Abstract: The present disclosure provides resonator networks adapted to a variety of applications. The networks include fluorophores, quantum dots, dyes, plasmonic nanorods, or other optical resonators maintained in position relative to each other by a backbone (e.g., a backbone composed of DNA). The networks may exhibit optical absorption and re-emission according to specified temporal decay profiles, e.g., to provide temporally-multiplexed labels for imaging or flow cytometry. The networks can include resonators that exhibit a dark state, such that the behavior of the network can be modified by inducing the dark state in one or more resonators. Such networks could be configured as logic gates or other logical elements, e.g., to provide multiplexed detection of analytes by a single network, to permit the temporal decay profile of the network to be adjusted (e.g., to use the networks as a controllable random number generator), or to provide other benefits.

Abstract: The present disclosure provides resonator networks adapted to a variety of applications. The networks include fluorophores, quantum dots, dyes, plasmonic nanorods, or other optical resonators maintained in position relative to each other by a backbone (e.g., a backbone composed of DNA). The networks may exhibit optical absorption and re-emission according to specified temporal decay profiles, e.g., to provide temporally-multiplexed labels for imaging or flow cytometry. The networks can include resonators that exhibit a dark state, such that the behavior of the network can be modified by inducing the dark state in one or more resonators. Such networks could be configured as logic gates or other logical elements, e.g., to provide multiplexed detection of analytes by a single network, to permit the temporal decay profile of the network to be adjusted (e.g., to use the networks as a controllable random number generator), or to provide other benefits.

Abstract: The present invention provides synthetic DNA strands that find use as process controls in DNA processing and nucleic acid testing methods. In particular, provided herein are synthetic methylated DNA strands of known composition for use as control molecules in DNA testing, e.g., of mutations and/or methylation of DNA isolated from non-fish samples, such as human samples.

Abstract: The invention provides a passive fluidics circuit for directing different fluids to a common volume, such as a reaction chamber or flow cell, without intermixing or cross contamination. The direction and rate of flow through junctions, nodes and passages of the fluidics circuit are controlled by the states of upstream valves (e.g. opened or closed), differential fluid pressures at circuit inlets or upstream reservoirs, flow path resistances, and the like. Free diffusion or leakage of fluids from unselected inlets into the common outlet or other inlets at junctions or nodes is prevented by the flow of the selected inlet fluid, a portion of which sweeps by the inlets of unselected fluids and exits the fluidics circuit by waste ports, thereby creating a barrier against undesired intermixing with the outlet flow through leakage or diffusion.

Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.

Abstract: Provided herein are methods of determining one or more modification(s) of the nucleic acid sequence of at least one nucleic acid and at least one epigenetic alteration of the at least one nucleic acid in a sample of a subject. The sample is derived from a body fluid of the subject. The methods link the one or more modification(s) to a specific cell type.

Abstract: Provided herein is the identification of markers associated with THCV, THCVA, CBDV, CBDVA, CBGV, or CBGVA production in Cannabis plants and their use in selecting Cannabis plants having modified THCV, THCVA, CBDV, CBDVA, CBGV, or CBGVA activity. The markers are useful for breeding plants having modified varin activity, including elevated THCV levels, by obtaining nucleic acids, detecting one or more markers that indicate modified varin activity, and establishing plant lines having such characteristics.

Abstract: The present disclosure provides methods and systems for generating and processing optically tagged beads. A nucleic acid probe comprising a fluorescent tag may be hybridized to a bead to generate an optically tagged bead. The nucleic acid probe hybridized to the optically tagged bead may be detectable by one or more signals and may be substantially unreactive to one or more chemical reactions performed with, or in the presence of, the optically tagged bead.

Abstract: Provided herein is a DNA analysis method comprising partitioning a sample into at least a first subsample and a second subsample, wherein the first subsample comprises DNA (e.g., cell-free DNA) with a cytosine modification in a greater proportion; the first subsample undergoes a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the first subsample; and DNA is sequenced to distinguish the first nucleobase from the second nucleobase. Also provided is a combination comprising first and second populations of captured DNA, wherein the first population comprises or was derived from DNA with a cytosine modification in a greater proportion than the second population, and wherein the first population comprises a form of a first nucleobase originally present in the DNA with altered base pairing specificity and a second nucleobase without altered base pairing specificity.

