Abstract: Particular forward and reverse primers may be used to link distant regions of the same large DNA molecule into a smaller DNA molecule. A reverse primer R1 can have a first portion complementary to an ending sequence of region A and can have a second portion having an overlapping sequence. A forward primer F2 can have a first portion complementary to a starting sequence of region B, where the forward primer includes a complementary overlapping sequence (e.g., the same first portion or a second portion) that is complementary to the overlapping sequence. The first portion of F2 may be the entire primer. The smaller DNA molecules can be used to determine haplotypes of regions. Kits including the particular forward and reverse primers are also described.

Abstract: Providing herein, among other things, is a method comprising incubating a double-stranded nucleic acid having a nick with a nick translating activity, a ligase, and a nucleotide mix comprising at least one modified nucleotide, to generate a product comprising a patch of a newly synthesized strand of a duplex nucleic acid containing a plurality of modified nucleoside monophosphates that are at or adjacent to the site of the nick. In some embodiments, the method may be used to map damaged nucleoside monophosphates in a nucleic acid. Compositions and kits for use in performing the method are also provided.

Abstract: The present invention provides a vaccine composition for treating or preventing cancer expressing VASH2, containing a peptide including an amino acid sequence represented by SEQ ID NO: 4.

Abstract: The present disclosure provides methods and materials for determining if antibiotic resistant H. pylori is present in a sample. The methods may comprise obtaining a threshold level of H. pylori DNA from the sample, amplifying a region of the H. pylori DNA to generate multiple copies of the region of the H. pylori DNA, sequencing the multiple copies of the region of the H. pylori DNA, comparing sequences of multiple copies of the region of the H. pylori DNA to a reference sequence, identifying the presence of a mutation in multiple copies of the region of the H. pylori DNA, and determining a number of the multiple copies of the region of the H. pylori DNA with the mutation, wherein antibiotic resistant H. pylori is present in the sample when the number of the multiple copies of the region of the H. pylori DNA with the mutation is above a predetermined amount.

Abstract: Provided is a biological information processing method and a device, a recording medium and a program that are able to predict and control changes in the state of an organism. The expression level of molecules in an organism is measured over a specific time interval; the measured time-series data is divided into a periodic component, an environmental stimulus response component and a baseline component; constant regions of the time-series data are identified from variations in the baseline component or from the amplitude or periodic variations of the periodic component; and causal relation between the identified constant regions is identified. The relation between the external environment and variations in the internal environment is identified and from the identified causal relation between the constant regions, changes in the state of the organism are inferred.

Abstract: Aspects of the invention relate to methods, compositions and algorithms for designing and producing a target nucleic acid. The method can include: (1) providing a plurality of blunt-end double-stranded nucleic acid fragments having a restriction enzyme recognition sequence at both ends thereof; (2) producing via enzymatic digestion a plurality of cohesive-end double-stranded nucleic acid fragments each having two different and non-complementary overhangs; (3) ligating the plurality of cohesive-end double-stranded nucleic acid fragments with a ligase; and (4) forming a linear arrangement of the plurality of cohesive-end double-stranded nucleic acid fragments, wherein the unique arrangement comprises the target nucleic acid.

Abstract: Provided herein are methods, compositions and kits for the generation of bisulfite-converted next generation sequencing (NGS) libraries. The methods, compositions and kits provided herein can be useful, for example, for the production of libraries from genomic DNA that allow for determination of the methylation status across the genome, i.e. the methylome. The methods, compositions and kits provided herein can also be utilized to query methylation status at a particular genomic locus or loci. Moreover, the methods provided herein can be employed for high-throughput sequencing of bisulfite-converted DNA while maintaining the directional (strandedness) information of the original nucleic acid sample.

Abstract: The majority of glioblastomas can be classified into molecular subgroups based on mutations in the TERT promoter (TERTp) and isocitrate dehydrogenase 1 or 2 (IDH). These molecular subgroups utilize distinct genetic mechanisms of telomere maintenance, either TERTp mutation leading to telomerase activation or ATRX-mutation leading to an alternative lengthening of telomeres phenotype (ALT). However, about 20% of glioblastomas lack alterations in TERTp and IDH. These tumors, designated TERTpWT-IDHWT glioblastomas, did not have well-established genetic biomarkers or defined mechanisms of telomere maintenance. The genetic landscape of TERTpWT-IDHWT glioblastoma includes tumors that have chromosomal rearrangements upstream of TERT. These rearrangements define a novel molecular subgroup of glioblastoma, that is a telomerase-positive subgroup driven by TERT-structural rearrangements (IDHWT-TERTSV).

