Abstract: Provided are methods of depleting a target nucleic acid from an initial collection of nucleic acids. Aspects of the methods include contacting the initial collection with a nucleic acid guided nuclease specific for the target nucleic acid in a manner sufficient to deplete the target nucleic acid from the initial collection. Depending on a given application, depletion of a target nucleic acid may vary, e.g., where depleting may include cleaving a target nucleic acid in, or selectively separating a target nucleic acid from, the initial collection of nucleic acids. Also provided are compositions and kits for practicing embodiments of the methods.

Abstract: Disclosed herein are methods and compositions for detecting differential expression of certain miRNAs in cancer cells or their surrounding normal tissues in the tumor microenvironment. The disclosure describes an automated, highly sensitive and specific method for detection of any cellular RNA molecule, including microRNA, messenger RNA and non-coding RNA. The technology includes probe design as well as probe use in an automated fashion for detection of RNA molecules in formalin-fixed paraffin-embedded tissue (FFPET) samples.

Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. This advantageously improves signal-to-noise ratios and increases the quality of results obtainable in a sequencing-by-binding protocol, and enables extended read lengths. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Abstract: Systems and methods for nucleic acid sequencing are provided. Nucleic acid is fixed in double-stranded linearized stretched form on a test substrate before being denatured into to single stranded form on the substrate to obtain adjacent fixed first and second strands of the nucleic acid. The strands are exposed to a respective pool of a respective oligonucleotide probe in a set of probes under conditions allowing for probes to form a heteroduplex with a corresponding complementary portion of the fixed first or second strand thereby giving rise to a respective instance of optical activity. An imager measures a location and duration on the substrate of this optical activity. The exposing and measuring is repeated for probes in the set of probes thereby obtaining a plurality of sets of positions. The nucleic acid sequence is determined from the plurality of sets of positions through compilation of the positions in the sets.

Abstract: The present invention relates to novel hybridization probes useful for rapid hybridization to realize a practicable and affordable pathogen diagnostic based on RNA signature detection, technology and hardware. In particular, the present invention relates to a nucleic acid structure which may comprise nucleic acid tiles, wherein each nucleic acid tile comprises nucleic acid oligomers, wherein each nucleic acid oligomer hybridizes to each other thereby forming a nucleic acid tile.

Abstract: The present disclosure relates to oligonucleotide sequences for amplification primers and their use in performing nucleic acid amplifications of HCV, in particular regions that encode the NS3 polypeptide. In some embodiments the primers are used in nested PCR methods for the detection or sequencing of HCV NS3. The oligonucleotide sequences are also provided assembled as kits that can be used to amplify and detect or sequence HCV NS3.

Abstract: Methods and compositions for the detection and quantification of nucleic acids are provided. In certain embodiments, methods involve the use of cleavable probes that comprise a ribonucleotide position that is susceptible to endoribonuclease (e.g., RNase H) cleavage in the presence of target nucleic acid molecules. Probes of the embodiments may also comprise non-natural nucleotide linked to a reporter and/or quenching moiety.

Abstract: In accordance with the disclosure, a method of forming a nanochannel is provided. The method includes depositing a photosensitive film stack over a substrate; forming a pattern on the film stack using interferometric lithography; depositing a plurality of silica nanoparticles to form a structure over the pattern; removing the pattern while retaining the structure formed by the plurality of silica nanoparticles, wherein the structure comprises one or more enclosed nanochannels, wherein each of the one or more nanochannels comprise one or more sidewalls and a roof; and partially sealing the roof of one or more nanochannels, wherein the roof comprises no more than one unsealed nanochannel per squared micron.

