Abstract: Compositions and methods comprising polynucleotides and polypeptides having glyphosate-N-acetyltransferase (GLYAT) activity are provided. In specific embodiments, the sequence has an improved property, such as, but not limited to, an improved specificity for glyphosate when compared to an appropriate control resulting in decreased off target acetylation of, e.g. an amino acid such as aspartate. Further provided are nucleic acid constructs, plants, plant cells, explants, seeds and grain having the GLYAT sequences. Various methods of employing the GLYAT sequences are provided. Such methods include methods for producing a glyphosate tolerant plant, plant cell, explant or seed and methods of controlling weeds in a field containing a crop employing the plants and/or seeds disclosed herein.

Abstract: The present invention pertains to methods, means and uses of nucleic acids and polypeptides for conferring, modifying or improving plant resistance against fungal infections. Particularly, the invention provides nucleic acids and polypeptides for conferring, modifying or improving plant resistance against fungal infections. The invention also provides vectors, cells and plants. Also, the invention provides methods for creating corresponding plant cells and plants, and for identification of agents for conferring, modifying or improving plant resistance against fungal infections.

Abstract: The present invention relates to a method of increasing resistance against fungal pathogens of the order Pucciniales, preferably the family Phacopsoraceae, in plants and/or plant cells. This is achieved by increasing the expression of an RLK1 protein or fragment thereof in a plant, plant part and/or plant cell in comparison to wild type plants, wild type plant parts and/or wild type plant cells. Furthermore, the invention relates to transgenic plants, plant parts, and/or plant cells having an increased resistance against fungal pathogens, in particular, pathogens of the order Pucciniales, preferably the family Phacopsoraceae, and to recombinant expression vectors comprising a sequence that is identical or homologous to a sequence encoding an RLK1 protein.

Abstract: This disclosure concerns nucleic acid molecules and methods of use thereof for control of coleopteran and/or hemipteran pests through RNA interference-mediated inhibition of target coding and transcribed non-coding sequences in coleopteran and/or hemipteran pests. The disclosure also concerns methods for making transgenic plants that express nucleic acid molecules useful for the control of coleopteran and/or hemipteran pests, and the plant cells and plants obtained thereby.

Abstract: Compositions and methods are provided for making rat pluripotent and totipotent cells, including rat embryonic stem (ES) cells. Compositions and methods for improving efficiency or frequency of germline transmission of genetic modifications in rats are provided. Such methods and compositions comprise an in vitro culture comprising a feeder cell layer and a population of rat ES cells or a rat ES cell line, wherein the in vitro culture conditions maintain pluripotency of the ES cell and comprises a media having mouse leukemia inhibitory factor (LIF) or an active variant or fragment thereof. Various methods of establishing such rat ES cell lines are further provided. Methods of selecting genetically modified rat ES cells are also provided, along with various methods to generate a transgenic rat from the genetically modified rat ES cells provided herein. Various kits and articles of manufacture are further provided.

Abstract: The present invention relates to recombinant viral vectors and methods of using the recombinant viral vectors to induce an immune response to influenza A viruses. The invention provides recombinant viral vectors based, for example, on the non-replicating modified vaccinia virus Ankara. When administered according to methods of the invention, the recombinant viral vectors are designed to be cross-protective and induce heterosubtypic immunity to influenza A viruses.

Abstract: The present invention relates to a Sendai virus or recombinant Sendai virus vector. In particular the present invention provides methods, vectors, formulations, compositions, and kits for a modified Enders strain Sendai viral vector. An immunogenic vector can be used in any in vitro or in vivo system. Moreover, some embodiments include vectors for imaging virus growth, location and transmission.

Abstract: The present invention includes the Paramyxovirus Parainfluenza Virus 5 (PIV5) as an oncolytic agent for treating various cancers, including, but not limited to breast cancer, lung cancer and melanoma. PIV5 oncolytic agents include both wild type PIV5 and various recombinant PIV5 constructs. Recombinant PIV5 constructs may include PIV5 lacking the conserved C-terminus of the V protein (PIV5V?C), PIV5 with mutations in the N-terminus of the V/P protein (PIV5CPI?), and PIV5 expressing MDA-7/IL-24 (rPIV5-MDA7), rPIV5-V/P-CPI?, rPIV5-CPI+, rPIV5-Rev, rPIV5-RL, rPIV5-P-S157A, rPIV5-P-S308A, rPIV5-L-A1981D, rPIV5-F-5443P, rPIV5-MDA7, rPIV5?SH-CPI?, or rPIV5?SH-Rev. Also included are methods of making and using such oncolytic agents and compositions including such oncolytic agents.