Abstract: The disclosure provides a high-fidelity polymerase with preference for gapped DNA and use thereof. The Klenow fragment (KlenDr) derived from Deinococcus radiodurans DNA polymerase I, which has the high-fidelity polymerization characteristics, is independent of 3?-5? proofreading exonuclease activity, has the preference for binding gapped DNA, and is different from the existing commercial high-fidelity polymerase. Due to the specific affinity of KlenDr to gapped DNA substrate, the 3? end of the forward primer will not be cut off, and the downstream nucleotide chain is rarely replaced.

Abstract: Disclosed herein, inter alia, are silicon containing detectable compounds and methods of use thereof.

Abstract: Methods for improving clinical diagnostic tests are provided, along with associated diagnostic techniques.

Abstract: Method for manufacturing a microarray and verifying the quality of said microarray, wherein the method comprises: —providing at least one reagent, —loading said at least one reagent in a dispensing print head, in a predetermined arrangement, —moving the print head with respect to a substrate and dispensing said at least one reagent on the substrate, during a print pass, to obtain a microarray, —illuminating the substrate using illumination means and obtaining an image of the printed microarray on the substrate, using a camera, —processing the obtained image to verify the quality of the microarray, wherein the step of obtaining an image of the printed microarray comprises: —illuminating the substrate and obtaining an image of the microarray by means of illumination means and a camera which are connected to and move together with the print head with respect to the substrate, the illumination means and the camera being adapted to move behind the print head.

Abstract: A method for mass spectral analysis of molecules based on full mass spectral profile or raw scan mode data, comprising the steps of specifying the basic building blocks for the molecule; estimating initial values including trial numbers of building blocks, charge states, and possible modifications; calculating discrete isotope distributions based on elemental compositions; calculating a profile mode theoretical mass spectrum using a target mass spectrum peak shape function; performing regression analysis between acquired profile mode mass spectrum data and calculated theoretical mass spectrum data and reporting regression statistics; using regression statistics as feedbacks to update initially estimated values including trial numbers of building blocks, charge states, and possible modifications; and repeating selected step to optimize the regression statistics. A mass spectrometer operating in accordance with the method.

Abstract: Disclosed herein are a group of gastric cancer VOC markers in saliva and an application thereof in the preparation of a diagnostic reagent of gastric cancer. The markers are a combination of compounds selected from the group consisting of acetaldehyde, 2-methylbutyraldehyde, isopropanol, hexanal, n-butanol, cineole, nonanal, menthone, 2-ethylhexanol, menthol, anethole and dodecanol. The diagnostic reagent is used for detecting the contents of the marker in a saliva sample of a subject to perform the diagnosis of gastric cancer.

Abstract: The present invention relates to gene expression profiles for B-cell lymphoma. More specifically, the present invention relates to gene expression profiles for diagnosis, prognosis or therapy selection for an aggressive B-cell lymphoma.

Abstract: Disclosed is a method for sequencing a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons, wherein the pool of amplicons is prepared by attaching a unique identifier to the target nucleic acid, and amplifying by PCR the target nucleic acid to which the unique identifier is attached; and sequencing the amplicons comprising the unique identifier and the target nucleic acid. In the method, a nucleotide sequence of the unique identifier comprises both a random nucleotide (N) and a predetermined nucleotide.

Abstract: Methods, kits, and compositions for evaluating the quality of nucleic acids within a biological sample for analysis in a molecular assay are provided.

Abstract: A method for exosome separation and extraction by stacked centrifugal filtration. It is used in molecular biology and clinical examination and comprises an exosome separation and extraction kit consisting of the stacked centrifugal filtration device, an incubation buffer and a protease K. The sample to be tested is incubated at room temperature using the incubation buffer and an appropriate amount of protease K, followed by centrifugation in a centrifuge matching the stacked centrifugal filtration device. After mixing thoroughly, the retained liquid in the ultrafiltration tube is collected to obtain the exosomes. The method needs no large experimental equipments except for a centrifuge, which has a low cost and which is convenient and fast, with short operation time and the possibility of carrying out parallel operations with a large number of samples. The high purity exosomes obtained by the method can meet the demand of large-scale clinical applications.

Abstract: A method utilizes an aluminum oxide support with a water-soluble neutral polymer adsorbed on a surface of the aluminum oxide support and is aimed to collect nucleic acids from a body fluid sample. The method includes a step of adsorbing nucleic acids on the support in the presence of a chaotropic agent and a step of adding a solution containing an anionic surfactant to the nucleic acid-adsorbed support.

Abstract: The invention relates to carrier screening and methods for describing a structural variant, such as a large rearrangement or chromosomal abnormality, in a person's genome using probes that are designed to determine the person's genetic sequence and reveal substitution mutations and small structural variants. Identifying a structural variant may include exposing a nucleic acid to a plurality of probes. Each probe has a linked pair of targeting arms designed to hybridize upstream and downstream of a target in a genome. The method includes hybridizing two of the probes to the nucleic acid and attaching the two probes together to create an inter-probe product as well as detecting the inter-probe product and reporting a structural variant of the genome in the nucleic acid.