Abstract: A bispecific antibody that simultaneously targets humanized p185 and VEGF, consisting of the four peptide chains: two identical antibody light chains that are the light chains of the antibody that identify the epitope or antigen of p185, and two identical antibody heavy chains that have the amino acid sequence of a recombinant antibody from N- to C-terminus, a light chain sequence of the antibody that recognizes the p185 epitope or the antigen; a constant heavy chain region; a flexible short peptide sequence; and either a single-stranded variable region sequence (ScFv) of anti-VEGF antibody which recognizes the VEGF epitope or antigen, or a receptor domain sequence that binds to VEGF. The bispecific antibody has the ability to bind p185 and VEGF at the same time, inhibits the proliferation of tumor cells, and promotes the expression of IFN-? by T lymphocytes; it may be applied as anti-tumor antibody drug.

Abstract: The present invention provides a method for diagnosing or detecting Idiopathic Scoliosis, in particular AIS, as well as a method for prognosticating this disease in a human subject.

Abstract: A method of limiting the spread of the norovirus within a cruise ship comprising: identifying a surface within a common area of a cruise ship that passengers are likely to touch; and applying a silane quaternary ammonium ion or salt thereof to the surface. The common area can be an elevator and the surface an elevator button. The common area can be a stairway and the surface a handrail. The common area can be a casino. The common area can be a dining room. The common area can be a walkway and the surface a handrail. The silane quaternary ammonium ion or salt thereof can be 3-(trimethoxysilyl)propyldimethyloctadecyl ammonium ion, 3-(trimethoxysilyl)propyldimethyloctadecyl ammonium chloride, 3-(trihydroxysilyl)propyldimethyloctadecyl ammonium ion, or 3-(trihydroxysilyl)propyldimethyloctadecyl ammonium chloride. Applying the silane quaternary ammonium ion or salt thereof to the surface comprises applying a solution including the silane quaternary ammonium ion or salt thereof and a solvent.

Abstract: Contemplated systems and methods allow for computational genomic analysis using paired-end sequence analysis and split read refinement to thereby identify high-confidence breakpoints associated with high copy numbers and orientation of rearrangements, which is then the basis for full reconstruction of double minutes (DM). In especially preferred aspects, the DM will also include an oncogene or tumor suppressor gene, and/or may be found in blood or blood derived fluids.

Abstract: Aspects of the present invention include methods and compositions related to the modulation of molecules regulating the regenerative potential of cells and tissues in the embryonic state and the loss thereof in later fetal and adult stages of development. Said methods and compositions have uses in research in stem cell biology and in increasing regenerative potential in fetal and adult tissues otherwise incapable of regeneration.

Abstract: A method of treating porphyria in a patient is provided comprising knocking down or reducing expression or activity of ?-catenin in the patient, e.g., in the liver of a patient, to an extent effective to treat porphyria in a patient.

Abstract: Herein are described 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These identified taxa can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.

Abstract: A method of detecting a target polynucleotide sequence in a given nucleic acid analyte characterised by the steps of: a. annealing the analyte to a single-stranded probe oligonucleotide A0 to create a first intermediate product which is at least partially double-stranded and in which the 3? end of A0 forms a double-stranded complex with the analyte target sequence; b. pyrophosphorolysing the first intermediate product with a pyrophosphorolysing enzyme in the 3?-5? direction from the 3? end of A0 to create partially digested strand A1 and the analyte; c. (i) annealing A1 to a single-stranded trigger oligonucleotide B and extending the A1 strand in the 5?-3? direction against B; or (ii) circularising A1 through ligation of its 3? and 5? ends; or (iii) ligating the 3? end of A1 to the 5? end of a ligation probe oligonucleotide C; in each case to create an oligonucleotide A2; d. priming A2 with at least one single-stranded primer oligonucleotide and creating multiple copies of A2, or a region of A2; and e.

Abstract: Methods of barcoding nucleic acids, such as genomic DNA, are provided herein. In some embodiments, a fragment of genomic DNA may comprise a first and a second barcode.

Abstract: The invention disclosed herein is based on the identification of novel mutations in the JAK2 gene and JAK2 protein. The invention provides compositions and methods useful for diagnosing hematopoietic diseases including, for example, myeloproliferative diseases. The invention also provides compositions and methods useful for determining a prognosis of an individual diagnosed as having a hematopoietic disease.

