Abstract: FRET-based fusion protein biosensors and methods for their use in measuring an NAD+/NADH ratio change in live cells are provided.

Abstract: The invention relates to methods for capturing a polynucleotide comprising a DNA target segment from a population of polynucleotide molecules. The method may use a mixture comprising the population of the polynucleotide molecules, one or more polynucleotide primers, nucleotides, biotinylated nucleotides, a polymerase enzyme and a buffered liquid medium. The method may denature the polynucleotide molecules in the mixture so as to create single stranded portions of the polynucleotide molecules which can be accessible to the polynucleotide primers; hybridizing the polynucleotide primers to the polynucleotide comprising the DNA target segment. The method may create an extended polynucleotide primer by using the nucleotides, the biotinylated nucleotides and the polymerase enzyme as a means for labeling with biotin and increasing the extent of hybridization of the extended polynucleotide primer to the polynucleotide comprising the DNA target segment.

Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Abstract: The disclosure relates to an adapter dimer-specific probe for detecting adapter dimers in a DNA library, the probe being labelled, particularly by a fluorophore, and being designed to bind specifically to a first adapter nucleotide sequence of a first adapter molecule and to a second adapter nucleotide sequence of a second adapter molecule.

Abstract: A reagent contains complex particles, each including a particle and a complex bound to the particle, and an aqueous liquid in which the complex particles are dispersed. The complex includes a Cas protein and a guide RNA bound to the Cas protein.

Abstract: The present disclosure describes compositions of matter comprising a ribonucleoprotein complex comprising a nucleic acid-guided nuclease and a guide RNA, and further comprising and a blocking nucleic acid molecule represented by Formula IV, wherein Formula IV in the 5?-to-3? direction comprises: T-D-M-A-Lp-C; wherein T is 17-31 nucleotides in length; D is 0-15 nucleotides in length; M is 1-25 nucleotides in length; A is 0-15 nucleotides in length and comprises a sequence complementary to D; and L is 3-25 nucleotides in length; p is 0 or 1; C is 4-15 nucleotides in length and comprises a sequence complementary to T; and wherein the blocking nucleic acid molecule comprises a sequence complementary to a gRNA.

Abstract: In some aspects, the present disclosure relates to methods for reducing the detection of false positive events during analysis of a biological sample. In some aspects, the method comprises use of a decoy oligonucleotide that can hybridize to a probe or to a target nucleic acid. The methods herein have particular applicability in reducing the detection of false positive events and in combining hybridization and ligation reactions into a single step. Also provided are kits comprising probes for use in such methods.

Abstract: The present disclosure relates in some aspects to methods for analyzing antigen receptor transcripts in a biological sample. In some aspects, nucleic acid molecules are generated from V(D)J transcripts in situ in the biological sample to enrich molecules comprising V(D)J joins. In some aspects, the presence, amount, and/or identity of a plurality of V(D)J transcripts are analyzed in situ. Also provided are oligonucleotides, sets of oligonucleotides, compositions, and kits for use in accordance with the methods.

Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a cell.

Abstract: Buffer compositions, such as two-part buffer compositions and buffer systems, methods, assays, kits and kits of parts comprising buffers, for rapid, non-hazardous and fully automated extraction of nucleic acids from various samples. The described buffers do not contain hazardous materials, yet unexpectedly provide more efficient nucleic acid extraction when compared to standard buffers containing harmful ingredients. The present technology provides superior nucleic acid extraction efficiency without the drawbacks associated with standard, hazardous extraction buffers.

Abstract: An object of the present invention is to provide a method for amplifying a nucleic acid using a PCR reaction solution with a volume as large as 30 mL or more, and an apparatus for amplifying a nucleic acid using a PCR reaction solution with a volume as large as 30 mL or more. The present invention provides a method for amplifying a nucleic acid, comprising performing polymerase chain reaction (PCR) by controlling a temperature of one or more reaction container(s) housing a reaction solution containing a DNA polymerase, deoxyribonucleotide triphosphates (dNTPs), a template DNA, a forward primer, a reverse primer, and a buffer solution, wherein the reaction solution is in an amount of 30 mL or more, and the polymerase chain reaction is performed while the reaction solution is stirred.

