Abstract: The present invention relates to a composition for forming an electrode, an electrochemical sensor comprising the same, and a method for determining an analyte using the electrochemical sensor.

Abstract: The present disclosure relates to methods and devices for providing accurate measurement of a property of a sample. The method comprises obtaining a plurality of independent measurements of the property. The plurality of values of the property of the sample obtained by the plurality of independent measurements is compared to determine whether one or more of the values is an outlier.

Abstract: Methods, apparatuses, and systems for screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, synthesizing microbial ensembles based thereon, and forming and administering endomicrobial feed supplements are disclosed. Methods for identifying and determining the absolute cell count of microorganism types and strains, along with identifying the network relationships between active microorganisms and environmental parameters, are also disclosed.

Abstract: The present invention relates to a measurement method for complement-dependent bactericidal activity against Streptococcus pneumoniae, and provides a measurement method capable of measuring complement-dependent bactericidal activity against Streptococcus pneumoniae of any capsular serotype. Complement-dependent bactericidal activity against Streptococcus pneumoniae is measured using capsule-deficient Streptococcus pneumoniae, that is, non-encapsulated or substantially non-encapsulated, or transparent Streptococcus pneumoniae. The measurement of the complement-dependent bactericidal activity against Streptococcus pneumoniae of any capsular serotype is enabled.

Abstract: The present invention provides methods for determining the antimicrobial susceptibility of a microorganism in a clinical sample said method comprising removing a test aliquot from a clinical sample culture before the culture reaches 0.5 McFarland units, isolating the microbial cells and transferring the cells into a suitable culture medium for microbial growth, and performing an AST assay using the isolated microbes, wherein the concentration of microbial cells in the microbial cells used to set up the AST assay is measured before the degree of microbial growth in the different growth conditions of the AST assay is measured. Devices for determining the antimicrobial susceptibility of a microorganism in a clinical sample are also provided.

Abstract: Provided is a compound that comprises the structure: where SIG is a signaling molecule and R3 is a formyl, a succinyl, a methyl succinyl, or a myristoyl. Also provided is a kit is provided that comprises the above compound, with instructions for determining the presence of the enzyme. Additionally, a method is provided for determining whether a sample has an enzyme that removes a succinyl, a methyl succinyl, a formyl, or a myristoyl moiety from an ?-amino of a lysine. Also provided is a method of determining whether a molecule inhibits an enzyme that removes a succinyl, a methyl succinyl, a formyl, or a myristoyl moiety from an ?-amino of a lysine.

Abstract: Functionalized chondroitin sulfate, cross-linked polymer matrices comprising functionalized chondroitin sulfate, and methods of making and using the same are provided. Such polymer matrices may be used for tissue engineering, reconstructing cartilage, and the like. Kits are also provided for detection of cartilage degrading enzymes.

Abstract: Described are coelenterazine analogues, methods for making the analogues, kits comprising the analogues, and methods of using the compounds for the detection of luminescence in luciferase-based assays.

Abstract: The present disclosure provides a system and method for depleting target nucleic acids from a nucleic acid sample. In one aspect, a kit according to the present disclosure includes a plurality of DNA probes. Each of the DNA probes is hybridizable to form a heteroduplex with at least one of a plurality of target RNA transcripts in a nucleic acid sample. The number of unique target RNA transcripts hybridized by the plurality of DNA probes is at least three. The kit further includes an enzyme having RNA-DNA hybrid ribonucleotidohydrolase activity, where degrades at least the RNA portion of the heteroduplex.

Abstract: This invention relates to the preparation of nucleic acid samples for analysis. The invention may be particularly useful for single stranded samples. Embodiments of the invention involve the attachment of double stranded or hairpin oligonucleotides using template independent polymerase enzymes in the preparation of nucleic acid sequencing libraries.

Abstract: Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.

Abstract: This disclosure relates to novel compounds for use in various compositions, kits and methods, including, for example, use in polymerase storage buffers and in nucleic acid synthesis or amplification reactions such as a polymerase chain reaction (PCR). Methods for preparing the novel compounds are also described.

