Abstract: A sample holder for annealing apparatus and electrically assisted annealing apparatus using the same are provided. The sample holder includes a heat conductive shell, high thermal conductive and electrical insulation blocks, first and second electrodes. The heat conductive shell includes a base frame and a top cover. The high thermal conductive and electrical insulation blocks are adjacent to the base frame and the top cover, respectively, and a sample pallet is sandwiched therebetween. Length and width of the sample pallet is smaller than that of the high thermal conductive and electrical insulation blocks. The first and the second electrodes are fixed to two sides of the sample pallet, and are connected to electrifying wire respectively. Thickness of the first and the second electrodes is smaller than that of the sample pallet, while the width of the first and the second electrodes is longer than that of the sample pallet.

Abstract: Methods for the rapid detection of the presence or absence of Mycoplasma genitalium (MG) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the target MG gene, along with kits are provided that are designed for the detection of MG.

Abstract: A composition for reducing the inhibitory effects of contaminants on nucleic acid amplification is provided. The composition includes effective amounts of ferric iron, an organic iron-chelating reagent, and a non-ionic surfactant. Optionally, the composition includes polyvinylpyrrolidone. The composition has a pH of about 8.45 to 8.85. The organic iron-chelating reagent has a first affinity constant greater than or equal to 104.2 with respect to ferric iron and a second affinity constant less than 103.8 with respect to magnesium. The first affinity constant and the second affinity constant are determined in deionized water at pH 8.45 and 20° C. Methods of using the composition to prepare a sample for nucleic acid amplification are also provided.

Abstract: A heating mechanism for use in DNA applications such as DNA amplification, extraction and sterilization is provided. Nanoparticles having photo-thermal properties are put in contact with a reaction mixture and irradiated with an activation light beam to activate these photo-thermal properties, thereby releasing heat. Nanoparticles of several types may be used. Use of the same nanoparticles or of different one to monitor the reaction using a different light beam is also presented.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: A cassette may include a substrate, a die coupled to the substrate, a reservoir defined in a first side of the substrate exposing a proximal side of the die to an external atmosphere, and an overflow reservoir defined in the first side of the substrate and surrounding at least a portion of a perimeter of the reservoir.

Abstract: The present invention is directed to a polymerase activity assay that produces a strong optical signal when a primer-template complex is extended to full-length product. The assay uses Cy3 as the molecular beacon and Iowa Black® RQ as the quencher. The signal-to-noise-ratio (STNR) of this donor-quencher pairing is ˜200-fold over background, which is considerably better than other donor-quencher pairs (STNRs ˜10-20-fold). The STNR allows for solution-based monitoring of polymerase activity. Because the sensor functions via Watson-Crick base pairing, the polymerase activity assay may also be used to evolve polymerases to accept xeno nucleic acids as substrates.

Abstract: The present invention provides compositions and methods for regulating the specificity and activity of immune effector cells for use in immunotherapy. In one embodiment, the invention provides a type of chimeric antigen receptor (CAR) wherein the CAR is termed a “NKR-CAR” which is a CAR design comprising a component of a receptor naturally found on natural killer (NK) cells. In one embodiment, the NK receptor includes but is not limited to a naturally occurring activating and inhibitory receptor of NK cells known as a killer cell immunoglobulin-like receptor (KIR).

Abstract: First and second sets of receptacles containing reagents for first and second amplification reactions, respectively, are placed in first and second receptacle holders, each associated with a thermal element. The receptacles are subjected to different first and second incubation processes resulting in the first and second amplification reactions in each of the first and second sets of receptacles that contain a first or a second target nucleic acid, respectively. The presence or absence of the first or second target nucleic acid, if any, is determined for each receptacle of the first and second sets of receptacles.

Abstract: Methods for amplifying a target nucleic acid by self-sustained amplification methods are described. The methods are designed, in particular, to be carried out without use of specialised lab facilities or instruments. Compositions, lyophilised formulations, and kits for carrying out the methods are also described.

Abstract: This disclosure provides methods for preparing a sequencing library including the steps of providing a template nucleic acid sequence, dNTPs, dUTP, a primer, a polymerase, a dUTP excising enzyme, and a plurality of beads including oligonucleotide adapter sequence segments; amplifying the template nucleic acid with the polymerase, dNTPs, dUTP and random hexamer to provide a complementary nucleic acid sequence including occasional dUTPs; and excising the incorporated dUTPs with the dUTP excising enzyme to provide nicks in the complementary nucleic acid sequence to provide a sequencing library.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: Sharing data is disclosed. In some cases, sharing data includes receiving a request to share data from a first account to a second account, receiving an indication of a plurality of first account profiles associated with the first account to share with the second account, and establishing sharing from the plurality of first account profiles to the second account, wherein sharing comprises the second account having read access to a subset of nonpublic data associated with the plurality of first account profiles.

