Abstract: Methods of using azide-modified biomolecules, such as fatty acids, carbohydrates and lipids, to treat a plant, an insect or an animal infected with a virus or to inhibit infectivity of a virus, such as the human immunodeficiency virus, are provided. Also provided are methods of labeling a virus, such as human immunodeficiency virus, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. Also, provided are methods of tracking a virus in vivo, with an azide-modified biomolecule, such as a fatty acid, a carbohydrate, or an isoprenoid lipid. The azide-modified biomolecules may be combined with a pharmaceutically acceptable excipient to produce a pharmaceutical composition, optionally containing another anti-viral agent and/or a delivery agent, such as a liposome.

Abstract: Methods are provided that operate on raw dissociation data and dissociation curves to generate calibrations of the detected data and to further improve analysis of the data. The data can be taken from each support region of a multi-region platform, for example, from each well of a multi-well plate. Each support region can be loaded with portions of the same sample. In some embodiments, a dissociation curve correction can be calibrated for the sample, prior to a run of an experiment using such sample. In some embodiments, a method is provided for generating a melting transition region of dissociation curves that show the melting characteristics of the sample. In some embodiments, dye temperature dependence correction can be performed on the dissociation curve data to further improve analysis. In some embodiments, a feature vector can be derived from the melt data, and the feature vector can be used to further improve genotyping analysis of the dissociation curves.

Abstract: A container includes a first wall made of a polymeric material, a second wall made of a polymeric material, and a plurality of elongated baffles, spacers or seam lines formed between the first wall and the second wall to form a plurality of separate fluid flow paths. Each of the plurality of fluid flow paths are separated from the other fluid flow paths by at least one of the baffles, spacers or seam lines. Each of the plurality of fluid flow paths have a first end in fluid communication with an inlet and have a second end in fluid communication with an outlet.

Abstract: This disclosure relates to methods, compositions, and related apparatuses for detection and quantification of nucleic acid molecules associated with a solid surface. Methods can include detecting or quantifying at least one nucleic acid molecule associated with a surface by contacting the at least one nucleic acid molecule with a fluorophore, wherein the fluorophore emits increased fluorescence at a wavelength when in contact with nucleic acid molecule, and detecting or measuring fluorescence from the fluorophore at the wavelength. Compositions can comprise a fluorophore and a nucleic acid molecule, wherein the nucleic acid molecule is associated with a surface, and the fluorophore has the property of emitting increased fluorescence at a wavelength when in contact with a nucleic acid molecule.

Abstract: Systems and methods for automated laser microdissection are disclosed including automatic slide detection, position detection of cutting and capture lasers, focus optimization for cutting and capture lasers, energy and duration optimization for cutting and capture lasers, inspection and second phase capture and/or ablation in a quality control station and tracking information for linking substrate carrier or output microdissected regions with input sample or slide.

Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.

Abstract: A bioreactor system includes a support housing having an interior surface bounding a compartment, the support housing having a sidewall with an opening extending therethrough and communicating with the compartment. A rack is secured to the support housing in alignment with the opening. An elongated first shaft has a first end and an opposing second end, the first end of the first shaft being secured to the rack so that the second end of the first shaft projects outwardly away from the sidewall of the support housing. A structure is secured to the first shaft towards the second end of the first shaft, the structure outwardly projecting away from the first shaft. A collapsible bag bounds a chamber and is at least partially disposed within the compartment of the support housing. A member projects from the collapsible bag and passes through the opening on the sidewall, the structure restraining movement of the member.

Abstract: A hydrogel network includes a hydrogel polymer having a coupling site, an oligonucleotide conjugated at a terminal end to the hydrogel polymer at the coupling site, and a functional moiety coupled between the terminal end of the oligonucleotide and the coupling site. Such a hydrogel network can be formed by a method including activating a coupling site of a substrate and binding a linker moiety coupled to a terminal end of an oligonucleotide to the activated coupling site, a functional moiety coupled between the terminal end of the oligonucleotide and the linker moiety.

