Abstract: The present invention relates to compositions and methods of target enrichment or selection of nucleic acids using hybridization, which can be used in, e.g., next-generation sequencing.

Abstract: An AC coupler for transmitting high-frequency components of a wideband signal includes a signal conductor and a shielding structure arranged as a transmission line. The signal conductor includes a conductive element and a capacitor configured to block direct current (DC) components of the wideband signal while transmitting high-frequency alternating current (AC) components of the wideband signal. The shielding structure is configured for conducting at least the AC components of the wideband signal while confining electric fields and currents in the shielding structure substantially to a region proximate to the signal conductor. The shielding structure has a width substantially greater than a width of the signal conductor. The difference between the shielding structure width and the signal conductor width may be substantially greater than an offset distance between the signal conductor and the shielding structure.

Abstract: The present invention provides a simple and rapid method for preparing purified transposase complexes that are highly suited for fragmenting DNA. The method includes forming transposase complexes with oligonucleotide adapters in cell lysate, then purifying the complexes from the other substance in the cell lysate. Purification is accomplished using a specific binding pair, in which one member of the pair is bound to an oligonucleotide adapter of the complex and the other member of the pair is bound to a solid substrate. The bound complexes can be immediately used in DNA fragmentation reactions to produce solid substrate-bound DNA fragments, which can be used for any number of purposes, including as templates for amplification and sequencing.

Abstract: A method comprising: synthesizing a set of overlapping oligonucleotides that comprises probe sequences that hybridize to unique sequences in a chromosome, assembling the overlapping oligonucleotides in a way that produces one or more double stranded polynucleotides that each comprises multiple probe sequences, labeling the one or more double stranded polynucleotides to produce one or more labeled probes, and hybridizing the labeled probes to an intact chromosome, in situ, is provided.

Abstract: Multiplexed spectrometry, such as multiplexed ion mobility spectrometry (IMS), time-of-flight mass spectrometry (TOFMS), or hybrid IM-TOFMS, is carried out on a sample, and the resulting measurement data are deconvoluted. Noise may be removed from the measurement data prior to deconvolution. Alternatively or additionally, noise may be removed from the deconvoluted data.

Abstract: Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided.

Abstract: An apparatus that includes a gain chip assembly, an external cavity, and a controller is disclosed. The gain chip assembly includes first and second gain chips that are coupled optically such that light travels serially between the first gain chip and the second gain chip, each gain chip is electrically biased. The electrical bias of the first gain chip is independent of the electrical bias of the second gain chip. The external cavity has a tunable wavelength selective filter that is changed in response to a control signal. Light in the external cavity passes through the gain chip assembly. The controller determines the tunable wavelength selective filter, and the electrical bias of each of the gain chips so as to cause the apparatus to lase at a wavelength specified by a control signal to the controller.

Abstract: A method for sequencing a nucleic acid is provided. In certain embodiments the method comprises obtaining a duplex comprising a nucleic acid and a primer, wherein the primer has a nuclease resistant 3? end, combining the duplex with a chain terminator nucleotide and a proof-reading polymerase to produce a reaction in which the polymerase idles on the added chain terminator nucleotide, identifying the chain terminator nucleotide added to the end of the primer; and adding a nuclease-resistant nucleotide to the end of the primer after the polymerase has idled on and removed the added chain terminator nucleotide, thereby producing a duplex comprising the template and an extended primer that has a nuclease resistant 3? end.

Abstract: A method and apparatus for measuring diffuse and specularly reflected light from a sample to provide a reflection spectrum as a function of wavelength and as a function of position on a sample is disclosed. The apparatus includes a MIR light source that generates an illumination beam of linearly polarized light. An illumination system illuminates a location on a specimen with part of the illumination beam. A linear polarization filter characterized by a polarization axis that defines a direction of polarization of linearly polarized light that is reflected by the linear polarization filter, a first detector that measures an intensity of light leaving the linear polarization filter and a light collection system collects light reflected from the location on the specimen and directs that light to the linear polarization filter. A controller measures an output from the first detector for each of a plurality of different polarization axis positions.

Abstract: A sample droplet generator transforms a segmented array of sample material into a continuous stream of droplets containing analytes. The droplets may serve as a sample source for a wide range of detectors and analytical instruments. As one example, the droplets may be introduced into an ion source of a spectrometer that measures ions produced from the droplets or photons emitted from the droplets.

Abstract: A method and apparatus for obtaining reference samples during the generation of a mid-infrared (MW) image without requiring that the sample being imaged be removed is disclosed. A tunable MIR laser generates a light beam that is focused onto a specimen on a specimen stage that moves the specimen in a first direction. An optical assembly includes a scanning assembly having a focusing lens and a mirror that moves in a second direction, different from the first direction, relative to the stage such that the focusing lens maintains a fixed distance between the focusing lens and the specimen stage. A light detector measures an intensity of light leaving the point on the specimen. A controller forms an image from the measured intensity. A reference stage is positioned such that the mirror moves over the reference stage in response to a command so that the controller can also make a reference measurement.

