Abstract: An object of the invention is to improve the crystallization speed of a PHA copolymer which is to be slowly crystallized, and improve the melt workability and productivity. A microorganism is used which has genes encoding two or more different PHA synthases derived from the genus Aeromonas. The genes encoding the PHA synthases derived from the genus Aeromonas preferably include genes encoding at least two PHA synthases which are capable of synthesizing a copolymer PHA including, as monomer unit species, 3-hydroxybutyric acid and 3-hydroxyhexanoic acid, and which are different in substrate specificity toward 3-hydroxyhexanoic acid from each other. When this microorganism is cultured, a PHA mixture can be produced which includes three or more PHA species different in melting point from each other.

Abstract: Methods are provided for obtaining a genetically modified plant, wherein the plant exhibits an increased oil yield relative to a corresponding control plant that is not so genetically modified. The methods comprise genetically modifying a plant progenitor cell to cause a decrease in triose-phosphate isomerase activity and an increase in glycerol-3-phosphate dehydrogenase activity. The methods also comprise culturing the genetically modified plant progenitor cell to obtain the genetically modified plant. Also provided are methods for increasing oil yield, comprising genetically modifying a plant to cause, in at least one oil-producing organ or tissue of the plant, a decrease in triose-phosphate isomerase activity and an increase in glycerol-3-phosphate dehydrogenase activity. The genetic modification is carried out across more than a single generation. The genetically modified plant exhibits an increased oil yield relative to a corresponding control plant.

Abstract: The present invention relates to methods for the production of oligosaccharides in genetically modified bacterial host cells, as well as to the genetically modified host cells used in the methods. The genetically modified host cell comprises at least one recombinant glycosyltransferase, and at least one nucleic acid sequence coding for a protein enabling the export of the oligosaccharide.

Abstract: Glycoproteins having particular sialylation patterns, and methods of making and using such glycoproteins, are described.

Abstract: The present invention relates to a method for selectively producing ginsenoside F2, compound Mc or compound O, which is originally present in ginseng in a trace amount, from a saponin of ginseng, and more specifically to a method capable of obtaining desired target compounds, that is, ginsenoside F2, compound Mc and compound O, in high yields, by treating saponins, obtained from ginseng, with particular enzymes to structurally convert the saponins.

Abstract: In various embodiments a molecular circuit is disclosed. The circuit comprises a negative electrode, a positive electrode spaced apart from the negative electrode, and an enzyme molecule conductively attached to both the positive and negative electrodes to form a circuit having a conduction pathway through the enzyme. In various examples, the enzyme is a polymerase. The circuit may further comprise molecular arms used to wire the enzyme to the electrodes. In various embodiments, the circuit functions as a sensor, wherein electrical signals, such as changes to voltage, current, impedance, conductance, or resistance in the circuit, are measured as substrates interact with the enzyme.

Abstract: The present invention relates to a novel gene regulating the virulence of Cryptococcus neoformans, and a use thereof. According to the present invention, anti-Cryptococcal or anti-fungal drug candidate materials can be effectively screened for. In addition, the present invention relates to a method for screening for drug candidate materials, which can bring a synergistic effect by being co-administered with a commercially available anti-Cryptococcal drug or anti-fungal drug. Furthermore, provided is a pharmaceutical composition having an anti-Cryptococcal or anti-fungal effect by increasing or decreasing the expression of transcription factors. The present inventors have performed a large-scale virulence test by using insect and animal models so as to identity transcription factors, and have analyzed a complex correlation between the transcription factors and in vivo and in vitro phenotypes of pathogenicity.

Abstract: A method for determining the bacterial charge in a liquid or semi-liquid product, including: preparing a quantity of liquid or semi-liquid product to be analyzed; keeping that quantity of liquid or semi-liquid product at a preset measuring temperature (Tm) and deriving values (?) representing an angle of electrical impedance of the liquid or semi-liquid product at predetermined time instants; deriving an indication of the presence of a bacterial charge in the liquid or semi-liquid product as a function of the time trend of the values (?) representing the angle of the electrical impedance.

Abstract: Disclosed herein are methods determining susceptibility of bacteria in a sample from a subject suspected of having an infection to a plurality of antibiotics simultaneously, wherein the sample is tested without first isolating the bacteria from the sample.

Abstract: The present invention provides a method for identifying a T6SS effector as well as the corresponding T6SS effector immunity protein. The present invention also provides a composition and uses there of that include T6SS effector and T6SS effector immunity protein that are identified using the method of the invention. In particular, the method of the invention utilizes a conserved domain sequence of T6SS of Gram-negative bacteria to identify a T6SS effector and its corresponding immunity protein.