Abstract: The present invention relates to methods and uses for the detection or quantification of newly-synthesized double-stranded target nucleic acid molecules in a sample during quantitative real-time polymerase chain reaction (qPCR) amplification. According to the invention, an intercalating dye recognizing double-stranded DNA molecules with higher affinity than single-stranded DNA molecules and a fluorophore-labeled oligonucleotide-probe being sequence specific for a target nucleic acid molecule are simultaneously employed, thus enabling quantification a specific target and total amount of a mixed nucleic acid population, and enabling assessing the cause of suboptimal PCR performance.

Abstract: Isolated or purified mammalian kidney-derived cell populations from mammalian kidney tissue are provided. Methods are provided for the isolation and purification of the mammalian kidney-derived cell population. Methods for treating kidney disease are provided by administration of the isolated or purified mammalian kidney-derived cell population to a mammalian subject.

Abstract: The present invention disclosed a Nosema bombycis HMG1 gene, a specific primer set used for rapidly detecting Nosema bombycis, a group of microsporidium universal detection primers, and uses thereof. The primer set comprises a primer HMG1-sF and a primer HMG1-sR, and nucleotide sequences of the primers are shown in SEQ ID No. 5-6 respectively. The universal detection primers comprise a primer HMG1F and a primer HMG1R, and nucleotide sequences of the primers are shown in SEQ ID No. 3-4 respectively.

Abstract: The subject invention pertains to a method of determining methylation state and chromatin structure of target loci. The method comprises treating the genetic material obtained from the cells with DNA methyltransferase, capturing target genetic loci using a set of oligonucleotides, ligating the target loci with oligonucleotide patches that flank the target loci, treating the target loci flanked by oligonucleotide patches with bisulfite, optionally amplifying the target loci by polymerase chain reaction, sequencing the PCR products, and analyzing the sequences to determine methylation state and chromatin structure of the target loci. The current invention also provides a method to identify genes associated with a disease. The invention also provides a method to detect cells suffering from a disease in a group of cells. The current invention also provides kits suitable for carrying out the method of determining methylation state and chromatin structure of the target loci.

Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimize sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimizing GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilizing flow cells.

Abstract: Sharing data is disclosed. In some cases, sharing data includes receiving a request to share data from a first account to a second account, receiving an indication of a plurality of first account profiles associated with the first account to share with the second account, and establishing sharing from the plurality of first account profiles to the second account, wherein sharing comprises the second account having read access to a subset of nonpublic data associated with the plurality of first account profiles.

Abstract: The invention concerns a method of analyzing the content of drops, involving then following step: providing a plurality of drops (6) contained in a carrier fluid, at least one of the drops (6) comprising at least one aggregate (10) of particles defining an object extending along a main axis, at least some of the drops (6) containing at least one target element capable of attaching to the aggregate (10). The method involves a step in which a physical parameter characteristic of the attachment of the target element to the aggregate (10) is measured.

Abstract: The present invention provides methods for the detection of cyanobacteria, and in particular, methods for the detection of cyanotoxic organisms. The invention further relates to methods of screening for compounds that modulate the activity of polynucleotides and/or polypeptides of the saxitoxin biosynthetic pathways.

Abstract: Provided herein are methods for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise producing a plurality of cDNAs from a plurality of polynucleotides, wherein at least one polynucleotide encodes a heavy and/or light chain, from a plurality of immune cells from a biological sample. Producing a plurality of cDNAs may comprise reverse transcription and template switching, such as to form a plurality of uniquely barcoded cDNAs. Methods described herein further comprise amplifying the plurality of uniquely barcoded cDNAs, thereby forming a library, and sequencing one or more of the sequences of the library.

Abstract: This invention relates to a kit for detecting NRAS gene mutation, and this kit can be used to detect cancer-related NRAS gene mutation. The said kit comprises: (1) the internal reference detection reagent, which includes the internal reference gene specific primers, internal reference gene specific probes and dNTP solution; (2) the NRAS mutation detection reagent, which includes the NRAS gene mutant type specific primers, NRAS gene mutant type specific probes, internal control gene specific primers, internal control gene specific probes and dNTP solution; (3) the Taq DNA polymerase; and (4) the NRAS positive quality control.