Abstract: The present invention relates to the field of CAdV vector vaccines, and especially to promoters suitable to express target antigens from such vector vaccines. Disclosed and claimed are recombinant canine adenoviruses, methods of making them, uses for them (including in immunological, immunogenic, vaccine or therapeutic compositions, or, as a vector for cloning, replicating or expressing DNA and methods of using the compositions and vector), expression products from them, and uses for the expression products. Additionally, disclosed and claimed are truncated EHV4 promoters, expression cassettes containing the promoters, and recombinant viruses and plasmids containing the promoters or expression cassettes.

Abstract: Methods of modulating expression of a target nucleic acid in a cell are provided including use of multiple orthogonal Cas9 proteins to simultaneously and independently regulate corresponding genes or simultaneously and independently edit corresponding genes.

Abstract: The invention relates to means and methods for the biomethanation of H2 and CO2. In particular, the invention relates to devices for producing methane by means of methanogenic microorganisms by converting H2 and CO2, wherein the devices comprise at least one reactor, an aqueous medium, which is provided in the at least one reactor, wherein the methanogenic microorganisms are contained in the aqueous medium, a feeding apparatus, which is designed to introduce H2 and CO2 into the at least one reactor, wherein H2 and CO2 form a gaseous mixture therein, and a reaction-increasing device, which is designed to enlarge the contact surface between the aqueous medium having the methanogenic microorganisms and the gaseous mixture. The invention further relates to methods for producing methane in a reactor device by means of methanogenic microorganisms.

Abstract: The present invention relates to a method for preparing bioethanol from lignocellulosic biomass. The method of the present invention is capable of: minimizing the impurity content of an enzymatic saccharification raw material, by extracting biomass using hot water, before pretreatment, and removing extractable substances such as inorganic salts; suppressing, to the greatest extent, the production of overdecomposition products of sugar, by pretreating the biomass, from which the hot water extractable substances have been removed, in a condition for maximizing xylan yield; preparing fermentable sugar at a low cost, without washing a pretreated solid obtained from subsequent solid-liquid separation, but by only concentrating a sugar solution obtained after enzymatic saccharification, using a separation film; and preparing bioethanol therefrom in high yield.

Abstract: There is provided a method of producing aminohexanoic acid and/or aminohexanoic acid ester from synthesis gas, the method comprising: A. contacting the synthesis gas with at least one bacteria capable of carrying out the Wood-Ljungdahl pathway and the ethanol-carboxylate fermentation to produce hexanoic acid; and B. contacting the hexanoic acid with a genetically modified cell to produce aminohexanoic acid and/or aminohexanoic acid ester, wherein the genetically modified cell has an increased activity, in comparison with its wild type, of alkane monooxygenase, alcohol dehydrogenase, and ?-transaminase.

Abstract: The present invention is related to a recombinant microorganism optimized for the fermentative production of methionine and/or its derivatives, wherein in said recombinant strain, the methionine efflux is enhanced by overexpressing the homologous logous genes of ygaZ and ygaH genes from Escherichia coli. It is also related to a method for optimizing the fermentative production of methionine or its derivatives comprising the steps of: a. culturing a recombinant microorganism wherein in said microorganism, the methionine efflux is enhanced by overexpressing the ygaZH homologous genes of ygaZ and ygaH genes from Escherichia coli, in an appropriate culture medium comprising a fermentable source of carbon and a source of sulphur, and b. recovering methionine and/or its derivatives from the culture medium.

Abstract: The present invention relates to application of a novel signal peptide in L-glutamate and its derivatives production from konjac powder, which belongs to the field of gene engineering, enzyme engineering and metabolism engineering. The signal peptide which mediated secretion of ?-mannanase was invented, and the recombinant strain with this signal peptide had advantages on utilizing konjac powder to produce related products, and its utilization efficiency of konjac powder, production efficiency, and yield were higher than other signal peptides. The recombinant strain possessing this new signal peptide had advantages on utilizing cheaper konjac powder as substrate to lower the process costs on L-glutamic acid and its high-value-added products.

