Abstract: The invention provides methods for isolating RNA from the soluble fraction of urine. The methods can be used for detecting the presence or absence of an RNA, or quantifying the amount of an RNA. The methods are useful for diagnosing an individual suspected of having a disease by detecting the level of RNA associated with the disease in the soluble fraction of urine. The methods are also useful for prognosing an individual diagnosed with a disease by detecting the level of RNA associated with the disease in the soluble fraction of urine.

Abstract: Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.

Abstract: Methods and kits for performing polymerase chain reaction (PCR) and melting analyses to determine copy number variation and/or gene expression are disclosed herein. Related uses of such methods and analyses are also disclosed herein.

Abstract: This document provides methods and materials related to assessing prostate cancer in mammals. For example, this document provides nucleic acids and polypeptides that can be analyzed to determine whether a male mammal having prostate cancer is susceptible to a good or poor outcome.

Abstract: Disclosed are a stabilizer for storage of a biological sample, a composition for storage of a nucleic acid and/or a polypeptide in a biological sample under non-freezing conditions, a kit comprising the composition, a mixture comprising the composition and a biological sample, and a method for storage of a nucleic acid and/or a polypeptide in a biological sample under non-freezing conditions. The integrity and stability of the nucleic acid and/or polypeptide in a biological sample can be stored for a long time under non-freezing conditions by using the stabilizer according to the invention, and therefore the stabilizer has a good application prospect.

Abstract: Oligonucleotide analogs conjugated to carrier peptides are provided. The disclosed compounds are useful for the treatment of various diseases, for example diseases where inhibition of protein expression or correction of aberrant mRNA splice products produces beneficial therapeutic effects.

Abstract: This invention relates to compounds, compositions, and methods useful for reducing Glycolate Oxidase (HAO1) target RNA and protein levels via use of dsRNAs, e.g., Dicer substrate siRNA (DsiRNA) agents.

Abstract: The present invention relates to an in vitro method for detecting methylated DNA comprising (a) coating a container with a polypeptide capable of binding methylated DNA; (b) contacting said polypeptide with a sample comprising methylated and/or unmethylated DNA; and (c) detecting the binding of said polypeptide to methylated DNA. In a preferred embodiment, said method further comprises step (d) analyzing the detected methylated DNA by sequencing. Another aspect of the present invention is a kit for detecting methylated DNA according to the methods of the invention comprising (a) a polypeptide capable of binding methylated DNA; (b) a container which can be coated with said polypeptide; (c) means for coating said container; and (d) means for detecting methylated DNA.

Abstract: The present disclosure relates to compositions and methods for randomly introducing codon-mutations in a target nucleic acid molecule and, more particularly, using wild-type and triplet-randomized oligonucleotides to introduce mutations uniformly across a target nucleotide of interest in a controlled fashion and with a low rate of insertions or deletions.

Abstract: The present invention relates to RNAi constructs and their use in gene silencing. RNAi constructs associated with the invention contain a double stranded region connected to a single stranded region of phosphorothioate modified nucleotides.

Abstract: Among other things, the present disclosure relates to chirally controlled oligonucleotides of select designs, chirally controlled oligonucleotide compositions, and methods of making and using the same. In some embodiments, a provided chirally controlled oligonucleotide composition provides different cleavage patterns of a nucleic acid polymer than a reference oligonucleotide composition. In some embodiments, a provided chirally controlled oligonucleotide composition provides single site cleavage within a complementary sequence of a nucleic acid polymer. In some embodiments, a chirally controlled oligonucleotide composition has any sequence of bases, and/or pattern or base modifications, sugar modifications, backbone modifications and/or stereochemistry, or combination of these elements, described herein.

Abstract: A method is provided herein, the method includes: applying a sample comprising target nucleic acids to a sample application zone of a substrate; and flowing a nucleic acid amplification reaction mixture across a length of the substrate through the sample application zone to amplify the target nucleic acid forming a nucleic acid amplification product; wherein the target nucleic acid having a first molecular weight is substantially immobilized at the sample application zone and wherein the amplification product having a second molecular weight migrates away from the sample application zone. An associated device is also provided.

Abstract: The invention relates to hetero-oligomeric pores derived from Msp. The invention also relates to polynucleotide characterisation using the hetero-oligomeric pores.