Abstract: The present invention relates to methods of making linear nucleic acid probes using rolling circle amplification methods.

Abstract: Disclosed is a method of preparing nucleic acid molecules, including: providing a pool of oligonucleotides, each containing restriction enzyme digestion sequences and generic flanking sequences; cleaving the restriction enzyme digestion sequence portions to provide a pool of mixtures comprising the oligonucleotides, each containing the generic flanking sequences at one end, and the oligonucleotides, each containing none of the generic flanking sequences at one end, and; assembling the oligonucleotides using the generic flanking sequences to randomly synthesize nucleic acid fragments.

Abstract: Provided are a method for constructing a nucleic acid single-stranded cyclic library and the reagents used therein. By the combination of interruption via a transposase with a restricted nick translation reaction, the method realizes a simple and rapid nucleic acid single-stranded cyclic library construction.

Abstract: There is provided an automated biological-sample-processing system comprising a pipette, a column of solid-phase material to which nucleic acid binds, a transport apparatus, an air-piston apparatus and an adaptor for coupling the pipette to the transport apparatus and to the air-piston apparatus, in which the adaptor is removably engageable with the transport apparatus and the air-piston apparatus for movement with the transport apparatus during processing of the sample, is couplable to the pipette so that the transport apparatus is controllable to position the pipette and so that the air-piston apparatus is controllable to draw a liquid into the pipette and to expel the liquid from the pipette, and is engageable with the column, in which the adaptor comprises a filter for preventing liquid or aerosol transfer between the pipette or column and the air-piston apparatus.

Abstract: In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.

Abstract: The present invention relates to methods and uses where a combination of (i) an enzyme exhibiting 5??3? exonuclease activity and specifically degrading 5?-phosphorylated strands of double-stranded nucleic acids is used, and (ii) one or more primer pair(s), each primer being 5? phosphorylated, in a method comprising at least a first and a second amplification reaction of a first and a second template, respectively, for preventing contamination of the second amplification reaction with amplification products of the first amplification reaction, as well as novel methods and kits using the combination. Also, the present invention relates to kits comprising the enzyme and either 5?-phosphorylated primers or a polynucleotide kinase.

Abstract: Transposon nucleic acids comprising a transposon end sequence and a calibration sequence for DNA sequencing in the transposon end sequence. In one embodiment, the transposon end sequence is a Mu transposon end. A method for the generation of DNA fragmentation library based on a transposition reaction in the presence of a transposon end with the calibration sequence providing facilitated downstream handling of the produced DNA fragments, e.g., in the generation of sequencing templates.

Abstract: A universally usable method for specific detection of target nucleic acid sequences, which method can be performed very rapidly and also simply and furthermore which does not need any expensive instrumental systems. The method is intended to be suitable as a molecular genetic rapid test and to respect the requirements of diagnostic specificity assurance. In this regard it is important that only one specific amplification product be detected and that amplification artifacts can be unambiguously discriminated. A nucleic acid amplification kit suitable for performing this method.

Abstract: Methods to formulate treatments for individual cancer patients by assessing genomic and/or phenotypic differences between cancer and normal tissues and integrating the results to identify dysfunctional pathways are described.

Abstract: The present invention provides DNA plasmids that find use as calibrators or reference standards for calculating DNA quantities in a sample. In particular, provided herein are DNA plasmids that contain multiple control fragments, and methods of their use in DNA quantitation.

Abstract: The invention relates to methods and compositions for estimating the absolute abundance individually for each unique rearranged lymphocyte receptor in a mixed sample.

Abstract: Provided herein are methods and compositions for labeling target nucleic acid molecules with molecular barcodes.

Abstract: The present invention generally relates to systems and methods for producing nucleic acids. In some aspects, relatively large quantities of oligonucleotides can be produced, and in some cases, the oligonucleotides may have a variety of different sequences and/or lengths. For instance, a relatively small quantity of oligonucleotides may be amplified to produce a large amount of nucleotides. In one set of embodiments, oligonucleotides may be amplified using PCR, then transcribed to produce RNA. The RNA may then be reverse transcribed to produce DNA, and optionally, the RNA may be selectively degraded or removed, relative to the DNA. In one set of embodiments, the oligonucleotides may be chemically modified. These modifications may include, but are not limited, to the adding of fluorescent dyes or other signaling entities.