Abstract: Described herein is a process for producing saccharides and ethanol from biomass feedstock that includes (a) producing an enzyme composition by culturing a fungal strain(s) in the presence of a lignocellulosic medium, (b) using the enzyme composition to saccharify the biomass feedstock, and (c) fermenting the saccharified biomass feedstock to produce ethanol. The process is scalable and, in certain aspects, is capable of being deployed on farms, thereby allowing local production of saccharides and ethanol and resulting in a reduction of energy and other costs for farm operators. Optional steps to improve the biomass-to-fuel conversion efficiency are also contemplated, as are uses for byproducts of the process described herein.

Abstract: This invention provides improved cell lines for manufacture of protein-based pharmaceutical agents, considerably reducing the cost of commercial production. The cell lines are obtained by fusing cells from one or more parental cell populations. The hybrid cells are then selected 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 hybrids or parental cells in the starting mixture. A gene encoding a therapeutic protein is 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 as much as eight grams or more of protein per liter of culture fluid.

Abstract: The current invention reports a promoter that has the nucleic acid sequence of SEQ ID NO: 02 or SEQ ID NO: 03 which is a human CMV major immediate-early (hCMV-MIE) promoter/enhancer with C to G point mutation at position ?41 and/or ?179 relative to the transcription start site. This new promoter is especially useful for the production of polypeptides at large scale as it shows reduced promoter silencing and improved polypeptide production.

Abstract: The invention provides means and methods for producing one or more Ig-like molecules in a single host cell. Novel CH3 mutations enabling the production of monospecific and/or bispecific Ig-like molecules of interest are also provided.

Abstract: A method of determining the presence of Pseudomonas involves establishing a gaseous headspace over a surface suspected of containing at least one Pseudomonas strain and contacting at least a portion of the gaseous headspace with a capillary microextraction of volatiles (CMV) sampling device to absorb at least one component of the headspace by the CMV sampling device. The component loaded CMV sampling device is coupled to an injection port of an analytical device where the components are desorbed into the analytical device, where components are separated, detected, and identified to determine if one or more of the identified components is a biomarker for at least one Pseudomonas strain.

Abstract: Methods and kits for preparing nucleic acid fragments from a sample of purified nucleic acid are provided. Alternatively, chromatin or other long polymers can be sheared with similar methods and kits.

Abstract: A molecular sensor that utilizes dichroism can be used to identify the presence of a target nucleic acid molecule in a sample, for example during or after amplification reactions such as PCR/thermocyling reactions and isothermal reactions. A sensor element for use in the molecular sensor may comprise an alignable scaffold/receptor complex, the receptor of said complex comprising a nucleic acid sequence which is complementary to at least a portion of a target nucleic acid molecule.

Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.

Abstract: This invention relates to compositions, methods and kits for detecting the presence or absence of a bacterial species in a biological sample using isothermal nucleic acid amplification.

Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes. Further, the improved processivity of the disclosed methods may allow amplification of DNA up to hundres of megabases in length.

Abstract: This disclosure describes related novel methods for Recombinase-Polymerase Amplification (RPA) of a target DNA that exploit the properties of recombinase and related proteins, to invade double-stranded DNA with single stranded homologous DNA permitting sequence specific priming of DNA polymerase reactions. The disclosed methods have the advantage of not requiring thermocycling or thermophilic enzymes, thus offering easy and affordable implementation and portability relative to other amplification methods. Further disclosed are conditions to enable real-time monitoring of RPA reactions, methods to regulate RPA reactions using light and otherwise, methods to determine the nature of amplified species without a need for gel electrophoresis, methods to improve and optimize signal to noise ratios in RPA reactions, methods to optimize oligonucleotide primer function, methods to control carry-over contamination, and methods to employ sequence-specific third ‘specificity’ probes.

