Abstract: The present invention provides a method and means that can specifically detect a target nucleic acid containing a modified nucleobase. Specifically, the present invention provides a method for measuring a target nucleic acid containing a modified nucleobase, the method comprising: (1) incubating a nucleic acid sample and a heterologous nucleic acid probe having a property of pairing with a modified nucleobase, in a solution; and (2) measuring the modified nucleobase using an antibody against a modified nucleobase having a property of heterologous pairing, in the solution obtained at (1). The present invention also provides a kit for measuring a target nucleic acid containing a modified nucleobase, the kit comprising: (I) a heterologous nucleic acid probe having a property of pairing with a modified nucleobase; and (II) an antibody against a modified nucleobase having a property of heterologous pairing.

Abstract: This disclosure is directed, in part, toward preparing and utilizing tunable electrostatic capture (“TEC”) ligands that have an ionizable function. The electrostatic nature of the ionizable functionality of the TEC ligands can be “tuned” or adjusted to either reversibly bind or release a desired target anion, such as a biomolecule, by varying the pH and/or the ionic strength of the binding conditions and release conditions. The TEC ligands can be bound to a solid support to form TEC binding surfaces. TEC surfaces, ligands, solid supports and the accompanying methods and buffer systems can be used to isolate polyanions, such as nucleic acids, from materials, for example in a size-selective manner.

Abstract: Compositions and methods useful in determining the major morphological types of lung cancer are provided. The methods include detecting expression of at least one gene or biomarker in a sample. The expression of the gene or biomarker is indicative of the lung tumor subtype. The compositions include subsets of genes that are monitored for gene expression. The gene expression is capable of distinguishing between normal lung parenchyma and the major morphological types of lung cancer. The gene expression and somatic mutation data are useful in developing a complete classification of lung cancer that is prognostic and predictive for therapeutic response. The methods are suited for analysis of paraffin-embedded tissues. Methods of the invention include means for monitoring gene or biomarker expression including PCR and antibody-based detection. The biomarkers of the invention are genes and/or proteins that are selectively expressed at a high or low level in certain tumor subtypes.

Abstract: A method is provided for generating single-stranded DNA circles from a biological sample. The method comprises the steps of: treating the biological sample with an extractant to release nucleic acids, thereby forming a sample mixture; neutralizing the extractant; denaturing the released nucleic acids to generate single-stranded nucleic acids; and contacting the single-stranded nucleic acids with a ligase that is capable of template-independent, intramolecular ligation of single-stranded DNA to generate the single-stranded DNA circles. All the steps of the method are performed without any intermediate nucleic acid isolation or nucleic acid purification. The single-stranded DNA circles may be amplified and further analyzed. Also provided is a kit which comprises compositions for carrying out the novel methods.

Abstract: Disclosed are devices, systems and methods of use utilizing interfacial effects enabling droplet actuation, inhibition and early sensing of molecular reactions, such as of polymerase chain reaction.

Abstract: A system and method for the processing of nucleic acids containing fluids involving manipulation of magnetically responsive particles contained therein are disclosed. In the system, a holder holds a plurality of containers containing the fluids, a heating device applies thermal energy to the fluids for incubation, and a separating device magnetically separates the particles. The heating and separating devices move into at least one operative position for processing the fluids and at least one inoperative position with respect to the containers, in which the containers are kept stationary at least during and in-between incubating the fluids and manipulating the magnetically responsive particles.

Abstract: A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

Abstract: Methods of cleaving double-stranded DNA that can be recognized and cleaved by a rationally-designed, I-CreI-derived meganuclease are provided. Also provided are recombinant nucleic acids, cells, and organisms containing such recombinant nucleic acids, as well as cells and organisms produced using such meganucleases. Also provided are methods of conducting a custom-designed, I-CreI-derived meganuclease business.

Abstract: Methods of cleaving double-stranded DNA that can be recognized and cleaved by a rationally-designed, I-CreI-derived meganuclease are provided. Also provided are recombinant nucleic acids, cells, and organisms containing such recombinant nucleic acids, as well as cells and organisms produced using such meganucleases. Also provided are methods of conducting a custom-designed, I-CreI-derived meganuclease business.