Abstract: The present invention provides methods and kits for performing microbial sensitivity tests. Specifically, the invention relates to methods for identifying the susceptibility, tolerance or resistance of a microorganism to one or more antimicrobial agents, and the level of tolerance. The method comprises exposing the microorganism grown on a plate surface to one or more antimicrobial agents and to at least one growth promoting agent.

Abstract: This invention relates to a capacitor comprising two electrical conductors separated by a dielectric, the dielectric comprising microorganisms. The dielectric may comprise a biological indicator. This invention relates to a process for determining whether the microorganisms are alive or dead. The number of microorganisms can be determined. This invention relates to a process for testing the efficacy of a sterilization process using the capacitor.

Abstract: A blood glucose measurement reagent includes: an enzyme having glucose as a substrate; a mediator; a chromogenic indicator; and an aromatic hydrocarbon having at least one sulfonic acid group. A sensor chip includes: a supply port through which blood is suppliable; a flow path having the supply port formed at one end thereof; and a reagent located in the flow path, the reagent being the blood glucose measurement reagent; wherein the sensor chip is mountable on a blood glucose meter for measuring blood glucose in the blood.

Abstract: The present invention provides inactivated microbes, methods of preparing and using the same, as well as compositions and kits containing the same. The inactivated microbes are useful in the formulation of internal control reagents for use in recombinant nucleic acid techniques, especially nucleic acid amplification, e.g., by the polymerase chain reaction (PCR).

Abstract: A method for extracting substances from a fecal sample using mass spectrometry or nuclear magnetic resonance spectrometry, and metagenomic analysis using a next-generation sequencer.

Abstract: Providing herein, among other things, is a method for preparing a nucleic acid for sequencing. In some embodiments, the method comprises a) amplifying a nucleic acid template using a dNTP mix that contains 5-methyl dCTP, thereby producing product nucleic acid molecules that contains methylcytosines; b) digesting the product nucleic acid molecules with a methylation-dependent restriction endonuclease, thereby cleaving the product nucleic acid molecules at sites that are adjacent to at least some of the methylcytosine and producing fragments of the product nucleic acid molecules; and c) ligating double-stranded adaptors onto the ends of the fragments to produce adaptor-ligated products.

Abstract: Methods of preparing double-stranded nucleic acids with single-stranded overhangs for amplification and sequencing are disclosed. Contacting a blunt-ended double-stranded nucleic acid molecules with Taq results in non-templated directed addition of a single nucleotide to the 3? ends of the nucleic acid with A added most frequently followed by G followed by C and T. G tailing is sufficiently frequent that the efficiency of ligation of nucleic acid molecules to adapters can be significantly increased by including adapters tailed with T and C. The ligation efficiency can be increased even further with blunted-ended adapters to ligate to blunt-ended nucleic acid molecules that failed to undergo tailing.

Abstract: Methods of detecting and amplifying short RNAs are provided.

Abstract: The present disclosure provides improved methods for bead beating and a bead beating system useful therefor. The bead beating system comprises a sample tube, beads, and a dry blocking agent, and methods for using the bead beating system to extract nucleic acids from cells containing the nucleic acids.

Abstract: A novel method for isolating DNA from juices and ciders is described. This method is low cost and yield large quantities of highly purified DNA even though one uses a small quantity of juice or cider. A method for determining if a juice or cider is safe to consume and/or the quality of the juice or cider are also described. For these methods, one can perform qPCR on the DNA which can be obtained using the disclosed method or any other prior art method, and comparing the amount of DNA from microorganisms is present in the juice and/or cider to determine the safety and/or quality of the juice and/or cider. These methods work even if the liquid was pasteurized.

Abstract: Disclosed herein are embodiments of a method for using estrogenic compounds to manipulate the bacterial composition of vaginal communities of female subjects. The method may include titrating a dose of an estrogenic compound to provide a female subject with a personalized effective dose, such as a minimum effective dose, sufficient to attain and/or maintain one or more determined target values of a relative abundance of vaginal Lactobacillus in the vaginal microbiota, an absolute abundance of vaginal Lactobacillus in the vaginal microbiota, a vaginal pH, a vaginal lactic acid concentration, or any combination thereof.

Abstract: The present invention relates to a method of detecting contaminants of microbial origin in a water distribution system and, more particularly, to a method of identifying the microbes contaminating the system, by manipulation of the DNA of the microbes. The microbes are collected, and a portion of the DNA sequence of a particular gene that is found in microbes is amplified. The portion of the DNA sequence that is amplified contains a highly variable region and the identity of the microbe can be determined by that DNA sequence. Each amplified DNA sequences is matched against the known sequences of corresponding regions in the DNA sequences of various microbes. Thus, the spectrum of microbial contaminants, and their relative quantities, can be identified in the liquid collected from different locations of the water distribution system.