Abstract: Described herein are standards and methods of normalizing amplicon size bias. These standards may comprise unique molecular identifiers. In some embodiments, the standards and methods are for use with next generation sequencing (NGS) assays. Also described herein are methods for quantifying DNA damage in a sample comprising DNA using fluorescence or for determining the presence of DNA damage in a library.

Abstract: The disclosure provides materials and methods for assessing the presence and level of polyanionic compounds in a sample that inhibit PCR reactions, including assays for the presence, and optionally the amount, of polyvinyl sulfonate, as well as materials and methods for the reduction or removal of such compounds from buffer solutions and from protein solutions using a variety of approaches, including titration-based techniques.

Abstract: Disclosed is a method of performing a non-isothermal nucleic acid amplification reaction, the method comprising the steps of: (a) mixing a target sequence with one or more complementary single stranded primers in conditions which permit a hybridisation event in which the primers hybridise to the target, which hybridisation event, directly or indirectly, leads to the formation of a duplex structure comprising two nicking sites disposed at or near opposite ends of the duplex; and performing an amplification process by; (b) using a nicking enzyme to cause a nick at each of said nicking sites in the strands of the duplex; (c) using a polymerase to extend the nicked strands to as to form newly synthesised nucleic acid, which extension with the polymerase recreates nicking sites; (d) repeating steps (b) and (c) as desired so as to cause the production of multiple copies of the newly synthesised nucleic acid; characterised in that the temperature at which the method is performed is non-isothermal, and subject to shu

Abstract: There is provided a method of preparing a lyophilized sample, comprising: (i) adding a sample comprising one or more molecules of interest in solution to a porous polymer matrix and allowing the sample to penetrate into the pores of the porous polymer matrix; and (ii) lyophilizing the sample within the pores of the porous polymer matrix thereby preparing a porous polymer matrix containing the lyophilized sample.

Abstract: The present invention relates to a loop mediated isothermal amplification (LAMP) method characterized in that the F3 nucleotide sequence and/or said B3 nucleotide sequence comprises one or more locked nucleic acid (LNA) nucleotides which are located within the first third of said F3 nucleotide sequence or said B3 nucleotide sequence, respectively. The present invention further relates to an in vitro method for detecting a nucleic acid sequence amplification product characterized by the use of a metallochromic indicator, preferably 5-Br-PAPS, and metal ions, preferably Zn2+ ions. The present invention further relates to a kit for carrying out the methods of the invention and a use of the kit.

Abstract: Provided herein are compositions and methods for the synthesis, amplification, and in vitro transcription of full-length cDNA, or cDNA fragments. Methods are provided for reverse transcription of RNA and amplification for in vitro transcription. Further provided are method for loading of dendritic cells with the RNA and homologous lysate for immune stimulation.

Abstract: This invention relates to methods and compositions for assessing an amount of total cell-free DNA, such as from a transplant subject. The methods and composition provided herein can be used to determine risk of complications following transplantation, including infection, cardiac arrest, and death, in a subject.

Abstract: The present disclosure generally relates to systems, compositions, kits, and methods for detection of nucleic acids in biological samples. The present disclosure also relates to ultrasensitive direct detection of pathogenic nucleic acids in various biological samples without the need to isolate the nucleic acids from the samples. The present disclosure further relates to detection of airborne or blood borne viruses directly from biological samples.

Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing biological samples involving active stripping of detectably labeled probes from hybridization complexes such as rolling circle amplification products (RCPs). In some embodiments, the present application provides a method wherein double-stranded hybridized complexes are dissociated by DNA helicases. In some embodiments, single-stranded binding proteins facilitate the dissociation and prevent hybridization of the dissociated strands.

Abstract: A method of labelling a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise contacting a sample comprising the nucleic acid of interest with a pool of oligonucleotides, the pool comprising oligonucleotides having at least 5 different lengths; and attaching an oligonucleotide from the pool on to one or each end of the nucleic acid of interest, wherein attachment of an oligonucleotide moves the read start and/or stop coordinate when the labelled NAOI is sequenced.

Abstract: The invention relates to new methods of attaching one or more polynucleotide binding proteins to a target polynucleotide. The invention also related to new methods of characterising target polynucleotides.