Abstract: A field terminator includes a plurality of electrode plates positioned around a guide axis at a radial distance therefrom. The plates generate a quadrupole DC field such that a polarity on each plate is opposite to a polarity on the plates adjacent thereto. The plates may be positioned at an axial end of a quadrupole ion guide such as a mass filter. In addition to an RF field, the ion guide may generate a quadrupole DC field. The DC field of the plates may be opposite in polarity to that of the ion guide.

Abstract: Systems and method for mass spectrometry are presented. In one embodiment, a method comprises: (a) acquiring one or more fragmentation signatures for a reference sample, wherein each fragmentation signature of the reference sample is acquired with a unique tandem mass spectrometry mode; (b) identifying one or more discriminate features across the plurality of fragmentation signatures of the reference sample; (c) acquiring one or more fragmentation signatures for an unknown sample, wherein each fragmentation signature of the unknown sample is acquired according to the discriminant features of step (b); (d) identifying one or more discriminate features across the plurality of fragmentation signatures of the unknown sample; (e) scoring the fragmentation signatures of step (c) by comparing the discriminate features of the reference sample, from step (b), against the discriminate features of the unknown sample, from step (d); and (f) identifying a structural isomer based on the score of step (e).

Abstract: An apparatus and method for generating images of specimens is disclosed. The apparatus includes an imaging system, controller, and user interface. The imaging system generates a plurality of component images of a specimen, each component image corresponding to a different viewing condition. Each image is represented by an intensity as a function of location on the specimen. The controller stores the component images and generates a compound image from a plurality of the component images. The compound image includes a weighted sum of first and second ones of the component images, the controller displaying the compound image on a display controlled by the controller. The user interface is adapted to control a weighting factor used in generating the weighted sum in response to user input. The controller redisplays the compound image after the weighting factor is changed in response to user input.

Abstract: The present invention provides mutants of DNA polymerases having an increased rate of incorporation of nucleotides into nucleic acids undergoing polymerization and having an enhanced resistance to inhibitors of DNA polymerase activity. The mutant polymerases are well suited for fast PCR applications, for PCR amplification of targets in samples that contain inhibitors of wild-type polymerases, and for fast PCR amplification of samples containing DNA polymerase inhibitors. In exemplary embodiments, the mutants are mutants of Taq DNA polymerase.

Abstract: An oligonucleotide derivative having the structure of formula (A) and methods for preparing the oligonucleotide derivative are disclosed. wherein R3 is a first oligonucleotide; R1 is selected from the group consisting of alkyl, cycloalkyl, aryl, heterocyclyl, heteroaryl, a polyethylene glycol, a peptide, a protein, a polysaccharide, and a second oligonucleotide; R2 is a linker or a direct bond; Z1 is NR4, S, or O, and Z2 is NR4 or S, wherein R4 is selected from H, alkyl, aryl, heterocyclyl, or heteroaryl. A method includes: synthesizing an oligonucleotide derivative comprising an amino or thiol group; and reacting a 3,4-dialkoxycyclobutene-1,2-dione with the oligonucleotide derivative to produce an oligonucleotide-squarate mono-conjugate.

Abstract: An injection device comprising: a housing defining a space; a seat located in said space, the seat being configured for receiving a flow path element capable of injecting a pressurized fluid into the injection device through the seat; a pressure source for pressurizing a medium in said space, thereby reducing the pressure difference between the pressurized fluid in said flow path element and said medium.

Abstract: The invention generally relates to ion-exchange chromatography. More particularly, the invention relates to compositions and methods that can substantially improve analytical sensitivity and/or selectivity of ion-exchange chromatography as well its efficiency and quality as a purification or preparation tool.

Abstract: The invention relates to the generation and characterization of stable MMLV reverse transcriptase mutants. The invention also discloses methods of using stable MMLV reverse transcriptase mutants.

Abstract: A fitting element is configured for coupling tubing to a fluidic device having a receiving cavity configured for receiving the fitting element, where the tubing has an inner contact surface of a biocompatible material, the inner contact surface being configured to contact a fluid to be conducted by the tubing, and the receiving cavity having a receiving contact surface of a bio-compatible material. The fitting element includes a first sealing element of a bio-compatible material configured for sealing to the bio-compatible material of the inner contact surface of the tubing, and a second sealing element configured for sealing against a pressure ambient to a pressure of the fluid in the tubing. Upon coupling of the tubing to the fluidic device, at least a portion of the receiving contact surface, the first sealing element, and the second sealing element enclose an interspace, each surface of the interspace being a bio-compatible material.