Abstract: A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3? sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a pair of tailed primers to produce asymmetrically-tagged library.

Abstract: Provided herein are compositions and methods to assess the genomic landscape of fixed cells using light activated oligonucleotides that can be directed to the nucleus, mitochondria, or cytoplasm of fixed cells and that, upon activation, can be extended for in situ copying of nuclear single-stranded DNA (i.e., open chromatin), open mitochondrial DNA, and/or cytoplasmic RNA into barcoded complementary DNA. These methods also provide for gene specific 3D chromatin structural niche analysis.

Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3? overhang of at least 8 nucleotides, wherein the 3? overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5? end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods are also provided.

Abstract: A device is provided in a supercritical fluid system, which uses a mobile phase output by a separation device, the mobile phase volumetrically expanding as it decompresses. The device includes a passive splitter and a shuttle valve. The passive splitter is configured to receive the mobile phase and to split the mobile phase into a primary flow stream and a split flow stream, where the primary flow stream is directed to a pressure maintenance device. The passive splitter is further configured to reduce pressure of the split flow stream, causing volumetric expansion of the split flow stream. The shuttle valve is configured to insert volumetric aliquots of the volumetrically expanded split flow stream into a dilution flow stream to provide a diluted split flow stream, and to direct the diluted split flow stream to a low pressure detector.

Abstract: Methods for making a synthetic nucleic acid which comprise: (a) identifying a conflicting nucleotide sequence in a target sequence; (b) inserting a masking sequence into the conflicting sequence to produce a disrupted target sequence, wherein: (i) the masking sequence comprises recognition sites for one or more Type IIS restriction endonucleases; and (ii) digestion of said disrupted target sequence by said one or more Type IIS restriction endonucleases followed by re-ligation reconstitutes the target sequence; (c) synthesizing a polynucleotide comprising the disrupted target sequence using polymerase chain assembly; and (d) removing the masking sequence from said polynucleotide by digesting said polynucleotide with said one or more Type IIS restriction endonucleases followed by re-ligation of the digestion product, thereby producing a polynucleotide comprising said target sequence.

Abstract: A scanning apparatus having a stage adapted to hold a specimen to be imaged and to move the specimen in a first direction, and a light source that includes a tunable laser that generates a light beam having an illumination wavelength that varies as a function of an input signal is disclosed. The apparatus includes an imaging system having a scanning assembly that includes a focusing lens that focuses the light beam to a measurement point on the specimen, a first mirror that moves in a second direction relative to the stage such that the focusing lens maintains a fixed distance between the focusing lens and the stage, and a displacement sensor that measures a distance between the scanning assembly at a mapping point on the specimen, and a light detector that measures an intensity of light leaving the measurement point on the specimen.

Abstract: An environmental chamber having an interior compartment, an augmented display, and a controller is disclosed. The interior compartment is adapted for isolating an experimental setup from an environment external to the interior compartment. The augmented display is positioned to allow a user in the external environment to view the interior compartment and an image generated on the augmented display. The controller generates the image. The image includes information about a component within the interior compartment. The augment display can include a touch-enabled display screen that allows the user to interact with controller.

Abstract: An injector, for injecting a fluidic sample into a flow path between a fluid drive and a sample separation unit, includes a sample accommodation volume, a sample drive, and a fluidic valve switchable to selectively couple the volume with the flow path or decouple the volume from the flow path. In an injection switching state, the fluid drive, the separation unit and the sample drive are coupled by the valve so that fluid driven by the sample drive and flowing from the volume to the separation unit and further fluid driven by the fluid drive and flowing from the fluid drive to the separation unit are combined at a fluidic connection upstream of the separation unit. A control unit controls a pressure of the fluid and/or the further fluid during injecting.

Abstract: In one embodiment, a system includes a mass analyzer, an ion source for providing ions to the mass analyzer, a detector for detecting an output of the mass analyzer, and a frequency-selectable power source. The frequency-selectable power source may include an energy supply configured to provide high-voltage radio-frequency (RF) energy to the mass analyzer at individually selectable first and second frequencies, and a frequency selector for switching between the individually selectable first and second frequencies.

Abstract: Described herein is a method for adding a counter sequence to the individual polynucleotide molecules of an initial nucleic acid sample. After addition of the counter sequence, the sample may be amplified and the number of initial target molecules in the sample can be estimated by counting the number of counter sequences associated with the amplified target molecules.

Abstract: The present invention relates to MHC-peptide complexes and uses thereof in the diagnosis of, treatment of or vaccination against a disease in an individual. More specifically the invention discloses MHC complexes comprising Mycobacterium tuberculosis antigenic peptides and uses there of.

Abstract: The present invention provides a method for making a large nucleic acid having a defined sequence in vivo. The method combines recombineering techniques with a CRISPR/Cas system to permit multiple insertions of defined sequences into a target nucleic acid at one time, double stranded cleavage of target nucleic acids in which the defined sequences were not successfully inserted, and selection of successful recombinant cells. The method further includes repeating the process one or more times, using a successful recombinant from one round as the host cell for the next round.

Abstract: Aspects of the present disclosure provide methods for determining the eligibility of a subject having a malignancy for treatment with an anti-PD therapeutic agent based on a Combined Positive Score (CPS) for a tumor tissue sample from the subject. Compositions and kits or performing the disclosed methods are also provided.

Abstract: A secondary electron multiplier includes: a conversion dynode for emitting a secondary electron in response to an incident ion; a plurality of dynodes configured to have multi-stages from second to final stages for receiving the secondary electron; and a first voltage applying device for applying a first negative voltage to the conversion dynode and sequentially dividing the first negative voltage to apply to each of the second-stage and subsequent dynodes, wherein the secondary electron multiplier is configured to sequentially multiply the emitted secondary electron by the second-stage and subsequent dynodes. In the secondary electron multiplier, any of the second-stage and subsequent dynodes have a second voltage applying device for applying a second negative voltage. The secondary electron multiplier has an improved ion detection efficiency without a large reduction of a usable period thereof, thereby enhancing the sensitivity of a mass spectrometer.

Abstract: An ATR scanner and method for calibrating the same are disclosed. The scanner includes an ATR objective having a reflecting face and an optical port adapted to receive a first light beam, and to focus the first light beam to a point, at a location on the reflecting face such that the first light beam is reflected by the reflecting face and no portion of the first light beam strikes the reflecting face at an angle greater than the critical angle. A detector measures an intensity of light reflected from the reflecting face. A controller controls the location of the focal point and determines an intensity of light that was incident on the reflecting face as a function of the position on the reflecting face and an intensity of light that was reflected from the reflecting face as a function of position on the reflecting face.

Abstract: A method of deprotecting a solid support bound polynucleotide comprising at least one 2?-protected ribonucleotide in which a step of contacting the polynucleotide with a composition comprising a diamine is performed under conditions sufficient to deprotect and cleave the polynucleotide which remains retained on the solid support.