Abstract: There is provided a method of identifying risk of cancer in a human subject, the method comprising: determining in a biological sample of the subject, whether a copy number amplification of at least one continuous genomic region specific to human chromosome 1q21 is present, wherein the presence of a copy number amplification of the region specific to human chromosome 1q21 represents an elevated risk of cancer in the subject and the at least one continuous genomic region is selected from the group consisting of: a human TUFT 1 gene or a gene from the human S100 family. It is also provided a method of treating cancer in a subject determined to have a copy number amplification of a region specific to human chromosome 1q21, the method comprising administering a therapeutic agent capable of suppressing IRAK1, IRAK4 or a S100 family member, such as Pacritinib. There are also provided a method of treating cancer, related polynucleotides, kits, therapeutic agents and use of the therapeutic agents.

Abstract: The invention provides compositions and methods related to selective inhibition of PPO11 and use for improving shelf life of a plant or parts thereof. In accordance with the invention, for example, compositions for topical application to a plant or part thereof, are provided that can reduce browning of the plant or part thereof to extend shelf life.

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: An example system includes a primary channel having a first end and a second end, at least two reagent reservoirs coupled to the first end, and a controller. Each reservoir contains a reagent in a fluid solution and is associated with an integrated pump to drive a reagent droplet from the corresponding reagent reservoir into the primary channel towards the second end. The controller is coupled to the integrated pumps and operates according to a sequence to actuate the integrated pumps, the sequence being indicative of reagents in the reagent reservoirs. The actuation of the pumps is to drive the reagent droplets from the reagent reservoirs into the primary channel in accordance with the sequence. The example system also includes a shell material reservoir with a shell material and an associated shell material pump to drive the shell material into the primary channel to encapsulate the reagent droplets.

Abstract: The present invention relates to complexes of oligonucleotide-encoded libraries and methods of tagging and using such libraries. In particular, the oligonucleotides and methods can include complexes having at least one linkage for which a polymerase has reduced ability to read or translocate through.

Abstract: A wavelength converter material and a method of A method of preparing a wavelength converter material may include providing an optionally oxide coated phosphor material, mixing the optionally oxide coated phosphor material with an optionally oxide coated paramagnetic nanoparticle, coating the optionally oxide coated phosphor material and the optionally oxide coated paramagnetic nanoparticle with an oxide coating, thereby preparing a coated phosphor-nanoparticle particle, and separating the coated phosphor-nanoparticle particle, thereby preparing a wavelength converter material. The separating of the coated phosphor-nanoparticle particle may be manipulated by applying a magnetic field. Furthermore, a wavelength converter material, as well as a light emitting diode are described herein.

Abstract: Disclosed is an adaptor for sequencing DNAs at ultratrace levels and its uses. The adaptor contains, from 5?terminus to 3?terminus, a Tag sequence, PolyNs, a first stem sequencing, a first loop sequence, dUTP(s), a second loop sequence, and a second stem sequence, wherein the second stem sequence is complementary to the first stem sequence when read in opposite directions, and the 5?terminus of the adaptor is phosphorylated. The adaptor is designed to form a hairpin structure itself in use and then ligated to a DNA molecule of interest, so that adaptor-adaptor ligation can be effectively avoided, eliminating the inefficient adaptor-DNA ligation problem. Such an adaptor is especially suitable for library construction and sequencing of DNAs at ultratrace levels, laying a good basis for accurate sequencing of ctDNAs.

Abstract: An example method includes identifying training data indicating features of a sample population and clinical outcomes of the sample population. The clinical outcomes are associated with a heterogeneous condition. The method further includes generating decision trees in a Random Forest (RF) based on the training data, each one of the decision trees being configured to divide the sample population into multiple categories based on the features of the sample population. In response to generating the decision trees, a proximity matrix comprising multiple entries is generated using the RF. One of the entries indicates a proportion of the decision trees that categorize a first individual among the sample population and a second individual among the sample population into the same categories among the multiple categories. The method further includes identifying subgroups of the heterogeneous condition by detecting communities of the proximity matrix.

Abstract: Methods and biomarker panels for detecting and treating pancreatic disease, including pancreatic cancer, are provided in association with determining and inhibiting expression levels of certain GPCRs, including GPR68, in particular in pancreatic cancer associated fibroblasts.