Abstract: The invention provides methods for determining the susceptibility of cancer patients to developing adverse reactions if treated with a telomerase inhibitor drug by measurement of telomere length in appropriate cells of the patient prior to initiation of the telomerase inhibitor treatment.

Abstract: Provided herein is a method for analyzing genomic DNA. In some embodiments, the method may comprise labeling a genomic sample by adding a capture tag to the ends of the DNA molecules in the sample and labeling molecules that comprise hydroxymethylcytosine with a first fluorophore, immobilizing the labeled DNA molecules on a support, and imaging individual molecules of hydroxymethylated genomic DNA on the support.

Abstract: Methods and compositions for the detection and quantification of nucleic acids are provided. In certain embodiments, methods involve the use of primers or probes that comprise a non-natural nucleotide linked to a reporter. Target nucleic acids are detected by the polymerization of a complementary probe or primer that incorporated a cognate non-natural nucleotide linked to a quencher.

Abstract: A method of analysing for a single stranded nucleic acid present, or potentially present, in a sample comprises a step in which the target nucleic acid (if present in the sample) displaces—and hybridises to—a reporter strand originally present in an interrogating duplex structure comprised of the reporter strand and a displaceable shorter strand. The reporter strand is tagged at or adjacent one end thereof with a reporter moiety capable of providing a detectable signal. The reporter/target duplex structure is such that the reporter strand may be selectively enzymatically digested (e.g. by means of ?-exonuclease) from its end opposite the reporter moiety to release that moiety for direct or indirect detection and regenerate single stranded target, which may then cycle through a plurality of the displacement and digestion steps to result in amplification of signal.

Abstract: Temperature sensitive transcriptional bioswitches and related genetic circuits and in particular bandpass and/or multiplex genetic circuits, vectors, cells, compositions methods and systems are described.

Abstract: Biosensors and methods for localized surface plasmon resonance biosensing are disclosed. The biosensor can include a substrate having a substrate surface to which a plurality of localized surface plasmon resonance (LSPR) antennae are affixed. The LSPR antennae can be affixed via an affixation surface of the LSPR antenna. The LSPR antennae can have a functional surface opposite the affixation surface. Each functional surface can be functionalized by a plurality of single-stranded DNA.

Abstract: The invention provides compositions and methods for determining whether a subject is predisposed to the disease or condition, or for diagnosing a disease or condition, or for detecting the state of a disease or condition, by detecting the methylation state of the subject's nucleic acids. In addition, the invention provides methods for determining the methylation age of a subject or tissue from a subject or for differentiation between nucleic acids originating from different subjects or tissues. The invention further provides methods for selecting nucleic acid molecules for use in the methods of the invention.

Abstract: The invention relates to the amplification of specific target nucleic acids. The invention provides methods, reagents, and kits for carrying out such amplification via the autoligation chain reaction (ACR).

Abstract: A technique for a nanodevice is provided. A reservoir is separated into two parts by a membrane. A nanopore is formed through the membrane, and the nanopore connects the two parts of the reservoir. The nanopore and the two parts of the reservoir are filled with ionic buffer. The membrane includes a graphene layer and insulating layers. The graphene layer is wired to first and second metal pads to form a graphene transistor in which transistor current flowing through the graphene transistor is modulated by charges or dipoles passing through the nanopore.

Abstract: The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.

Abstract: The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample.

Abstract: Described are devices and methods for forming one or more nanomembranes including electroactive nanomembranes within a nanowell or nanotube, or combinations thereof, in a support material. Nanopores/nanochannels can be formed by the electroactive nanomembrane within corresponding nanowells. The electroactive nanomembrane is capable of controllably altering a dimension, a composition, and/or a variety of properties in response to electrical stimuli. Various embodiments also include devices/systems and methods for using the nanomembrane-containing devices for molecular separation, purification, sensing, etc.