Abstract: An improved device and system for facilitating polymerase chain reaction including a light source, detector, waveguide, and filters that occupy minimal space and facilitate reduced sample read time and rapid reading of multiple light wavelengths.

Abstract: The invention relates to a method of determining an infection of a patient with Morganella species potentially resistant to antimicrobial drug treatment, a method of selecting a treatment of a patient suffering from an antibiotic resistant Morganella infection, and a method of determining an antibiotic resistance profile for bacterial microorganisms of Morganella species, as well as computer program products used in these methods. In an exemplary method, a sample 1, is used for molecular testing 2, and then a molecular fingerprint 3 is taken. The result is then compared to a reference library 4, and the result 5 is reported.

Abstract: The invention provides a method for detecting a low-virulence infection in a patient, by distinguishing true infections from false positives. The method comprises testing for the presence or amount of commensal microorganism(s) in a patient sample, and in particular, the commensal microorganism is one that may be causative of a low-virulence infection. Since testing for commensal microorganisms will lead to a large number of false-positives due to frequent sample contamination, the sample is also tested to discriminate true chronic infection from these false positives. In accordance with the invention, false positives are discriminated by evaluating a nucleic acid profile from the sample.

Abstract: Methods for analyzing the bacterial microbiome of a subject and triaging the subject into treatment for head and neck squamous cell cancer from a saliva or tissue sample are provided. The methods also provide means for differentiation of different cancer patient cohorts from the bacterial microbiome of a subject.

Abstract: The present invention discloses methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes. The methods and systems allow for detecting, identifying and quantitating a plurality of biomolecules or microorganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes. Some embodiments provide methods of selecting an oligonucleotide probe specific for a node on a clustering tree. Other embodiments provide methods of selecting organism-specific or OTU-specific oligonucleotide probes for use in accurately detecting a plurality of organisms in a sample with high confidence. Some embodiments provide methods and systems to detect the presence of a rare OTU in a sample.

Abstract: This disclosure describes techniques to improve the accuracy of random access of data stored in polynucleotide sequence data storage systems. Primers used in polynucleotide sequence replication and amplification can be scored against a number of criteria that indicate the fitness of sequences of nucleotides to function as primers. Primers having scores that indicate a particular fitness to function as primers can be added to a specific group of primers. The primers from the group of primers can be used in amplification and replication of polynucleotide sequences that encode digital data. Additionally, an amount of overlap between primer targets and payloads encoding digital data can be determined. Minimizing the amount of overlap between primer targets and payloads can improve the efficiency of polynucleotide replication and amplification. The bits of the digital data can be randomized to minimize the amount of overlap between payloads encoding the digital data and primer targets.

Abstract: This disclosure describes techniques to improve the accuracy of random access of data stored in polynucleotide sequence data storage systems. Primers used in polynucleotide sequence replication and amplification can be scored against a number of criteria that indicate the fitness of sequences of nucleotides to function as primers. Primers having scores that indicate a particular fitness to function as primers can be added to a specific group of primers. The primers from the group of primers can be used in amplification and replication of polynucleotide sequences that encode digital data. Additionally, an amount of overlap between primer targets and payloads encoding digital data can be determined. Minimizing the amount of overlap between primer targets and payloads can improve the efficiency of polynucleotide replication and amplification. The bits of the digital data can be randomized to minimize the amount of overlap between payloads encoding the digital data and primer targets.

Abstract: The present disclosure provides methods and systems for nucleic acid processing. A method for preparing a sequencing set may include providing a template nucleic acid and amplifying the template nucleic acid to provide a complementary nucleic acid. Next, the complementary nucleic acid may be fragmented and barcoded to produce a first set of barcoded fragments comprising a plurality of first barcoded fragments. Next, the plurality of first barcoded fragments may be fragmented to yield a second set of barcoded fragments comprising a plurality of second barcoded fragments.

Abstract: Oligonucleotides for detecting and profiling expression products at transcriptome scale.