Abstract: The present disclosure provides methods and compositions for tracking nucleic acid fragment origin by target-specific barcode tagging when original nucleic acid targets break into small fragments. Nucleic acid targets are captured in vitro on a solid support with clonally localized nucleic acid barcode templates. Many nucleic acid targets can be processed simultaneously in a massively parallel fashion without partition. These nucleic acid target tracking methods can be used for a variety of applications in both whole genome sequencing and targeted sequencing in order to accurately identify genomic variants, haplotype phasing and assembly, for example.

Abstract: The disclosure provides methods and related compositions and kits for mapping DNA-protein interactions (DPIs). In one aspect, the disclosed methods comprise contacting a double stranded DNA molecule with a target protein; coupling a double stranded DNA deaminase (DddA) to the target protein, before or after the contacting step; permitting deamination of one or more cytosine residues in a domain of the double stranded DNA molecule by the DddA to provide one or more uracil residues, wherein the domain comprises a site of interaction between the target protein and the double stranded DNA molecule; determining the sequence of at least a portion of the double stranded DNA molecule; and detecting the domain comprising one or more cytosine deamination events. The method can be controlled by use of DddA inhibitors. The method can also incorporate use of inhibiting a base-excision repair pathway when addressing DPIs in a cellular context.

Abstract: The present disclosure relates in some aspects to methods and compositions for manufacturing molecular arrays using a hybrid approach comprising using non-contact printing (e.g., using inkjet printing, slot die coating, and/or blade coating) and photolithography-guided oligonucleotide hybridization and ligation. In particular, the molecular arrays can be used for determining spatial patterns of abundance and/or expression of a biological target in a sample.

Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.

Abstract: Despite the advance of screening technology, omic-based studies with spatial resolution still requires laborious efforts, hampering the analysis of biology and disease. The present disclosure provides methods, systems, reagents, and platforms to increase the throughput of analyte screening with spatial resolution.

Abstract: A method of assessing the circadian rhythm of a subject and/or assessing and predicting the athletic performance of said subject, including the steps of providing at least three samples of saliva, more preferably four samples of saliva, from the subject, wherein the samples have been taken at different time points over the day and determining gene expression of at least two members of genes for the core-clock network, in particular of at least two members of the group including ARNTL (BMAL1), ARNTL2, CLOCK, PER1, PER2, PER3, NPAS2, CRY1, CRY2, NR1D1, NR1D2, RORA, RORB, RORC, in particular ARNTL (BMAL1) and PER2, in particular of BMAL1 and PER2, in each sample. And the step of assessing and predicting by a computational step based on the expression levels of BMAL1 and PER2 over the day the circadian rhythm of the subject and/or the individual diurnal athletic performance times.

Abstract: The present disclosure relates in some aspects to methods and compositions for in situ analysis using nucleic acid complexes comprising a detectable label and a moiety that can be activated to extinguish signals of the detectable label. In some embodiments, the activatable moiety comprises a photosensitizer. The nucleic acid complexes may allow for improved detection and decreased signal carryover between detection cycles.

Abstract: Methods of determining infection type are disclosed based on the amount of CD177 RNA and the amount of IFI44L RNA in a sample obtained from the subject. Additional RNA markers for determining infection type are also disclosed. Kits capable of determining infection type are also disclosed.

Abstract: The present invention refers to methods of detecting an infection with pathogens causing tuberculosis comprising the steps of a) contacting a first aliquot of a sample of an individual with at least one antigen of a pathogen causing tuberculosis, b) incubating the first aliquot with the at least one antigen for about 15 to about 23 hours, c) adding a cell lysing reagent which is preferably able to stabilize RNA in a temperature range of about 0° C. to about 40° C.