Abstract: In one embodiment, the present invention relates to a method for optimizing cell-type specific protein expression. In another embodiment, the present invention relates to a method for creating a tRNA profile of a cell.

Abstract: The disclosure concerns a method for measuring and reporting vascularity in a biological tissue sample. The method generally includes: within a digital image of a tissue section, (i) identifying endothelial cells, lymphatic cells, or a combination thereof; (ii) mapping one or more proximity regions, each of the proximity regions defining an area between detected vessels and a first distance outwardly therefrom; and (iii) calculating one or more of: a vessel proximity score or a hypoxia score, wherein the vessel proximity score relates a composition of objects within the proximity regions, and wherein the hypoxia score relates a composition of tissue within or outside of the proximity regions, respectively.

Abstract: The invention relates to the field of immunology and immunodiagnostics. Provided is a method for determining the replicative history of a lymphocyte, preferably a B cell, the method comprising detecting a signal joint nucleotide sequence on an extrachromosomal circular excision product in the lymphocyte, wherein the excision product is deleted from a chromosome to give a chromosomal-coding joint nucleotide sequence, wherein the coding joint is retained in the chromosome, and detecting the coding joint nucleotide sequence in the lymphocyte. Also provided are primers, probes and a control cell for use in a method of the invention.

Abstract: According to one aspect, systems and processes for assaying a plurality of nucleic acid samples are provided. In an exemplary process, a matrix is generated including pools and samples using a pooling scheme with decoding capability equal to a number D. Matrix organization includes assigning one pool in a set of pools per row by one sample in a set of samples per column. Sample assignment creates a known pattern of pools, wherein each sample in the set of pools is assigned a total number of D+1 times and any two pools have at most one sample in common. Samples are pooled based on a pooling scheme, where pooled samples are assayed. Positive pools are determined and one or more positive samples are identified. The matrix is displayed as a visual pattern representing the known pattern of pools, the identified positive samples, and the determined positive pools.

Abstract: Methods and uses for diagnosing and treating rhabdoid tumors such as Atypical Teratoid Rhabdoid Tumors are provided. In particular, the present disclosure provides methods of identifying and treating subgroups of rhabdoid tumors. In one embodiment, an inhibitor that targets Notch signaling or targets an epigenetic regulator selected from a BET domain protein, G9a or EZH2, is used for treating a subject with a Group 1 type rhabdoid tumor. In another embodiment, an inhibitor that targets BMP or PDGFR? signaling is used for treating a subject with a Group 2 type rhabdoid tumor.

Abstract: The present invention describes methods for determining the risk that a breast precursor lesion will progress to invasive breast cancer and/or the risk of recurrent non-invasive disease in a patient, comprising detecting the presence and/or level of PAPA and/or PAPPA functional activity in a breast tissue sample obtained from the patient, wherein if PAPPA is not present, or is present at a reduced amount compared to a control, the is the risk of progression to invasive cancer and/or the risk or recurrent disease. The present invention also enables the chemosensitisation of mitotically delayed breast cancer cells to anti-proliferative agents, preferably anti-mitotic agents, by restoring normal progression through mitosis. In this embodiment a first drug is applied to release breast cancer cells from the mitotic block and, sequentially, a second drug affecting proliferating cells is administered for cancer cell killing.

Abstract: Provided herein is technology for colorectal neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of colorectal neoplasia in 1) individuals at, older or younger than 50 years of age, or 2) individuals having Lynch Syndrome.

Abstract: The disclosure provides methods of improving the effectiveness of an immunomodulatory cancer therapy by selecting a patient population amenable to immunomodulatory cancer therapy and methods of selecting cancer patient populations amenable to immunomodulatory therapy by measuring T cell repertoire clonality as well as methods of selecting cancer patients at reduced risk of developing an adverse event in response to such therapy. Also provided are methods of screening for adjuvants for immunomodulatory cancer therapy by measuring the frequency or severity of at least one adverse event that develops in response to the therapy.