Abstract: A kit for detecting live cells of a microorganism in a test sample by distinguishing the live cells from dead cells or injured cells by a nucleic acid amplification method includes the following components: 1) an agent capable of covalently binding to DNA or RNA of the microorganism by irradiation with light having a wavelength of 350 nm to 700 nm; 2) an agent for suppressing a nucleic acid amplification inhibitory substance; and 3) a primer or primers for amplifying a target region of the DNA or RNA of the microorganism to be detected by a nucleic acid amplification method. The agent for suppressing a nucleic acid amplification inhibitory substance is one or more selected from albumin, dextran, T4 gene 32 protein, acetamide, betaine, dimethyl sulfoxide, formamide, glycerol, polyethylene glycol, soybean trypsin inhibitor, ?2-macroglobulin, tetramethylammonium chloride, lysozyme, phosphorylase and lactate dehydrogenase.

Abstract: A method for detecting a low-occurrence mutation in isolated DNA adds a blocking probe to reagents during amplification of the isolated DNA. The blocking probe is an oligonucleotide complementary to wild-type DNA corresponding to the sample. The blocking probe spans a site of a suspected mutation within a region of interest in the isolated DNA. After amplification, fragments of the amplified DNA is sequenced using next generating sequencing and an output is generated to display the sequenced fragments. In some embodiments, the blocking probe is locked nucleic acid (LNA).

Abstract: Disclosed herein are methods and kits for selectively amplifying, detecting or quantifying a DNA fragment with a specific end sequence, especially generated following restriction enzyme digestion. This method can be used, for example, to detect a hypomethylated DNA fragment. This methods and kits are especially useful in detecting or quantifying a hypomethylated fetal DNA fragment in a maternal plasma sample containing a corresponding hypermethylated maternal DNA fragment.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Abstract: A method for characterizing at least a portion of the biodiversity of a sample. The method includes the steps of: (i) obtaining a sample having nucleic acid from a plurality of different organisms; (ii) extracting at least a portion of the nucleic acid from the sample; (iii) optionally performing a whole-genome amplification of the extracted nucleic acid; (iv) optionally performing a second, targeted amplification; (v) sequencing the amplified nucleic acid to obtain sequence data comprising a nucleic acid sequence for at least some of the plurality of different organisms; (vi) querying, using the obtained sequence data, a sequence database, where querying the sequence database identifies one or more of the plurality of different organisms; and (vii) determining, using the identified one or more of the plurality of different organisms, a characteristic of the sample.

Abstract: A paired-end sequencing method for sequencing a string of oligonucleotides is disclosed. The method includes preparing a template that includes a substrate with a plurality of wells. Each well includes a pair of strands, formed of a forward strand and a corresponding reverse strand, from the string of oligonucleotides. Each pair of strands are sequenced simultaneously to obtain a reads pairs set, where each reads pair includes a read and a corresponding read-pair. The reads pairs set is processed by generating a sequences pairs set, where each sequences pair has a read sequence and a read-pair sequence respective to a pair of reads of the set of pairs of reads, mapping the sequences pairs set along a reference genome, and re-sequencing the mapped sequences pairs set to obtain the sequence of the string of oligonucleotides.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.

Abstract: The invention provides a novel additive for improved analysis by mass spectrometry. More specifically, ascorbic acid has been found to reduce or eliminate the presence of adducts commonly present in mass spectra. The improved processes and compositions of the invention allow for increased accuracy, sensitivity and throughput for samples analyzed by mass spectrometry.

Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.

Abstract: This disclosure describes, in one aspect, methods for DNA sequencing and performing epigenomic analyses. Generally, the methods include immobilizing a plurality of copies of a DNA molecule on a surface, stretching at least a portion of the immobilized DNA molecules, and sequencing at least a portion of the immobilized, stretched DNA molecules.

Abstract: A method for nucleic acid sequencing, comprising: exposing a plurality of clusters of a plurality of template polynucleotide strands to a series of flows of a plurality of nucleotide or oligonucleotide solutions, wherein the nucleotide solutions or oligonucleotide solutions are flowed in an order of flow which is not a continuous repeat of an ordering of a single flow of each of the nucleotide solutions or oligonucleotide solutions; and obtaining a fluorescence signal indicative of which, if any, nucleotide species or oligonucleotide species incorporated to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands. This method enables dephased amplicons to return in-phase.