Abstract: Provided herein are nucleic acid-based nanoswitches that can detect specific nucleic acids and other analytes types by for example a simple gel electrophoresis readout. Binding of the target to the nanoswitches induces a conformation change from a linear, open conformation to a looped, closed conformation. These nanoswitches may be used in diagnostic assays such as nucleic acid-based diagnostic assays, to detect, measure and/or purify a variety of targets including low abundance targets.

Abstract: This invention provides biochip cartridges and instrument devices for the detection and/or analysis of target analytes from patient samples.

Abstract: Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.

Abstract: Novel methods for making high resolution oligonucleotide paints are provided. Novel, high resolution oligonucleotide paints are also provided.

Abstract: The invention generally relates to methods for distinguishing a rare genetic variation in a nucleic acid sequence.

Abstract: Provided herein are methods for generation and amplification of a single-stranded DNA circle in a single reaction vessel from a linear DNA without any intervening purification steps. The single-stranded DNA circle is generated via a template-independent single-stranded DNA ligation. Whole-genome amplification of linear chromosomal DNA in a single tube using ligation-assisted DNA amplification is also provided.

Abstract: This invention pertains to the creation of a complex pool of adapters that contain complementary barcodes to be utilized in next generation sequencing library prep methods and methods of using barcoded adapters for next generation sequencing.

Abstract: This disclosure provides systems and methods for molecular identification and polymer (e.g., nucleic acid) sequencing using nanopores. The polymer may be passed through or in proximity to the nanopore and various subunits of the polymer may affect the current flowing through the nanopore. The various subunits may be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. In some cases, the polymerization of tagged nucleotides presents tag molecules to the nanopore that can be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. Also provided herein are systems and methods for sequencing both the sense and anti-sense strand of a double stranded nucleic acid molecule with a nanopore and methods for using ribonucleic acid (RNA) speed bump molecules to slow the passage of a nucleic acid molecule through or in proximity to a nanopore.

Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include enhanced performance with large nucleotide analogs, increased stability, increased readlength, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.

Abstract: Methods of loading a molecule of interest into a sample well are provided. In some aspects, methods of loading a molecule of interest into a sample well involve loading a molecule of interest into a sample well in the presence of a crowding agent and/or a condensing agent. In some aspects, methods of loading a sequencing template into a sample well are provided.

Abstract: Apparatus and methods to a DNA sequencing device and related methods that includes a substrate, a nanochannel formed in the substrate, a first electrode, a second electrode arranged opposite the first electrode, a distance between the first and second electrodes defining an electrode gap that is exposed within the nanochannel, and at least one actuator operable to move at least one of the first and second electrodes to adjust a size of the electrode gap.

Abstract: The invention relates to a process for parallel high throughput sequencing of nucleic acid molecules, in particular in the single molecule format.

Abstract: A device for electronic sequencing of polymers consisting of a tunnel gap that is self-aligned with a nanochannel.

Abstract: A method of sequencing a nucleic acid strand includes receiving particles having nucleic acid strands coupled to a polymer matrix, exposing the particles to a solution including a condensing agent, and applying the particles to a surface, the particles depositing on the surface.

Abstract: The invention provides compositions and methods for sequencing nucleic acids and other applications. In sequencing by synthesis, unlabeled reversible terminators are incorporated by a polymerase in each cycle, then labeled after incorporation by binding to the reversible terminator a directly or indirectly labeled antibody or other affinity reagent.

Abstract: A method of conjugating a substrate includes exchanging a counter ion associated with a biomolecule with a lipophilic counter ion to form a biomolecule complex, dispersing the biomolecule complex in a nonaqueous solvent, and coupling the biomolecule complex to a substrate in the presence of the nonaqueous solvent.

Abstract: This document provides methods and materials related to treating a disease. For example, this document provides methods for treating a subject's disease based on identifying the risk of progressive multifocal leukoencephalopathy PML using a genetic test.

Abstract: Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.

Abstract: The present invention relates generally to methods for predicting progression, initiation and susceptibility of osteoarthritis in human subjects using their genotype test results.

Abstract: The present invention relates to methods that are useful for predicting the response of hepatitis B virus (HBV) infected patients to pharmacological treatment.