Abstract: This invention relates to compounds, compositions, and methods useful for reducing Glycolate Oxidase (HAO1) target RNA and protein levels via use of dsRNAs, e.g., Dicer substrate siRNA (DsiRNA) agents.

Abstract: The present invention, among other things, provides technologies for detecting and/or quantifying nucleic acids in cells, tissues, organs or organisms. In some embodiments, through sequential barcoding, the present invention provides methods for high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci.

Abstract: This invention generally relates to particle-assisted nucleic acid sequencing. In some embodiments, sequencing may be performed in a microfluidic device, which can offer desirable properties, for example, minimal use of reagents, facile scale-up, and/or high throughput. In one embodiment, a target nucleic acid may be exposed to particles having nucleic acid probes. By determining the binding of the particles to the target nucleic acid, the sequence of the target nucleic acid (or at least a portion of the target nucleic acid) can be determined. The target nucleic acid may be encapsulated within a fluidic droplet with the particles having nucleic acid probes, in certain instances. In some cases, the sequence of the target nucleic acid may be determined, based on binding of the particles, using sequencing by hybridization (SBH) algorithms or other known techniques.

Abstract: The present invention lies in the field of molecules known as “small interfering RNA” with therapeutic applications. siRNAs have the ability to reduce gene expression in an extremely specific way (1). These are small sequences of double-strand RNA, normally used in laboratory to modify cell function, which revolutionized cell biology by allowing previously precluded molecular manipulations.

Abstract: Methods and materials are described for human genome prophylaxis and therapy of diseases using myoblast transfer. These methods result in gene transcript changes in multiple pathways. Linking the myoblast transfer technology development from DMD, cardiomyopathy, and Type-II diabetes, the myoblast transfer demonstrably mediates its effect through transfer of the normal myoblast nuclei that supply the complete human genome, in addition to just replenishing the missing gene(s) or the aberrant gene(s). The replacement genes then transcribe to produce the necessary proteins or factors for genetic repair. A variety of uses of this technology are described, including that for disease treatment, disease prevention, drug discovery, and selection of superior cells and clones for therapy.

Abstract: Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. Also provided herein are compositions generated using the blocking oligonucleotide adapters, including circularized polynucleotides, that may be manipulated, for example, through nick translation, to yield a linear mate pair construct.

Abstract: The present invention relates to novel nucleic acid molecules, called aptamers, that bind specifically to a small molecule fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.

Abstract: The invention relates to improving the movement of a target polynucleotide with respect to a transmembrane pore when the movement is controlled by a polynucleotide binding protein. The invention also relates to improved transmembrane pores and polynucleotide binding proteins.

Abstract: Provided are a target region enrichment method based on multiplex PCR, and a reagent, the method comprising: connecting a first linker and a second linker respectively at two ends of a nucleic acid segment containing target regions to be enriched so as to obtain a linker-connected product; performing a PCR amplification on the linker-connected product using a first primer specifically bound to the first linker and a second primer specifically bound to the second linker to obtain an amplified product, the first primer or the second primer having a first affinity label; capturing a single strand having the first affinity label in the amplified product using a solid phase carrier; performing single primer linear amplification using a third primer with the captured single strand as a template; performing exponential amplification using the third primer and the first primer, with the linearly amplified product as the template, to obtain a product containing the target regions.

Abstract: Provided herein are methods of measuring C19MC miRNA amount and/or expression in a post-natal cell and/or tissue. Provided herein are methods of measuring CpG methylation of the upstream C19MC miRNA promoter region in a post-natal cell and/or tissue. Also provided herein are methods of treating a cell, population thereof, and/or a subject in need thereof by administering a C19MC miRNA inhibitor or CRISPR to suppress the expression of specific miRNA within the C19MC or the entire C19MC cluster, population thereof, and/or the subject in need thereof.

Abstract: Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.

Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.

Abstract: The present invention relates to the identification of nucleic acid and amino acid sequences that are characteristic of tumor tissues, in particular tumors of the central nervous system (CNS) such as glioma, in particular glioblastoma and which represent targets for therapy or diagnosis of tumor diseases in a subject.

Abstract: This disclosure describes, in one aspect, a method of amplifying an RNA template. Generally, the method includes synthesizing an oligonucleotide from the RNA template, isolating at least a portion of the oligonucleotide, and subjecting the isolated product to treatment with an RNase and/or glycosylase.

Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

Abstract: Provided are compositions and methods for detecting RNase activity.