Abstract: The present disclosure relates to a primer set for preparation of a library used for next generation sequencing (NGS), and a method and a kit for making an NGS library using the same. The method for making the next generation sequencing (NGS) library using the primer set according to the present disclosure is able to simply analyze large amounts of samples as compared to the existing method for making a library, which is effectively usable for analysis of target DNA sequences or for database construction, in large amounts of samples.

Abstract: The invention generally features compositions and methods for modulating an immune response. In particular embodiments, such compositions and methods modulate regulatory T cell suppressive activity.

Abstract: Disclosed herein are biomarkers of platelet function and methods for assessing platelet function in response to anti-platelet therapy and for determining a prognosis, diagnosis, or risk identification in a patient by detecting at least one biomarker of platelet function in the patient as well as determining amounts thereof. The biomarkers may be used to identify a patient as a candidate for treatment with an antiplatelet agent and to monitor and adjust antiplatelet therapy in a patient.

Abstract: This document provides methods and materials for detecting genetic and/or epigenetic elements. For example, methods and materials for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, methods and materials for detecting the amount of target nucleic acid containing a genetic or epigenetic element within a sample, kits for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, kits for detecting the amount of target nucleic acid containing a genetic or epigenetic element present within a sample, and methods for making such kits are provided.

Abstract: The present invention relates, in part, to methods and kits for treating cardiovascular disease.

Abstract: The present invention provides methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples, and in particular in the lymph nodes. The invention further relates to DNA methylation as a predictor of disease recurrence and patient prognosis, specifically in the field of cancer biology.

Abstract: Compositions and methods for detecting bladder cancer are provided. In some embodiments, methods of detecting low grade bladder cancer are provided. In some embodiments, methods of monitoring recurrence of bladder cancer are provided. In some embodiments, the methods comprise detecting androgen receptor (AR) and/or uroplakin 1B (UPK1B).

Abstract: The disclosed embodiments include methods to form STC and STMC for use in determining presence of cancer, and methods to detect presence of cancer. In one embodiment, A portion of a STC is stained. The STC includes normal cells and cancer cells of a type of cancer co-cultured based on at least one cell culturing factors. The at least one co-culture factors includes a type of the cancer cells being cultured, a ratio of the cancer cells to the normal cells being co-cultured, seeding density of the normal cells and the cancer cells being co-cultured, a type of cell growth supplement used to facilitate culturing the cells, and a concentration of the cell growth supplement used to facilitate co-culturing the cells. The stained portion is observed to determine presence of one or more biomarker types that indicate presence of cancer.

Abstract: Methods and compositions for the identification of breast cancer grade signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages and/or grades of breast cancer.

Abstract: The present invention relates to methods, devices, combinations, kits, and systems for predicting and treating clinically significant prostate cancer in a urine sample of an individual suspected of suffering from prostate cancer based on expression analysis of normalized prostate tumor markers. The present methods, devices, combinations, kits, and systems are especially suitable for predicting and treating prostate cancer with a Gleason score of seven or more in individuals with a serum prostate-specific antigen (sPSA) level lower than 15 ng/ml.

Abstract: The present invention features a method for determining the prognosis for survival of a cancer patient. Methods for measuring the level of NOL3 expression in a cancer cell-containing sample from a patient, and comparing the level of NOL3 expression in the sample to a reference level of NOL3 expression are also included. A higher level of NOL3 relative to the reference level correlates with decreased survival of the patient, and an equivalent or lower level of NOL3 relative to the reference level correlates with increased survival of the patient.

Abstract: A method for analyzing cell free DNA (cfDNA) from the bloodstream of a cancer patient is provided. In some embodiments, the method may comprise sequencing at least part of the coding sequences of TP53 and KRAS in a sample of the cfDNA, analyzing the sequences to identify nucleotide transversions in the coding sequences of the genes, relative to reference sequences of the genes. In some embodiments, the method may comprise counting the total number of identified nucleotide transversions. The presence of nucleotide transversions indicates that the patient will be more responsive to the immune checkpoint inhibitor, whereas a decreased number of transversions or no transversions indicates that the patient will be less responsive to the immune checkpoint inhibitor.