Abstract: Provided are a composition for diagnosing Down syndrome, a kit including the composition, a diagnostic method, and a method of providing information for diagnosing Down syndrome, the composition including an agent for measuring a methylation level of any one gene selected from the group consisting of MXRA8, MIB2, KIF26B, SP5, ZIC4, ENPEP, PITX2, SH3BP2, SEPP1, FLJ32255, SHROOM1, LINC00574, LOC154449, PRRT4, TMEM176B, MNX1, LOC101928483, EGFL7, NACC2, C9orf69, TLX1, FGF8, TACC2, CPXM2, NKX6-2, TLXINB, IQSEC3, PCDH8, F7, SOX9, PNMAL2, THBD, MAPK81P2, KLHDC7B, GPR143, IGHMBP2, MRGPRD, CHODL, NCAM2, CYYR1, GRIK1, OLIG2, CLIC6, SIM2, HLCS, MX2, MX1, TMPRSS2, SLC37A1, PDE9A, CBS, CRYAA, C21orf2, TRPM2, TSPEAR, LINC00162, SSR4P1, SLC19A1, LOC100129027, MCM3AP, YBEY, PRMT2, and ITSN1. Thus, Down syndrome can be diagnosed early with high accuracy, and the disclosure is expected to be applied as key a technology in the field of Down syndrome diagnosis.

Abstract: In one aspect, methods of diagnosing a subject as having Alzheimer's disease and prognosing a subject as being at risk of progressing to Alzheimer's disease are provided. In some embodiments, the method comprises determining one or more of the level of expression of rhotekin 2 (RTKN2), the level of expression of microtubule-associated Ser/Thr kinase 4 (MAST4), the level of binding of forkhead box O1 (FOXO1) to the RTKN2 promoter, and the level of binding of amyloid precursor protein (APP) to the MAST4 promoter in a sample from the subject.

Abstract: Methods and systems for genetic and epigenetic profiling of DNA samples and detecting genetic and epigenetic changes in DNA samples are provided, which involve digestion of DNA with methylation-sensitive restriction enzymes, followed by high-throughput sequencing and analysis of sequence reads. Advantageously, the methods and systems of the present invention are sensitive yet accurate, and enable working with very low amounts of DNA and receive vast amount of information, including methylation data, mutation data and more, based on sequencing data from a single run.

Abstract: The present invention relates to: a method for providing information that enables early diagnosis and prediction of a risk group for Alzheimer's disease by providing an SNP marker that can predict high risk of Alzheimer's disease in Korean people; a composition for predicting the risk of Alzheimer's disease; and a microarray and a kit including the composition.

Abstract: The present disclosure relates generally to methods of diagnosing Benign Paroxysmal Positional Vertigo (BPPV) in a subject. In particular, the present disclosure relates to methods of genotyping a subject in order to determine the presence or absence of a genetic variation or variations indicative of BPPV. In other embodiments, an inhibitor is administered to a subject, wherein the inhibitor prevents aggregation of proteins in neural cells such as the vestibular ganglia. The disclosure further includes methods of identifying an agent that inhibits the aggregation of proteins in neural cells. Methods of monitoring protein aggregation in neural cells are also provided.

Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.

Abstract: The invention relates to the field of clinical molecular diagnostics, in particular to the application of NOTCH family gene variation in predicting the sensitivity of solid tumor patients to immune checkpoint inhibitor therapy and predicting the degree of tumor mutation load of solid tumor patients. This method is helpful to simplify the detection content, reduce the detection cost of patients, speed up the issuance time of detection report, and the detection of gene mutation status is more reliable.

Abstract: Present invention provides methods for determining sensitivity or resistance to treatment with an antineoplastic agent in a subject diagnosed with a neoplastic disease, the method comprising determining in a biological sample obtained from said subject the presence or absence of a genetic or epigenetic alteration leading to reduced or abolished expression or function of FAT1, or determining whether FAT1 expression or function is reduced or abolished in a biological sample obtained from said subject; wherein said antineoplastic agent is selected from the group consisting of an epidermal growth factor receptor (EGFR) inhibitor, a mitogen-activated protein kinase (MEK) inhibitor, a Ca2+/calmodulin-dependent protein kinase (CAMK) inhibitor, and a SRC kinase inhibitor. Present invention further also provides methods of treating a subject diagnosed with a neoplastic disease, comprising determining the sensitivity or resistance of said subject to treatment with an antineoplastic agent.