Abstract: Provided are methods for diagnosing an increased risk of failure in a female pelvic organ prolapse surgery. Also provided are devices and kits for detection of a SNP associated with increased risk of failure in a female pelvic organ prolapse surgery.

Abstract: The disclosure relates to the identification and the use of compounds which regulate the expression of at least one Sestrin gene, for preventing and/or attenuating skin ageing, and/or for hydrating the skin and/or for regulating skin pigmentation. The method includes the following steps: a. bringing at least one test compound in contact with a sample of human keratinocytes or melanocytes; b. measuring the expression of at least one Sestrin gene chosen from SESN3, SESN2 and SESN1 in the keratinocytes or melanocytes; c. selecting the compounds for which an activation of at least 1.6 fold of the expression of at least one of the genes is measured in the keratinocytes treated in a. compared with the untreated keratinocytes, or for which a significant modulation of the expression of at least one of the genes is measured in the melanocytes treated in a. compared with the untreated melanocytes.

Abstract: The present invention relates generally to the field of cancer. In particular, the present invention relates to cancer prognostic and treatment protocols.

Abstract: The present invention provides a method and single-tube assay for identification and quantitative analysis of differentially methylated MLH1 promoter sequences that are associated with certain types of cancer in an individual by obtaining a biological sample comprising DNA from the individual, detecting the presence of and measuring the level of methylated MLH1 promoter sequences, and comparing the presence of and level of methylation in the sample to a normalization reference of “normal” beta-actin gene promoters, wherein a difference in the level or pattern of MLH1 methylation of the sample compared to the Actin gene reference level identifies abnormally methylated MLH1 promoter sequences associated with cancer.

Abstract: The invention relates generally to methods for diagnosis and treatment of follicular lymphoma or diffuse large B cell lymphoma. Specifically, the invention relates to detecting a lysine (K)-specific methyltransferase 2D (KMT2D) alteration to diagnose or treat follicular lymphoma or diffuse large B cell lymphoma.

Abstract: Clinical tests for testing therapeutic sensitivity of cancerous breast tissue and methods and kits for performing the same are described herein. Embodiments of the present invention are directed to methods for predicting the efficacy of treatment of breast cancer. In addition, certain embodiments are directed to a kit for testing therapeutic sensitivity of breast cancer tissue.

Abstract: An miRNA expression signature comprising a set of one or more miRNAs associated with metastatic cancer is provided. In one embodiment, the expression signature is selected from the group consisting of miR-10b, miR-139-5p, miR-130b and miR-199b-5p. In some aspects, miR-199b-5p and miR-130b are overexpressed in metastatic cancer; and miR-10b and miR-139-5p are downregulated in metastatic cancer. Such an expression signature may be used in methods for predicting metastasis, risk for developing metastasis or a prognosis in a cancer. In another embodiment, a method for establishing such a cancer miRNA expression signature is provided.

Abstract: A method of selecting a subject suffering from a cancer for a therapeutic regimen of administration of a pharmaceutical composition comprising an effective amount of an FGFR inhibitor is described, which method comprises (1) the taking of a tumor or liquid biopsy from the subject; (2) determination of the level of expression of any or all of FGFR1, FGFR2 and FGFR3, and (3) comparison of the determined level of expression of at least one of FGFR1, FGFR2 and FGFR3 with a pre-established threshold value, and declaring the subject eligible for the therapeutic regimen if the determined level exceeds the threshold value. The invention also relates to a method of personalized cancer therapy comprising selection of a subject by the above-described method and subjecting the subject to a therapeutic regimen that comprises administration of a pharmaceutical composition comprising an effective amount of an FGFR inhibitor.

Abstract: The present invention provides biomarkers for identifying tumors likely to respond to treatment with Wnt pathway inhibitors. Also provided are methods for identifying tumors and/or patients that are likely to be responsive or non-responsive to treatment with a Wnt pathway inhibitor. Methods for treating a patient with cancer are provided, wherein the cancer is predicted to respond to a Wnt pathway inhibitor.