Abstract: Provided herein are DNA-glycan conjugates that include a glycan and a covalently attached polynucleotide. The polynucleotide includes a plurality of modules. Each module includes a nucleotide string, and the plurality of modules includes a monomer module that corresponds to each carbohydrate monomer present in the DNA-glycan conjugate, and a linkage module that corresponds to each glycosidic linkage present between each carbohydrate monomer in the DNA-glycan conjugate. The nucleotide sequence of the plurality of modules corresponds to the glycan structure. Also provided herein are methods for making and using the DNA-glycan conjugates. Further provided is a computer-implemented method for translating data from a nucleotide sequence to a glycan structure, a system for converting data from a glycan structure to a nucleotide sequence, and a system for translating data from a nucleotide sequence to a glycan structure.

Abstract: Compositions and methods of capturing one or more nucleic acid molecules of a cell or subcellular compartment are described. In certain aspects, the compositions comprise a caged molecule comprising one or more photolinkers and an antisense oligonucleotide, which when uncaged hybridizes to a target nucleic acid molecule.

Abstract: The present application relates to methods for determining the proportion or quantity of DNA contributed by individual animals to a volume of milk collected from a plurality of individual animals, wherein the method employs allele sampling for DNA sequence polymorphisms in DNA extracted from a sample of the volume of milk by shallow whole genome sequencing (SWGS). The present methods are useful for example in detecting mastitis or subclinical mastitis in animals contributing milk to the volume of milk.

Abstract: Provided is a nucleic acid sample-contained container including; a first nucleic acid molecule including an intended base sequence and a base sequence for detection different from the intended base sequence; and a second nucleic acid molecule free of the intended base sequence but including the base sequence for detection, wherein the nucleic acid sample-contained container includes the first nucleic acid molecule in a predetermined number. In a preferable mode, the copy number of the intended base sequence is less than 1,000, and the coefficient of variation (CV value) for the copy number is lower than 20%. In a more preferable mode, the nucleic acid molecules are artificially synthesized nucleic acid molecules. In a yet more preferable mode, the first nucleic acid molecule includes the intended base sequence in a plural number in the same molecule.

Abstract: Provided is a method for a two-step multiplex DNA amplification reaction which allows bacterial or fungal DNA analysis without first extracting DNA from the sample, nor without need to enrich microbes by laboratory culture prior to analysis. Without additional DNA purification or analysis, the PCR amplified DNA is administered directly to a microarray designed to interrogate a large panel of meaningful bacteria or fungi as a single multiplex test. Microarray analysis is then performed at ambient temperature, thus enabling substantial simplification of the testing process. It is contemplated that analysis may be conducted on unprocessed and processed leaf wash and similar surface sampling of plant material, cannabis, vegetables, fruit, nuts, spices, grains, other agriculture samples, food samples, or water samples, so as to detect bacterial, yeast, mold or viral, plant or human pathogen contamination.

Abstract: Provided herein are methods, compositions, and kits for the detection of immune cell clonotypes and immune cell analytes within a biological sample.

Abstract: This disclosure provides methods and compositions for removing one or more high abundance species from a plurality of nucleic acid molecules. In some embodiments, the methods and compositions can be used for normalizing nucleic acid libraries. In some embodiments, molecular labels are used in conjunction with the methods and compositions disclosed herein to improve sequencing efficiency.

Abstract: A method of DNA fragmentation is provided. The method comprising incubating a semi-solid biological sample which comprises the DNA with an auxiliary domain-directed nuclease having a binding affinity and selectivity to pre-defined sites in the DNA so as to yield a DNA fragment-of-interest, to thereby fragment the DNA.

Abstract: The present invention relates to a method for predicting clinical outcome for a subject diagnosed with colorectal cancer, skin cancer, head and neck cancer or lung cancer. It also relates to a method for predicting whether a subject has a predisposition to develop such cancers as well as to a method for aiding the staging of such cancers in a subject. The methods of the present invention apply to the biomarkers MYO5B and/or RAB8A and optionally in addition to RAB9A, RAB10, RAB11A, RAB25, CDC42, RAC and/or RhoA.

Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.

Abstract: The present teachings relate to the extraction of nucleic acid from solid materials. Provided are useful compositions, methods, and kits for obtaining nucleic acids from a solid biological sample or an adhesive material having a biological material adherent or embedded within the adhesive substrate. The extracted nucleic acid can be used in downstream applications such as genotyping, detection, quantification, and identification of the source of the biological material.