Abstract: For high spatial resolution imaging a structure marked with luminescence markers, light that has an effect on the emission of luminescence light by the luminescence markers is directed onto a sample with an intensity distribution having a central zero point. Scan areas of the sample are scanned with the zero point. Luminescence light emitted out of a local area including the zero point is registered and assigned to the respective location of the zero point in the sample. Several copies of an object of interest are arranged in the scan areas and subjected to varying surrounding conditions. The individual scan areas are scanned with the respective zero point at least two times at two different stages of reactions to the varying surrounding conditions. Dimensions of the scan areas are limited such that they are not larger than 75% of a distance of intensity maxima delimiting the zero point.

Abstract: A method of analyzing a molecule is disclosed. A lipid bilayer is formed such that it divides a first reservoir characterized by a first reservoir osmolarity from a second reservoir characterized by a second reservoir osmolarity. An electrolyte solution is flowed to the first reservoir that tends to make a first change to a ratio of the first reservoir osmolarity to the second reservoir osmolarity. A voltage is applied across the lipid bilayer, wherein the lipid bilayer is inserted with a nanopore, and wherein a net transfer of ions between the first reservoir and the second reservoir tends to make a second change to the ratio of the first reservoir osmolarity to the second reservoir osmolarity, and wherein the first change to the ratio and the second change to the ratio tends to counter-balance each other.

Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.

Abstract: The invention herein describes a method to purify a target oligonucleotide using hydrophobic interaction chromatography (HIC). The method includes adding a salt to a mixture of the target oligonucleotide and product-related impurities, applying the diluted mixture, at a particular dynamic loading capacity, to the hydrophobic interaction chromatography resin (or hydrophobic adsorbent), washing the hydrophobic adsorbent with an aqueous salt solution, eluting the target oligonucleotide with a eluting solution, and collecting the eluent comprising the target oligonucleotide.

Abstract: The subject invention provides methods, assays, and products for visual detection of small-molecule targets in a sample in both clinical and field settings within minutes. The subject invention is based on an aptamer sensor that reports the presence of small-molecule target via a sensitive colorimetric signal for naked-eye detection. The aptamer sensor is a CBSAzyme-based sensor having both target-mediated cooperative behavior of the CBSA and peroxidase-mimicking catalytic activity of DNAzyme. The subject invention also provides methods of using the CBSAzyme-based sensor.

Abstract: Disclosed are a gene detection device including gold nanoparticles and a gene detection method using gold nanoparticles. The use of the gene detection device and the gene detection method avoids the need for special equipment, such as a thermal cycler, which is essential for 3-stage heating in conventional PCR-based gene amplification techniques. In addition, the gene detection device and the gene detection method enable rapid and sensitive quantitative analysis and multiple detection.

Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR), generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification d

Abstract: System for performing chemical spectroscopy on samples from the scale of nanometers to millimeters or more with a multifunctional platform combining analytical and imaging techniques including dual beam photo-thermal spectroscopy with confocal microscopy, Raman spectroscopy, fluorescence detection, various vacuum analytical techniques and/or mass spectrometry. In embodiments described herein, the light beams of a dual-beam system are used for heating and sensing.

Abstract: A polynucleotide expression system is provided that is capable of alternative splicing of RNA transcripts of a polynucleotide sequence to be expressed in an organism.

Abstract: Provided herein are methods of using photocleavable labels for multiplex and serial antigen detection. The methods comprise detecting the presence of photocleavable labels, which are conjugated through functional linkers to antigen-binding complexes, which in turn non-covalently bind to antigens. The presence of a photocleavable label is indicative of the presence of an antigen specifically or selectively bound by an antigen-binding complex. Also provided are apparatuses for using photocleavable labels for multiplex and serial antigen detection.