Abstract: The present invention generally relates to the methods and use of clonal evolution analysis of the kinetics and genetic alterations associated with the development of resistance to a therapy using whole-exome and deep targeted sequencing in treating patients in need thereof.

Abstract: The present invention relates to a method for predicting whether a patient with a cancer is likely to respond to an epidermal growth factor receptor (EGFR) inhibitor, which method comprises determining the expression level of hsa-miR-31-5p (SEQ ID NO:2) miRNA in a sample of said patient. The invention also relates to kits for measuring the expression of hsa-miR-31-5p and at least one other parameter positively or negatively correlated to response to EGFR inhibitors. The invention also relates to therapeutic uses of an EGFR inhibitor in a patient predicted to respond to said EGFR inhibitor.

Abstract: Prognostic and predictive biomarkers are disclosed that can be used in systems and methods for predicting the prognosis of a subject with a cancer and to direct therapy based on that prognosis.

Abstract: The present invention provides methods for accessing the risk of developing breast cancer.

Abstract: A method of investigating the monotypia of a population of T-cells comprising detecting expression of the T cell receptor beta chain constant region TRBC1 and TRBC2, and/or the T cell receptor gamma chain constant region TRGC1 and TRGC, in a population of T-cells.

Abstract: Biomarkers and methods are disclosed that identify patients being treated with a BTK inhibitor that have acquired a mutation that will cause resistance to the BTK inhibitor. Therefore, also disclosed is a method for treating a hematological cancer in the patient that involves detecting an acquired mutation that causes resistance to a BTK inhibitor and then selecting an alternative treatment if resistance is detected.

Abstract: Described herein are polynucleotides associated with prostate and lung cancer. The polynucleotides are miRNAs and miRNA precursors. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of prostate and lung cancer.

Abstract: A method of detecting a predisposition to, or the incidence of, colorectal cancer in a fecal sample comprises, in a first step (a), detecting the presence of blood in the fecal sample, wherein detection of the presence of blood is indicative of a predisposition to, or the incidence of, colorectal cancer. The method additionally comprises, in second step (b), detecting an epigenetic modification in the DNA contained within the fecal sample, wherein detection of the epigenetic modification is indicative of a predisposition to, or the incidence of, colorectal cancer. Based upon a positive result obtained in either (a) or (b) or in both (a) and (b) a predisposition to, or the incidence of, colorectal cancer is detected. Related methods and kits involve detecting an epigenetic modification in a number of specific genes.

Abstract: The invention provides arrays, systems, devices, methods, computer-readable media and kits that enable expression-based classification of B-precursor acute lymphoblastic leukemia (ALL) as being either responsive or non-responsive to tyrosine kinase inhibitor mono or co-therapy.

Abstract: Provided herein are compositions aid methods for barcoding mammalian cells. The compositions and methods provided herein further provide methods for tracing such barcoded cells ex vivo or in vivo during the life time of an organism. In one aspect, a method of forming a barcoded cell is provided. The method includes expressing in a cell a heterologous cleaving protein complex including a sequence-specific DNA-binding domain and a nucleic acid cleaving domain. The sequence-specific DNA-binding domain targets the nucleic acid cleaving domain to a genomic nucleic acid sequence, thereby forming a genomic nucleic acid sequence bound to the heterologous cleaving protein complex.

Abstract: The subject disclosure relates in part to endpoint TaqMan® PCR assays for the detection and high throughput zygosity analysis of the fad-3c gene in canola. The subject disclosure further relates, in part, to the use of wild type DNA as a reference for use in determining zygosity. These and other related procedures can be used to uniquely identify the zygosity and variety of canola lines comprising the subject gene. The subject disclosure also provides related kits for determining zygosity from a sample of a canola plant or seed, for example.

Abstract: Soybean plants, germplasm and seed comprising at least one native locus conferring improved Carlavirus tolerance, molecular markers useful for identifying and, optionally, selecting soybean plants displaying tolerance, improved tolerance, or susceptibility to Carlavirus, and methods of their use are provided. Also provided are isolated polynucleotides, probes, kits, systems, and the like, useful for carrying out the methods described herein.