Abstract: An object of the present invention is to provide a kit and a method which are capable of measuring a measurement target substance in a biological sample with high precision in a measurement range from a low concentration range to a high concentration range. According to the present invention, there is provided a kit for measuring a measurement target substance in a biological sample, including a labeled particle having a first binding substance capable of binding to a measurement target substance in a biological sample, and a substrate having a second binding substance capable of binding to any one of the measurement target substance or the first binding substance, in which the labeled particle is a luminescent labeled particle containing at least one kind of compound represented by Formula (1) and a particle. Each symbol in Formula (1) has the meaning described in the present specification.

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

Abstract: Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

Abstract: Disclosed are compositions and methods for template-free nucleic acid synthesis.

Abstract: Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.

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: Compositions and methods for generating maize plants that exhibit resistance to northern leaf blight are provided herein. Isolated polynucleotides encoding a polypeptide that confers resistance to northern leaf blight, polynucleotide constructs comprising such, and maize plants comprising the polynucleotide constructs are provided. The methods include expressing an isolated polynucleotide in a maize cell via standard transformation methods and obtaining a maize plant from said maize cell.

Abstract: The disclosure provides various systems and methods for identifying individuals from one or more samples. In particular, improved systems and methods of analysis are provided for handling multiple contributors, as well as systems and methods that model not only individual error rates per locus but factor in amplification of errors induced through PCR cycles. In some embodiments, modeling of error rates can be applied in multi-contributor settings to more accurately establish real alleles from artifacts. Other aspects involve application of sequencing in error modeling. Further, methods are provided for determining the presence of common individual DNA profiles in one or more complex DNA mixtures and for deconvolution of multiple complex DNA mixtures into shared individual components.

Abstract: The present invention relates to methods of detecting novel mutations in a PKD1 and/or PKD2 gene that have been determined to be associated with autosomal dominant polycystic kidney disease (ADPKD) in order to detect or predict the occurrence of ADPKD in an individual.

Abstract: 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 hybridization event in which the primers hybridize to the target, which hybridization 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 so as to form newly synthesized 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 synthesized nucleic acid.

Abstract: Disclosed are compositions and methods for increasing virus production. In particular, disclosed herein are cell or cell line comprises reduced expression of one or more cellular genes selected from the group comprising COQ9, FGF2, NAT9, NDUFA9, NEU2, PLA2G1B, PYCR1, RAD51AP1, STRADA, SVOPL, and/or ZFYVE9 for use in increasing viral production.

Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.

Abstract: Determining relative relationships of people who share a common ancestor within at least a threshold number of generations includes: receiving recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using one or more computer processors, the recombinable DNA sequence information of the plurality of users in parallel; determining, based at least in part on a result of processing the recombinable DNA information of the plurality of users in parallel, a predicted degree of relationship between the first user and a user among the plurality of users, the predicted degree of relative relationship corresponding to a number of generations within which the first user and the second user share a common ancestor.

Abstract: This disclosure provides improved cell lines for manufacture of protein-based pharmaceutical agents, considerably reducing the cost of commercial production. The cell lines are obtained by selecting cells from a mixed population for one or more characteristics that support protein production on a non-specific basis, such as the level of endoplasmic reticulum, Golgi apparatus, and/or other desired phenotypic features, compared with other cells in the starting mixture. Particularly effective producer cell lines can be obtained by preparing the cells for functional selection by making cell hybrids. A gene encoding a therapeutic protein of interest may be transfected into the cells before or after one or more cycles of fusion and selection. Depending on the protein product being expressed, cell lines may be obtained that produce eight grams or more of protein per liter of culture fluid.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: Provided are a nucleic acid sequencing method and a nucleic acid sequencing kit. The kit comprises a nucleic acid probe, a ligase, dNTP having a blocking group attached to a 3? end, a polymerase, a reagent 1 for excising the blocking group attached to the 3? end of the dNTP, and a reagent 2 for excising the remaining nucleotides on the nucleic acid probe that are not bound to a to-be-tested base group.

Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.

Abstract: The present invention relates to substituted benzene compounds. The present invention also relates to pharmaceutical compositions containing these compounds and methods of treating cancer by administering these compounds and pharmaceutical compositions to subjects in need thereof. The present invention also relates to the use of such compounds for research or other non-therapeutic purposes.

Abstract: The present invention relates to a method for detecting C. perfringens induced diseases in animals, the method comprising: a) collecting sample material of a specific animal or of a specific group of animals at consecutive points in time; b) determining the amount of a first marker and a second marker contained in the sample material; and c) determining the ratio of the first marker to the second marker contained in the sample material; wherein the first marker comprises a polynucleotide sequence being specific for the C. perfringens sub-species inducing the targeted disease; and the second marker comprises a polynucleotide being specific for the species C. perfringens; and wherein an increase in the ratio of the first marker to the second marker in the analyzed sample material over time is an indication of the targeted disease.

Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.