Abstract: A rotor assembly includes a rotor plate to rotate around a first axis; a bucket rotatably attached to the rotor plate and to rotate around a second axis; and a stop plate to rotate around the first axis relative to the rotor plate between an open position and a closed position, when in the closed position, the stop plate is to engage the bucket to fix an angular position of the bucket relative to a plane of rotation of the rotor assembly.

Abstract: Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.

Abstract: A method of preparing a discrete polymer network array include mixing a plurality of nucleic acid polymer networks with a plurality of color-activated polymer networks to form a dispersion, applying the dispersion to an array of wells, the nucleic acid polymer networks selectively depositing into wells of the array of wells, and rinsing the array of wells to selectively remove the plurality of color-activated polymer networks.

Abstract: A method for calibrating a biological instrument is provided. The method comprises the steps of acquiring an image of at least one biological sample array, determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.

Abstract: A polymer substrate, such as a polymer coating or a polymer hydrogel network, includes carboxyl moieties that can be used as conjugation sites to which receptor or analyte molecules can be attached. In an example, the polymer substrate includes a polyacrylamide polymer network having alkanoic acid moieties or derivatives thereof, which can react with carboxyl activating compounds to provide an activated alkanoate moieties on the polyacrylamide network. Amine-terminated nucleic acids can react with the activated alkanoate moieties to capture the nucleic acid to the polymer network through an alkylamide moiety.

Abstract: The present invention provides a method for measuring cellular nascent nucleic acid synthesis by dual pulse labeling of nucleic acid. The first pulse labeling of nucleic acid with a nucleoside analog allows establishment of a baseline nucleic acid synthesis rate. Pulse labeling of the nucleic acid with a second nucleoside analog then allows measurement of any changes to nucleic acid synthesis. The nucleic acid synthesis can be measured as cell proliferation, DNA, or gene expression, RNA. This method does not require a potentially artifact-inducing intermediary wash step between pulse labels. Additionally, this method may be used to screen compounds for their affect on cellular proliferation by treating cells or an organism with the test compound simultaneous to or before treatment with a competitive nucleoside analog.

Abstract: A method for performing polymerase chain reactions (PCR) for improving thermal non-uniformity is provided. The method includes measuring a first temperature, by a first sensor, of a first sample block sector of a sample block and measuring a second temperature, by a second sensor, of a second sample block sector of the sample block that is adjacent to the first sample block sector. The method further includes calculating, by a thermoelectric controller, a difference in temperature between the first temperature and the second temperature and adjusting, by the thermoelectric controller, the first temperature of the first sample block sector based on the difference in temperature by using one or more thermoelectric coolers. The one or more thermoelectric coolers is configured to heat or cool the first sample block sector by adjusting power output from the thermoelectric controller.

Abstract: A method of treating a sensor array including a plurality of sensors and an isolation structure, where a sensor of the plurality of sensors has a sensor pad exposed at a surface of the sensor array and the isolation structure is disposed between the sensor pad and sensor pads of other sensors of the plurality of sensors, comprises exposing the sensor pad and the isolation structure to a non-aqueous organo-silicon solution including an organo-silicon compound and a first non-aqueous carrier; applying an acid solution including an organic acid and a second non-aqueous carrier to the sensor pad; and rinsing the acid solution from the sensor pad and the isolation structure.

Abstract: According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I): In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.

Abstract: A proximity binding assay (PBA) is performed on at least one test sample, at least one reference sample, a background sample, and one or more calibration samples using a thermal cycler instrument. Ct values are determined for at least one set of test sample data and at least one set of reference sample data. Background corrected Ct values are calculated using a corresponding value in a background sample data set. A linear range is determined for the background corrected Ct values as a function of sample quantity. A linear regression line is calculated for each linear range. One or more parameter values of an exponential model (EM) fold change formula are estimated from the one or more sets of calibration sample data. A target protein quantity and associated confidence interval are calculated using the linear regression lines and the EM fold change formula.