Abstract: Disclosed herein are methods for identifying patients with pancreatic cancer and subjects at risk for developing pancreatic cancer, methods for monitoring a patient with an identified pancreatic lesion, methods for evaluating the effectiveness of a treatment used for a patient with pancreatic cancer, and methods for selecting a therapy for treating pancreatic cancer in a particular patient. The invention makes use of hydroxymethylation biomarkers, which in combination with one or more clinical parameters and optionally one or more additional types of biomarkers and/or patient-specific risk factors, exhibit a hydroxymethylation level that correlates with pancreatic cancer. Kits and other methods of use are also provided.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Methods are described herein for identifying and/or treating lymphoma patients that have one or more genomic mutations in a coding region of at least one BCL10 allele. Such patients can be resistant to commonly used cancer treatments and can benefit instead from treatment with at least one MALT1 inhibitor.

Abstract: The present disclosure provides a method, a system and a kit for assessing the homologous recombination deficiency (HRD) status of a subject. The present disclosure further provides a method, a system and a kit for identifying a treatment based on the HRD status for the human subject.

Abstract: A method of reporting a diagnoses of cancer in a subject is provided. The method can include obtaining a biological sample from the subject, and measuring a presence or amount of a combination of biomarkers in the biological sample. The combination of biomarkers includes ACSL4, IGSF8, ITGA2, ITGA5, ITGB3, and MYOF, and optionally STX4 and/or optionally FOLR1. The presence of the biomarkers in the sample indicates the presence of cancer cells in the subject, and/or an increased amount of the biomarkers in the sample indicates presence of cancer cells in the subject. The method can include determining whether the presence or amount of the combination of biomarkers indicates the presence of cancer cells in the subject, and then preparing a report on the presence of cancer cells in the subject.

Abstract: Determining whether a particular sample is what it is labeled or sold as is an important concept, particularly to those who buy or sell food products. Particularly for end users, a fast, efficient, accurate way of determining whether a sample is being accurately marketed and sold is necessary. This invention allows a user to rapidly determine if a product is from a certain species or not, based on genetic markers for that product.

Abstract: Disclosed herein are primers and probes related to the detection of Neisseria gonorrhoeae via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of N.gonorrhoeae nucleic acids present in test samples. Specifically the present disclosure describes primers and probes that bind to Cytochrome C or ccpA gene of N.gonorrhoeae for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.

Abstract: Cell-based DNA sensors, compositions comprising the cell-based DNA sensors, and methods of detecting DNA and cells. The cell-based DNA sensors include competent cells that include genetic circuits. Each genetic circuit includes homology arms separated by an interstitial region that comprises at least one element of a reporter switch and/or a kill switch. The compositions include one or more cell-based DNA sensors. The cell-based DNA sensors can be used to detect DNA and cells by the genetic circuits undergoing homologous recombination with target regions of target DNA to activate or deactivate the reporter switch and/or kill switch.

Abstract: Disclosed are methods of identifying a methicillin-resistant Staphylococcus aureus (MRSA) in a sample wherein the methods involve detecting a S. aureus-specific nucleic acid sequence, mecA and mecC, in the sample. Kits for determining the presence of MRSA in a sample are also provided.

Abstract: This disclosure relates generally to the field of taxonomic profiling of microbial organisms such as bacteria, and, more particularly, to system and method for simultaneous interpretation of taxonomic distribution and replication rates of microbes constituting microbial communities. The present disclosure extracts bacterial genomic DNA from a plurality of bacterial organisms comprised in collected microbiome sample. Maps the plurality of the DNA sequence fragment reads to a precomputed reference sequence database of a plurality of all available completely sequenced bacterial genomes. Based on the mapping, the read coverage is measured at the genomic locations of the phylogenetic marker genes, wherein measured read coverage is used for interpretation of taxonomic distribution of the plurality of bacterial organisms. A plurality of slopes is obtained by fitting a linear function.

Abstract: A method of identifying a target microbe in a specimen and including the steps of a) obtaining a specimen, b) lysing the specimen to release a plurality of rRNA molecules from one or more first target microbes in the specimen, c) contacting the specimen with a plurality of first oligonucleotide probe sets configured to selectively bind to rRNA molecules released from the target microbe thereby forming a plurality of first hybridized complexes, each first hybridized complex including one first capture probe and one first detector probe and one of the plurality of rRNA molecules, and d) analyzing the first hybridized complexes to identify a first target microbe in the specimen.