Abstract: A system for classifying thyroid nodule tissue as malignant or benign is provided that is based on the identification of sets of gene transcripts, which are characterized in that changes in expression of each gene transcript within a set of gene transcripts can be correlated to with either malignant or benign thyroid nodule disease. The thyroid classification system provides for sets of “thyroid classifying” target sequences and further provides for combinations of polynucleotide probes and primers derived there from. These combinations of polynucleotide probes can be provided in solution or as an array. The combination of probes and the arrays can be used for diagnosis. The invention further provides further methods of classifying thyroid nodule tissue.

Abstract: Methods for typing a strain of an organism are provided, the methods comprising the steps of amplifying, in a single reaction mixture containing nucleic acid from the organism, dividing the reaction mixture into a plurality of sets of second-stage reaction wells, each set of second-stage reaction wells containing a different pair of second-stage primers, subjecting each of the second-stage reaction wells to amplification conditions to generate a plurality of second-stage amplicons, melting the second-stage amplicons to generate a melting curve for each second-stage amplicon, and identifying the strain of the organism from the melting curves.

Abstract: Disclosed are processes that use DNA polymerases to extend primers annealed to templates, wherein a standard nucleotide in the template guiding the extension directs the incorporation of a nonstandard nucleotide analog into the product duplex opposite that standard template nucleotide, and processes wherein a nonstandard nucleotide in the template guiding the extension directs the incorporation of a standard nucleotide analog opposite the nonstandard template nucleotide. Conditions, including the pH of the mixture where the primer extension is done and the composition of triphosphate mixtures where the primary extensions done, are disclosed.

Abstract: In one embodiment, compositions and methods are provided for the detection and/or quantification of epigenetic modifications in DNA. In particular aspects, probes are provided comprising fluorescent metal nanocluster beacons, which can selectively detect nucleic acids including an epigenetic modification.

Abstract: A solid-state imaging element including: a sensor substrate in which a photoelectric conversion section is arranged and formed; a circuit substrate in which a circuit for driving the photoelectric conversion section is formed, the circuit substrate being laminated to the sensor substrate; a sensor side electrode drawn out to a surface of the sensor substrate on a side of the circuit substrate and formed as one of a projection electrode and a depression electrode; and a circuit side electrode drawn out to a surface of the circuit substrate on a side of the sensor substrate, formed as one of the depression electrode and the projection electrode, and joined to the sensor side electrode in a state of the circuit side electrode and the sensor side electrode being fitted together.

Abstract: Some embodiments described herein relate to modified nucleotide and nucleoside molecules with novel 3?-hydroxy protecting groups. Also provided herein are methods to prepare such modified nucleotide and nucleoside molecules and sequencing by synthesis processes using such modified nucleotide and nucleoside molecules.

Abstract: Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca2+. In addition to Li+, the fluid can contain polyethylenimine (PEI) with or without betaine.

Abstract: The invention provides methods for amplifying nucleic acids, particularly methods for reducing density-dependent GC bias and for reducing nucleic acid damage in a bridge amplification of a nucleic acid template. The invention also provides methods for evaluating the effect of reagents and/or additives on nucleic acid damage during bridge amplification of nucleic acid template strands. The methods are suited to solid phase amplification, for example, utilizing flow cells.

Abstract: A moving section that moves in the horizontal plane direction at above a collection container section where collection containers are set is provided with a nozzle holding section for holding a nozzle, and a waste port holding section for holding a waste port. The moving section is capable of moving the nozzle holding section or the waste port holding section. Accordingly, one of a state where the waste port is at a position immediately below the tip of the nozzle and a state where the waste port is not at the position immediately below the tip of the nozzle may be achieved.

Abstract: Methods, systems and computer-readable storage media relate to generating quantitative genomic information. The methods may include processing at least one dataset obtained from a data repository, the at least one dataset including raw genomic data and descriptive data. The descriptive data may include experiment data. The methods may also include determining quantitative information for each group of one or more genes of the at least one dataset based on experiment data and/or at least one coordinate system. The quantitative information may correspond to one or more quantitative measures of one or more biological properties associated with a processed genomic dataset. The quantitative information can provide a normalized value that can be compared across different experiment types and thus can provide biological knowledge and insights.