Abstract: Based on the structural features of KIR full genomic sequences, the distribution of single nucleotide polymorphisms in their coding regions and the length of flanking intronic sequence of each exon, a method for high-throughput simultaneous sequence-based typing of all the 14 functional killer cell immunoglobulin-like receptor (KIR) genes is disclosed including: developing a scientific and reasonable polymerase chain reaction (PCR) amplification strategy; simultaneously amplifying the complete coding sequence of each functional KIR gene using 3˜5 pairs of KIR gene-specific PCR primers that have similar annealing temperature; and determining the nucleotide sequences of the exons carried by each PCR amplicon in both directions using the forward and reverse sequencing primers, respectively, as shown in FIG. 1.

Abstract: Disclosed are a systemic lupus erythematosus (SLE) biomarker and diagnostic kit thereof. The SLE biomarker is a segment within 1500 bp upstream from a transcription start site of a human IFI44L gene, namely chr1: 79,085,190-79,085,311 (hg19), and a DNA sequence thereof is represented by SEQ ID NO.1. The SLE diagnostic kit in the present invention comprises primers having sequences represented by SEQ ID NO.2 and SEQ ID NO.3, and a probe having a sequence represented by SEQ ID NO.4.

Abstract: The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3? OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.

Abstract: The invention generally relates to assemblies for displacing droplets from a vessel that facilitate the collection and transfer of the droplets while minimizing sample loss. In certain aspects, the assembly includes at least one droplet formation module, in which the module is configured to form droplets surrounded by an immiscible fluid. The assembly also includes at least one chamber including an outlet, in which the chamber is configured to receive droplets and an immiscible fluid, and in which the outlet is configured to receive substantially only droplets. The assembly further includes a channel, configured such that the droplet formation module and the chamber are in fluid communication with each other via the channel. In other aspects, the assembly includes a plurality of hollow members, in which the hollow members are channels and in which the members are configured to interact with a vessel.

Abstract: Methods and systems for array-based methods for genotyping multiallelic markers are disclosed. Also disclosed herein are methods for whole genome amplification and locus specific multiplex PCR for selectively biasing amplification for reducing effects of undesired pseudogenes in resulting data.

Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment after protective adapters are ligated to target polynucleotides to degrade unincorporated adapters prior to amplification and sequencing.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5? and 3? ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.

Abstract: The present disclosure relates to a biomarker for diagnosis of drug addiction and a kit for diagnosis of drug addiction. The biomarker for diagnosis of drug addiction and the kit for diagnosis of drug addiction according to the present disclosure can determine drug addiction by using a molecular biological method. Especially, the present disclosure has investigated molecular biologically how microRNA functions in the human brain due to drug addiction and how the microRNA is transferred to blood or serum by using an exosome as a means of transport. Therefore, the problem that, even though the change in the expression pattern of the microRNA in the brain is validated, it is difficult to apply the change in the expression pattern in the brain for clinical purposes directly and simply, was solved.

Abstract: The disclosure describes the effects of transcription mediated from a promoter on the transcription mediated by divergently coupled supercoiling-sensitive promoter. Transcription initiated from a promoter inhibits transcription mediated by a specific supercoiling-sensitive promoter that is divergently coupled to the promoter. A gyrase inhibitor relieves this inhibition and substantially increases the transcription mediated by the specific supercoiling-sensitive promoter that is divergently coupled to another promoter. Accordingly, the invention pertains to a method for identifying a compound as a gyrase inhibitor or not a gyrase inhibitor based on differential expression of genes under the control of divergently coupled promoters in the presence of the compound. Another embodiment of the invention provides an assay for identifying one or more compounds from a library of compounds as a gyrase inhibitor.

Abstract: The present invention provides a method for genotyping alleles in at least one homologous genetic loci set, comprising: (i) providing a DNA-containing sample that includes said at least one homologous genetic loci set; (ii) performing PCR amplification of regions of said homologous genetic loci set using consensus sequence-specific primers, wherein said consensus sequence-specific primers bind to consensus sequences that are common to a plurality of genes within the genetic loci set, thereby generating a pool of amplification products; (iii) sequencing a plurality of said amplification products in order to determine the relative proportion of each nucleotide at each position in a sequencing read; (iv) performing a sequence alignment between the sequencing read results of (iii) and at least one reference sequence, which reference sequence corresponds to one of the genes in said homologous genetic loci set; and (v) performing genotype calling of the allele or alleles in said sample based on the relative proport

Abstract: Methods for determining a genetic identity of a cell, tissue, organ, or organism, based on type, position, and size of every occurrence of at least one repetitive element in the genome of the cell, tissue, organ, or organism. The methods can include using a computer to generate a graphical representation of the genetic identity of the cell, tissue, organ, or organism, and comparing genetic identity at different times/spaces. Also described herein is a computer implemented Universal Genome Information System, which serves as a genome-RE/TRE information management and analysis platform.

