analysis. The present invention has applications with targets such as circulating epithelial, cells, circulating tumor cells, circulating endothelial cells, leukocytes, lymphocyte subsets, cells containing an organelle or receptor of interest, cellular debris, disrupted cells and their debris, or any other formed element that might be captured and imaged.

Abstract: Methods for performing a direct enzymatic reaction involving a nucleic acid molecule include performing the enzymatic reaction directly using a biological specimen in a reaction mixture containing a zwitterionic buffer and/or a non-reducing carbohydrate to prevent the biological specimen from inhibiting the enzymatic reaction, in which a nucleic acid molecule present in the biological specimen is not purified before the enzymatic reaction, and obtaining a product from the enzymatic reaction.

Abstract: A method of filling a cartridge that includes a reaction chamber, a biochip mounted in the reaction chamber and a compensation chamber connected so as to communicate with the reaction chamber. The method includes placing a filling nozzle, which is connected so as to communicate with the reaction chamber, such that it is facing upwards, filling a liquid biological sample into the filling nozzle, pressing a stopper into the filling nozzle in order to force sample liquid into the reaction chamber, so that the reaction chamber is filled from bottom to top and an air bubble remains in the compensation chamber downstream of the reaction chamber.

Abstract: Compositions, methods, and systems for detecting small molecules using chemiluminescent signaling assay technology are provided. One system provided herein comprises a chromophore; an oxalate ester, a peroxide, and a modulating agent, wherein the modulating agent will perturb a chemiluminescent signal generated by an interaction among the chromophore, the oxalate ester, and a peroxide; and the perturbation will occur in response to an analyte. One method provided herein comprises combining a chromophore, an oxalate ester, a peroxide, and a modulating agent, wherein: the modulating agent will perturb a chemiluminescent signal generate by an interaction among the chromophore, the oxalate ester, and a peroxide; and the perturbation will occur in response to an analyte. Another method provides a colorimetric or fluorometric signal response in the presence of an analyte.