Abstract: In one aspect, a thermal cycler system is disclosed. The thermal cycler can be comprised of a device housing and a cover that is operably connected to the device housing. The cover can include a handle portion, a device lid portion, a sample block platen, and a link bar. The device lid portion is attached to the proximal side of the handle portion with a first pin. The sample block platen is operably connected to the handle portion such that the sample block platen is positioned against the sample block when the handle portion is flush with the device lid portion and the cover is in a closed position. The link bar is pivotably connected to the device housing at a first terminal end portion and a second pin at an opposite second terminal end portion, wherein the handle portion is elevated away from the device lid portion before the cover is moved to an open position.

Abstract: Disclosed herein are methods and compositions (e.g., oligonucleotide primers) for isothermal amplification and detection of M. pneumoniae nucleic acids in a sample. In some embodiments, the methods include contacting a sample with a set of LAMP primers specific for a M. pneumoniae CARDS toxin-encoding nucleic acid under conditions sufficient to produce an M. pneumoniae nucleic acid amplification product and detecting the resulting M. pneumoniae amplification product. Kits including sets of LAMP primers for detection of M. pneumoniae CARDS toxin nucleic acids are also provided herein.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: The present invention relates to a formulation of a thermostable DNA polymerase which is completely free of detergents and its particular use in real time polymerase chain reaction (PCR). Such a formulation may be obtained if the selected purification method does not require the addition of a detergent at any purification step.

Abstract: The present invention provides reagents, kits, and methods for single-cell whole genome amplification using Phi 29 DNA polymerase.

Abstract: A method for detecting toxigenic Clostridium difficile (C. difficile) by strand-invasion based DNA amplification is provided, together with oligonucleotides, compositions and kits suitable for use in this method.

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Abstract: The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.

Abstract: Described herein are cell-based analytic methods, including a method of incorporating nucleic acid sequences into reaction products from a cell population, wherein the nucleic acid sequences are incorporated into the reaction products of each cell individually or in small groups of cells individually. Also described herein is a matrix-type microfluidic device that permits at least two reagents to be delivered separately to each cell or group of cells, as well as primer combinations useful in the method and device.

Abstract: A direct chemical lysis composition includes an assay compatible buffer composition and an assay compatible surfactant. When combined with a specimen storage composition, such compositions prevent undesired modifications to nucleic acid and proteins lysed from cells in the biological sample. Assays of samples from such compositions do not require expensive and time-consuming steps such as centrifugation and prolonged high temperature processing. The direct chemical lysis composition of the present invention permits direct nucleic acid extraction from the cells in the biological sample without the need to decant off the transport media or otherwise exchange the transport media with assay compatible buffers. There is no need to combine the sample with proteinase K or another enzyme to extract nucleic acids from the cells. A method for lysing cells to obtain target nucleic acid for assay and a kit for combining the direct chemical lysis composition with a sample are also contemplated.

Abstract: A method for identification of circulating tumor cells (CTCs) in a blood sample uses magnetic enrichment and a nanowell assay. The CTCs are magnetically labeled with cancer cell markers conjugated to magnetic nanoparticles and then separated by passing the blood sample through a magnetic sifter. The enriched CTCs are then loaded into a microfluidic single-cell molecular assay comprising an array of 25,600 or more nanowells, each containing at most a single one of the CTCs. Using multiple fluorescent gene markers, simultaneous multiple-color multiplexed gene expression of the CTCs is performed, preferably using RT-PCR. Images of fluorescence signals from individual nanowells are analyzed to identify CTCs.

Abstract: This document provides methods and materials for detecting contaminated food products. For example, methods and materials for using an enzymatic amplification cascade of restriction endonucleases to detect nucleic acid of a microorganism or virus (e.g., a pathogen) within a sample (e.g., food product sample) being tested, thereby assessing a food product for possible contamination are provided.

Abstract: Methods and systems are provided for amplifying target nucleic acids by means of a polymerase with strand displacement activity, using two or more stem loop primers, each with a 3?-end portion comprising sequence complementary to a target homology site of a target nucleic acid and 5?-end portion with a sequence comprising a stem sequence, a loop sequence and a sequence which is reverse complementary to the stem sequence, the said 5?-end portion being capable of forming a stem loop. Such methods and systems can be used to amplify target nucleic acids isothermally by means of a polymerase with strand displacement activities.