Abstract: The purpose of the present invention is to provide double-stranded oligonucleotides comprising the CpG oligonucleotide mentioned below, as a nucleic acid derivative having an immunostimulatory activity. An adjuvant comprising a double-stranded oligonucleotide, wherein a first strand is a CpG oligonucleotide consisting of 8 to 50 nucleotides, a second strand is an oligonucleotide consisting of 8 to 60 nucleotides and comprising a sequence capable of hybridizing with the first strand, and a lipid binds to the second strand through a linker.

Abstract: This invention relates to a diagnostic test measuring circulating SCN5A proteins or gene transcripts in a test sample as a biomarker for pulmonary hypertension.

Abstract: The present invention provides a novel nucleic acid molecule that can be used for detection of a wheat allergen. The wheat allergen-binding nucleic acid according to the present invention is characterized in that it binds to a wheat allergen with a dissociation constant of 20 nM or less, and preferably includes a polynucleotide consisting of either of base sequences of SEQ ID NOs: 1 and 2, for example.

Abstract: A pathogen detection device is provided. The pathogen detection device may include a pathogen detector circuit configured to detect a target analyte in a patient sample, determine the presence of a pathogen from the target analyte, and generate a detection result including the identity of the pathogen and resistance genes (if any); and a decision support generator circuit configured to generate decision support information for the pathogen by application of user configurable rules to the detection result, wherein each of the configurable rules include a logic expression that indicates the corresponding decision support information of the rule to be included in the detection report.

Abstract: Provided are methods for site selective conjugation of an oligonucleotide conjugate to a metal binding protein comprising a metal binding site and for site selective conjugation of a small molecule conjugation compound (SMCoC) to an antibody comprising a metal binding site, metal binding protein conjugates obtainable by said methods, and uses of said metal binding protein conjugates.

Abstract: Provided herein are tissue-specific differential methylated regions (T-DMRs) and cancer-related differential methylated regions (C-DMRs) and methods of use thereof. In one embodiment of the invention, there are provided methods of detecting a cell proliferative disorder by detecting altered methylation in one or more DMRs identified herein. In another embodiment of the invention, there are provided methods of determining clinical outcome by detecting altered methylation in one or more DMRs identified herein.

Abstract: The present invention provides asymmetrical duplex RNA molecules that are capable of effecting sequence-specific gene silencing. The RNA molecule comprises a first strand and a second strand. The first strand is longer than the second strand. The RNA molecule comprises a double-stranded region formed by the first strand and the second strand, and two ends independently selected from the group consisting of 5?-overhang, 3?-overhang, and blunt end. The RNA molecules of the present invention can be used as research tools and/or therapeutics.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: Provided herein are compositions and methods for determining the structure of individual targets using by determining long-range distances within such targets.

Abstract: Provided herein are methods and compositions for synthesizing 5?Capped RNAs wherein the initiating capped oligonucleotide primers have the general form m7Gppp[N2?Ome]n[N]m wherein m7G is N7-methylated guanosine or any guanosine analog, N is any natural, modified or unnatural nucleoside, “n” can be any integer from 0 to 4 and “m” can be an integer from 1 to 9.

Abstract: The invention provides methods and apparatus for carrying out multiple amplification reactions in a single reaction chamber by successive cycles of loading reaction mixture, amplifying, and removing spent reaction mixture in a fluidly closed reaction system. In particular, the present invention allows amplification of a plurality of target polynucleotides from a single sample by carrying out under closed-loop control successive amplifications of different target polynucleotides from different portions of the sample.

Abstract: Translation modulating agents that modulate expression of one or more translation start sites for expanded repeat (e.g., DPR) protein synthesis are provided. Compositions and methods for treating translation start sites for expanded repeat (e.g., DPR) protein synthesis-associated disorders are also provided.