Abstract: Systems and methods (S/M) to detect stress in stem cells are described. The S/M, including modified stem cells, assays and high throughput screens, can be used to identify compounds or other potential stressors that can negatively affect development potential.

Abstract: A method useful for identifying and isolating live circulating tumor cells is described. The method utilizes an adenoviral vector comprising a replication-competent adenovirus in which the E1 gene region is expressed under the control of a telomerase-specific promoter and further comprises a second expression cassette containing a marker protein, optionally fused to a detectable cell surface marker to permit detection of circulating tumor cells lacking cell surface markers. The method involves combining ex vivo a test sample from a patient suspected of having circulating tumor cells, an adenoviral probe system, and culture media for the cells. The test sample is incubated with the adenoviral system for a sufficient time to permit expression of the reporter protein. The marker gene expression can thereafter be quantitated and the marker-expressing cells may optionally be collected for further analysis.

Abstract: An expression vector, comprising a first reporter nucleic acid sequence operably linked to a first expression control sequence comprising a promoter; and a second reporter nucleic acid sequence operably linked to a second expression control sequence that comprises a response element that is activated or inactivated as one or more of the cells differentiate or dedifferentiate. Methods and kits for imaging and monitoring stem cells comprising the expression vector are also provided.

Abstract: The system described herein for bacterial identification can be used as a point-of-care or lab-based diagnostic system. In some implementations, the system can be used to detect other foreign agents within blood or other samples. The system can include disposable microfluidic cartridges that are removable from the system. The microfluidic cartridges can receive a sample, such as a blood sample, that is suspected of containing bacterial cells and separate the bacterial cells from the blood sample. Once the bacterial cells are separated from the blood, the system can introduce the recombinant detector bacteriophages into the system that can infect the bacterial cells. The system can then detect the expression of reporter genes from the recombinant detector bacteriophages.

Abstract: The present invention relates to a bacterial cell with texturizing property, starter cultures comprising the cell, and diary products fermented with the starter culture.

Abstract: A process to produce an aqueous solution of carbohydrates that contains C6-sugar-containing oligomers, C6 sugar monomers, C5-sugar-containing oligomers, C5 sugar monomers, or any combination thereof is presented. The process includes the steps of reacting biomass or a biomass-derived reactant with a solvent system including a lactone and water, and an acid catalyst. The reaction yields a product mixture containing water-soluble C6-sugar-containing oligomers, C6-sugar monomers, C5-sugar-containing oligomers, C5-sugar monomers, or any combination thereof.

Abstract: Processes for recovering sugars and nicotine from a tobacco biomass include feeding a biomass of tobacco plants and subcritical water to a reactor, hydrolyzing the biomass of tobacco plants with the subcritical water at a temperature between about 150° C. and 305° C. and recovering a liquid product and a solid product from the reactor, wherein the liquid product contains water-soluble sugars and nicotine.

Abstract: Stevia compositions are prepared from Stevia rebaudiana Bertoni extracts. The compositions are able to provide a superior taste profile and can be used as sweeteners, sweetness enhancers, flavors, flavor enhancers in foods, beverages, cosmetics and pharmaceuticals.

Abstract: A method for producing steel in which iron ore is reduced with hydrogen and the resulting intermediate product of reduced iron ore is subjected to further metallurgical processing; the hydrogen is produced through electrolysis of water; the electrical energy required for the electrolysis is regenerative energy from hydroelectric, wind, and/or photovoltaic sources and the hydrogen and/or the intermediate product is produced regardless of demand, whenever enough regeneratively produced electrical energy is available; and unneeded intermediate product is stored until there is demand or it is used so that the regenerative energy that is stored therein is also stored; and using a calculation model to calculate a required discharge rate in a reduction shaft to achieve a desired metallization grade of the steel by tracing batches of the iron ore in the reduction shaft, and using the calculation model to calculate the amount of carbon-containing gas or hydrogen-containing gas to add to the hydrogen for the reduction.