Abstract: The present invention relates to methods, monitors and systems, useful, for example, for advanced detection of sepsis in a subject.

Abstract: The invention relates to the use of a cell-free nucleosome as a biomarker in a fecal sample for the diagnosis or detection of cancer, adenoma, autoimmune disease or inflammatory disease. The invention also relates to methods of detecting said cell free nucleosomes in fecal samples, in particular in methods of diagnosis.

Abstract: Disclosed are compositions, methods and apparatus for diagnosing and/or monitoring a virus-associated systemic inflammation by measurement of a host immune response. The invention can be used for diagnosis including early diagnosis, monitoring, making treatment decisions, or management of subjects suspected of having systemic inflammation associated with an infection. More particularly, the present disclosure relates to peripheral blood RNA and protein biomarkers that are useful for specifically distinguishing between the host systemic immune response to viruses as compared to the host immune response to other causes of systemic inflammation.

Abstract: The present invention relates to methods and kits for the prediction and diagnosis of intrauterine-transmission of viral pathogens, specifically, hCMV in a mammalian subject, by calculating the ability of a subject to prevent transmission of said hCMV based on determining the expression of ISG15, IFIT3 and USP18 genes and optionally of EIF2AK2, HERC5, RSAD2 and MX1 genes in a sample of said subject.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with cardiovascular disorders, particularly acute coronary events such as myocardial infarction and stroke, and genetic polymorphisms that are associated with responsiveness of an individual to treatment of cardiovascular disorders with statin. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: The invention provides a method for identifying or detecting small RNA (sRNA) predictors of a disease or a condition. The method comprises identifying one or more sRNA sequences that are present in one or more samples of an experimental cohort, and which are not present across a comparator cohort; and optionally identifying one or more sRNA sequences that are present in one or more samples of a comparator cohort, and which are not present across an experimental cohort. In contrast to identifying dysregulated non-coding RNAs (such as miRs that are up- or down-regulated), the invention identifies sRNAs that are binary predictors, that is, present in one cohort (e.g., an experimental cohort) and not another (e.g., a comparator cohort). Further, by quantifying reads for individual sequences (e.g., iso-miRs), without consolidating reads to annotated reference sequences, the invention unlocks the diagnostic utility of miRs and other sRNAs.

Abstract: The present disclosure relates to methods and systems for assessing the risk of a human female subject for developing breast cancer. In particular, the present disclosure relates to combining clinical risk assessment and genetic risk assessment to improve risk analysis.

Abstract: The present invention relates to methods of diagnosing bladder cancer in a patient, involving determining the methylation status of Methylation Variable Positions (MVPs) in DNA from the patient and providing a diagnosis based on methylation status data. The invention also relates to methods of treating bladder cancer comprising providing a diagnosis of bladder cancer by the diagnostic methods defined herein followed by administering one or more anti-cancer agents to a patient. The invention also relates to methylation-discriminatory arrays comprising probes directed to the MVPs defined herein and kits comprising the arrays.

Abstract: Provided herein are non-invasive methods and biomarkers that identify progression and clonal evolution of plasma cell dyscrasias. Also provided are materials and methods for the diagnosis, prognosis, staging, and monitoring of plasma cell dyscrasias based on the presence of the bio markers in a blood biopsy, as well as methods for monitoring the progression of a plasma cell dyscrasia, determining the efficacy of a therapeutic agent, determining a targeted therapy related to a plasma cell dyscrasia, and/or treating a plasma cell dyscrasia. The methods provided herein provide several advantages over invasive biopsies.

Abstract: This document provides methods and materials involved in using measles viruses. For example, methods and materials for identifying mammals (e.g., humans) likely to respond to standard measles virus vaccines or standard measles virus-based therapies as well as methods and materials for identifying mammals (e.g., humans) unlikely to respond to standard measles virus vaccines or standard measles virus-based therapies are provided.

Abstract: The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein.

Abstract: The methods described herein allow for the classification of patients into groups for receiving optimized radiation treatment based on patient specific biomarker signature. The biomarker signature includes markers that have been shown to correlate with TGF-B expression and to be associated with tumor aggressiveness, radioresistance and poor prognosis. The markers play a key role in the epithelial-mesenchymal transition. The methods described herein provide the dual benefits of anti-tumor efficacy plus normal tissue protection when combining TGF-B inhibitors with ionizing radiation to treat cancer patients.

Abstract: The present disclosure relates to methods for the diagnosis and evaluation of neoplastic disorders, particularly non-small cell lung cancer. Assays are described in which patient test samples are analyzed for the presence of one or more specific EML4-ALK fusion genes associated with neoplastic disorders.

Abstract: The present invention relates to transcriptional systems and method of uses thereof for identifying and/or assessing cancer cells from biological fluid(s) of cancer patients.