Abstract: Compositions and methods for enhancing delivery of molecules, e.g. biological agents, into cells are described. The composition is a conjugate of the biological agent, preferably a nucleic acid analog having a substantially uncharged backbone, covalently linked to a peptide transporter moiety as described. Conjugation of the peptide transporter to a substantially uncharged nucleic acid analog, such as a morpholino oligomer, is also shown to enhance binding of the oligomer to its target sequence and enhance antisense activity.

Abstract: An integrated neuron circuit structure comprising at least one thin-film resistor, one Metal Insulator Metal capacitor and one Negative Differential Resistance device.

Abstract: The present invention relates to a method for rapidly detecting copies of at least one RNA molecule expressed in individual cells and uses thereof.

Abstract: This disclosure related to methods of detecting mechanical forces required to separate ligand and receptor interactions. In certain embodiments, this disclosure relates to methods of detecting mechanical forces between a ligand and receptor, where the ligand is immobilized on a surface using weaker forces. Ligand-receptor forces lead to dissociation of the ligand that can be detected and amplified. In certain embodiments, the disclosure relates to methods of detecting ligand and receptor interactions comprising linking a ligand to one of two binding partners, wherein the binding partners have attracting forces that are less than the forces between the ligand and a receptor of the ligand such that when the ligand binds the receptor, the binding partners will separate. Separation of the binding partners can be detected.

Abstract: Disclosed are kits and methods for determining the presence or absence of an antibody of interest in a biological sample of a subject. In particular, the methods may detect either pathological or beneficial antibodies. The method may include the step of contacting a biological sample from a subject with a substrate conjugated to an antigen and an Fc receptor operatively linked to a detectable label. Detection of the label may indicate the presence or absence of an antibody of interest.

Abstract: The object is to provide a method that enables detection of unknown virus sequences and efficient detection and search of viruses. The method comprises the step of randomly fragmenting an objective double-stranded (ds) RNA to obtain dsRNA fragments; the step of subjecting the obtained dsRNA fragments to a reverse transcription reaction and then performing polymerase chain reaction (PCR) to obtain corresponding DNA fragments; and the step of subjecting the obtained DNA fragments to a sequence analysis operation to determine the sequences. The reverse transcription reaction is preferably started from the 3? ends of the dsRNA fragments.

Abstract: A method for amplifying a CYP21A2 gene and/or a CYP21A2 gene chimera from a sample is provided. In some embodiments, the method may comprise amplifying a product from a sample comprising human genomic DNA by PCR using a forward primer that is complementary to a sequence that is duplicated in a bimodular human RCCX locus and a reverse primer that is complementary to a sequence that occurs only once in the bimodular human RCCX locus at a position that is downstream of the CYP21A2 gene. Methods for analyzing the amplification product are also provided.

Abstract: A flow cytometry apparatus includes a flow cytometer having a suction or negative-pressure intake probe, a support for a microplate having a plurality of sample wells, and motive elements operatively connected to at least one of the probe and the support for moving the intake probe and the support relative to one another so that the intake probe is sequentially aligned with different sample wells of the microplate. The apparatus has no fluid pumping elements between the support and the flow cytometer so that a bubble-separated sample stream is forced to the flow cytometer solely by virtue of a negative pressure communicated via the intake probe.

Abstract: The present invention discloses a tumor molecular detection/diagnostic reagent, which takes excrement as a detection sample and includes an SDC2 gene methylation detection reagent. The methylation level of the SDC2 gene detected in the excrement has an extremely high relevance to the onset of the colorectal cancer. The sensitivity of the SDC2 gene in the excrement is 87 percent and the specificity is up to 98 percent or even higher than that in tissue.

Abstract: A double-stranded nucleic acid molecule includes a first polynucleotide chain including a base sequence represented by Chemical Formula (1) (SEQ ID NO:1) and a second polynucleotide chain including a base sequence complementary to the first polynucleotide chain. A method for preventing and/or treating a tumor includes a step in which the double-stranded nucleic acid molecule is administered to a test subject.