Abstract: A method for producing silicate-containing magnetic particles having a closed and tight silicate layer and high purity. In addition, the novel method prevents an uncontrolled formation of aggregates and clusters of silicates on the magnetite surface, thereby having a positive influence on the properties and biological applications. The method enables depletion of nanoparticulate solid substance particles on the basis of a fractionated centrifugation. The silicate-coated magnetic particles exhibit optimized magnetization and suspension behavior as well as advantageous run-off behavior from plastic surfaces. These highly pure magnetic particles coated with silicon dioxide are preferably used for isolating nucleic acids from cell and tissue samples, whereby the separating out from a sample matrix ensues by means of magnetic fields.

Abstract: The invention relates to polynucleotide combinations and their use in allele-specific enrichment, amplification, and detection. The disclosure also provides methods to multiplex various target DNA molecules in a single tube with high sensitivity and specificity. The disclosure provides a polynucleotide competitor that comprises a sequence that is fully complementary to a first target DNA polynucleotide region (T1) such that the competitor polynucleotide will hybridize to the first target DNA polynucleotide region under appropriate conditions. In another aspect, the polynucleotide competitor comprises a mismatch to a non-target DNA polynucleotide that is a sequence variant of the first target DNA polynucleotide region (T1*).

Abstract: A method for labeling concentration density differentials of an analyte in a biological sample is provided. The method may including the steps of: binding an enzyme to an analyte contained in a sample, the enzyme capable of acting on at least two chromogens; incubating the sample with a first chromogen for a first time period to generate a first color chromogen-enzyme product, the first color chromogen-enzyme product reflecting light observable as a first color; and incubating the sample with a second chromogen for a second time period to generate a second color chromogen-enzyme product, the second color chromogen-enzyme product reflecting light observable as second color. A combination of the light observable as the first color and the light observable as the second color may be observable as a third color, and each color may describe a different analyte density in the biological sample.

Abstract: Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Abstract: A biochip for detecting or sequencing biomolecules and a method of making the same. The biochip comprises a base member; a dielectric layer being deposited on the base member and having at least two rows of discrete recesses being formed thereon; and two or more electrodes being sandwiched between the base member and the dielectric layer and running under respective row of discrete recesses, the two or more electrodes are separated from each other along length by a portion of the dielectric layer; wherein the dielectric layer defines a continuous operation surface above the electrodes and on which the discrete recesses are deposited for detecting or sequencing of biomolecules, when an electric field is applied through the electrodes, a field gradient is created to draw biomolecule towards a preferred part of the operation surface.

Abstract: Disclosed are methods of using d8 square planar metal complexes containing tridentate ?-conjugated ligands and ancillary ligand of N-heterocyclic carbene or di-phosphine ligand to target mismatched DNA. Targeting of mismatched DNA can be revealed by monitoring the differences in emission enhancement of metal complexes toward mismatched DNA and matched DNA; or the gradually heat release from isothermal titration calorimetry (ITC) when complexes bind toward mismatch DNA; or the significant increase in melting temperature of the mismatched DNA after adding complexes.

Abstract: Methods for amplification and sequencing of at least one nucleic acid comprising the following steps: (1) forming at least one nucleic acid template comprising the nucleic acid(s) to be amplified or sequenced, wherein said nucleic acid(s) contains at the 5? end an oligonucleotide sequence Y and at the 3? end an oligonucleotide sequence Z and, in addition, the nucleic acid(s) carry at the 5? end a means for attaching the nucleic acid(s) to a solid support; (2) mixing said nucleic acid template(s) with one or more colony primers X, which can hybridize to the oligonucleotide sequence Z and carries at the 5? end a means for attaching the colony primers to a solid support, in the presence of a solid support so that the 5? ends of both the nucleic acid template and the colony primers bind to the solid support; (3) performing one or more nucleic acid amplification reactions on the bound template(s), so that nucleic acid colonies are generated and optionally, performing at least one step of sequence determination of

Abstract: Methods and reagents suitable for conducing polymerase chain reaction are described. In particular, the disclosure provides probes and primers that are suitable in dynamic flux amplification procedures. In aspects, the disclosure provides long oligonucleotide probes and primers, as well as triplex forming probes and primers, which function within the narrow Tm ranges used with dynamic flux amplification. However, embodiments are also provided wherein the probes and primers taught herein can be utilized in standard PCR.

Abstract: Described herein are aptamers capable of binding to growth differentiation factor 8 (GDF8) protein; compositions comprising a GDF8 binding aptamer; and methods of making and using the same.

Abstract: The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations.

Abstract: Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample.