Abstract: The invention relates to nucleic acids encoding a p-coumaroyl-CoA:monolignol transferase and to inhibitory nucleic acids adapted to inhibit the expression and/or translation of a p-coumaroyl-CoA:monolignol transferase RNA. Inhibition of p-coumaroyl-CoA:monolignol transferase in plants improves the incorporation of monolignol ferulates into the lignin of plants, giving rise to plant biomass that is more easily processed into useful products such as paper and biofuels.

Abstract: The present invention relates to mutant gibberellin 2-oxidase (GA2ox) genes and uses thereof. In particular, the effective mutations disclosed herein can reduce GA2ox enzymatic activity to different extents, leading to various degrees of GA deficient yet beneficial agronomic traits in transgenic plants.

Abstract: Disclosed herein are methods for production of fully-processed mature Factor X in an expression system producing a controlled amount of furin between 50 U/mL and 300 U/mL of culture supernatant. Also disclosed are transformed cells, expression systems, and expression vectors for the expression of furin and Factor X.

Abstract: The present invention includes methods for effecting phenotype conversion in a cell by transfecting the cell with phenotype-converting nucleic acid. Expression of the nucleic acids results in a phenotype conversion in the transfected cell. Preferably the phenotype-converting nucleic acid is a transcriptome, and more preferably an mRNA transcriptome.

Abstract: The present invention provides a method of direct germline mutagenesis of a non-human animal.

Abstract: Methods and compositions are provided for generating targeted genetic modifications on the Y chromosome or a challenging target locus. Compositions include an in vitro culture comprising an XY pluripotent and/or totipotent animal cell (i.e., XY ES cells or XY iPS cells) having a modification that decreases the level and/or activity of an Sry protein; and, culturing these cells in a medium that promotes development of XY F0 fertile females. Such compositions find use in various methods for making a fertile female XY non-human mammal in an F0 generation.

Abstract: The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multi-cellular organisms.

Abstract: This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof.

Abstract: This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof.

Abstract: Disclosed are methods for forming ammonia and ammonium that can be utilized in certifiably organic farming productions according to most if not all known certification standards. Also disclosed are bioreactors that can be utilized in carrying out disclosed methods. Methods and systems utilize obligate anaerobic bacteria to breakdown organic protein substrates, i.e., compounds containing bound nitrogen, to provide nitrogen in an unbound plant available form, and particularly, ammonia and/or ammonium. Obligate anaerobic bacteria include high ammonia producing bacteria such as Peptostreptococcus anaerobius, Clostridium sticklandii, and Clostridium aminophilum.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) is processed for use in the production of useful products, such as fuels. For example, systems can use biomass materials, such as cellulosic and/or lignocellulosic materials, to enhance the production of a product, e.g., the production of ethanol and/or butanol by fermentation.

Abstract: A method for producing fermentation products from lignocellulosic biomass is provided. Lignocellulosic biomass is composed of lignocellulosic fibers which are hollow and primarily contain cellulose, hemicellulose and lignin. Lignin is concentrated in the outer fiber wall and glues the fibers into bundles, but the inner fiber wall has a much lower concentration of lignin and has more easily accessible cellulose and hemicellulose. This method uses vacuum infusion to infuse enzymes into the lumen (hollow center) of lignocellulosic fibers to hydrolyze the hemicellulose and cellulose to produce sugars and oligomers, and then uses cycles of vacuum pressure to pump these homogeneous reagents and sugars and oligomers into and out of the lumen. These reagents are homogenized by mixing the reagents with process water using turbulent mixing to produce a homogeneous reagent. The sugars may be fermented, such as with yeast, to a fermentation product, such as ethanol or butanol.

Abstract: Fungi, such as Aspergillus niger, having a dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase (Alg3) gene genetic inactivation, increased expression of a loss of aflR expression A (LaeA), or both, are described. In some examples, such mutants have several phenotypes, including an increased production of citric acid relative to the parental strain. Methods of using the disclosed fungi to make citric acid are also described, as are compositions and kits including the disclosed fungi. Further described are Aspergillus terreus fungi overexpressing the LaeA gene and the use of such fungi for the production of itaconic acid.

Abstract: A bacterial strain secreting fatty acids, the strain inducing fatty acids to be extracellularly secreted by using phospholipase expressed in the periplasmic space of cell. When a method of producing fatty acids by using the bacterial strain secreting fatty acids is used, fatty acids extracellularly secreted are continuously obtained without apoptosis, leading to lower costs and higher production efficiency. Phospholipase, unlike thioesterase, which is a typical fatty-acid degrading enzyme, decomposes phospholipid to produce free fatty acids. Accordingly, by using the substrate specificity of two different phospholipases, a fatty acid having a specific composition can be selectively produced. Unlike in a typical method in which fat is obtained from cells or tissues, fatty acids secreted during cell growth are obtainable by biding to a hydrophobic material without an extraction process using an organic solvent in large quantities.

Abstract: Provided is a method for producing 5-aminolevulinic acid or a salt thereof at a high yield using 5-aminolevulinic acid-producing microorganisms. The method for producing 5-aminolevulinic acid or a salt thereof comprises culturing 5-aminolevulinic acid-producing microorganisms in a medium comprising one or more components selected from the group consisting of L-arginine, glutamic acid, and a salt thereof. The content of glutamic acid or the salt thereof is from 42 to 100 mM in the medium as the glutamic acid.

Abstract: This invention relates to DNA encoding a novel enzyme having activity of synthesizing D-serine from formaldehyde and glycine, recombinant DNA constructed by integrating such DNA into a vector, a transformant transformed with the recombinant DNA, and a method for producing D-serine from formaldehyde and glycine with the use of the enzyme.

Abstract: The present invention relates to thermostable pullulanases useful for industrial and scientific purposes. The present invention provides methods for producing the modified pullulanase, enzymatic compositions comprising the modified pullulanase, and methods for use of the enzymatic compositions.

Abstract: Provided are compositions and methods for use in assembling and expressing a plurality of transcription units using, in one aspect, homologous recombination in yeast. Yeast containing the plurality of transcription units, and isolated transcription units, are also provided. Kits for use in making the yeast and the transcript units are further included.

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 provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using renewable initiators coupled to a solid support. 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.

Abstract: Methods for making cDNA molecules, for amplification of RNA by PCR and for preparation of cDNA libraries are provided. Kits for making cDNA molecules also are provided. Compositions are also provided comprising mixtures of reagents, including reverse transcriptases, buffers, cofactors and other components, suitable for immediate use in conversion of RNA into cDNA and RT PCR without dilution or addition of further components. These compositions are useful, alone or in the form of kits, for cDNA synthesis or nucleic acid amplification (e.g., by the Polymerase Chain Reaction) or for any procedure utilizing reverse transcriptases in a variety of research, medical, diagnostic, forensic and agricultural applications.

Abstract: Use of at least one chromogenic and/or fluorogenic phosphatase substrate for the detection and/or enumeration of enterobacteria in a sample likely to contain them, such as a food sample.

Abstract: The present invention relates to methods and apparatuses for amplifying, detecting, and optionally quantifying, nucleic acids. In one aspect the method comprises (a) providing a reaction volume comprising (i) a first electrode comprising an electrochemically-active conducting polymer, a first single-stranded nucleic acid molecule capable of hybridizing to a target nucleic acid, wherein the first nucleic acid molecule is covalently attached to the electrochemically-active conducting polymer, and (ii) a second electrode, (b) providing a reaction mixture to the reaction volume, the reaction mixture comprising a target nucleic acid, a nucleic acid polymerase, a redox couple, and nucleic acid amplification reagents, (c) amplifying the nucleic acid, and (d) measuring the impedance of the first electrode at least once during the nucleic acid amplification reaction.

Abstract: This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof.

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for determining copy number variation of one or more nucleic acids present in a sample. In some aspects, the method includes various target-specific primers that allow for the selective amplification of one or more target nucleic acids in the sample. In yet another aspect, the invention relates to determining copy number variation with respect to gene or chromosome representation of a nucleic acid in the sample. In some aspects, the method for determining copy number variation of different target nucleic acids in a sample using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including diagnosis, predictive therapeutic regimes or other therapeutic purposes.

Abstract: Transposon nucleic acids comprising a transposon end sequence and a calibration sequence for DNA sequencing in the transposon end sequence. In one embodiment, the transposon end sequence is a Mu transposon end. A method for the generation of DNA fragmentation library based on a transposition reaction in the presence of a transposon end with the calibration sequence providing facilitated downstream handling of the produced DNA fragments, e.g., in the generation of sequencing templates.

Abstract: Nucleic acids comprising ?-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.

Abstract: In one aspect, compositions and methods for reducing reverse transcriptase (RT) inhibition in RT-PCR are provided. In some embodiments, the RT inhibition reducer is a phosphorothioate oligodeoxycytosine (SdC), phosphorothioate oligodeoxyadenine (SdA), phosphorothioate oligodeoxythymine (SdT), or phosphorothioate oligodeoxyguanosine (SdG).

Abstract: The present invention provides a method of specifically detecting the presence of one or more Mycobacteria of the M. tuberculosis complex, said method comprising detecting ilvC nucleic acid of one or more Mycobacteria of the M. tuberculosis complex in a sample under conditions that do not detect ilvC nucleic acid of the M. avium complex. The invention also provides methods of diagnosis and treatment of tuberculosis in a subject employing the specific detection ilvC nucleic acid of one or more Mycobacteria of the M. tuberculosis complex.

Abstract: Methods of detecting nucleic acids, including methods of detecting nucleic acids in situ, are provided. The methods can detect even target nucleic acids that are partially degraded and/or masked by extensive crosslinking.

Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: Provided herein is technology relating to next-generation sequencing (NGS) and particularly, but not exclusively, to methods and compositions for preparing NGS libraries, e.g., to prepare NGS libraries for use in a NGS workflow.

Abstract: Provided herein is technology relating to detecting and identifying nucleic acids and particularly, but not exclusively, to compositions, methods, kits, and systems for detecting, identifying, and quantifying target nucleic acids with high confidence at single-molecule resolution.

Abstract: An in vitro method of prognostically assessing tissue regeneration capacity and/or cellular potency and/or the prospects of success of an implantation and/or transplantation, wherein the transcriptome and/or the gene expression of cells, said gene expression originating from the transcriptome, are analyzed.

Abstract: The present invention relates generally to genetic markers for autism spectrum disorders and other childhood developmental delay disorders, in particular to copy number variant genetic markers for autism spectrum disorders.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with liver fibrosis and related pathologies. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, including groups of nucleic acid molecules that may be used as a signature marker set, 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: Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.

Abstract: The present application relates to methods of detecting a mutation in a target nucleic acid molecule. Two phosphorodiamidate morpholino oligomer probes that differ by at least one base are each covalently coupled to a nano article and hybridised to a target sequence. The melting temperature of the complexes between each of the two probes and the target nucleic acid are measured and compared to determine whether the sample contains a nucleic acid with the mutation. Further, the present invention relates to kits comprising a first and second conjugate as described herein and to the use of such kits for the detection of mutations in a target nucleic acid molecule or for assigning a genotype to a target nucleic acid molecule.

Abstract: This disclosure describes a novel CD177 haplotype and its involvement in HNA-2 deficiency. Methods of determining the CD177 haplotype of an individual are provided.

Abstract: Nucleic acid constructs and methods that provide superior prevention of primer-dimers and other artifacts of false priming events are disclosed. In particular, there is disclosed a hairpin primer having a target-specific primer region, wherein the target-specific region comprises a target-binding dependent cleavage sequence; a first stem forming region 5? of the target-specific primer region; and a second stem forming region 3? of the target-specific primer region, wherein the second stem forming region is complementary to the first stem forming region. Methods of using the hairpin primer to amplify a target nucleic acid are also disclosed.

Abstract: Compositions and methods useful for the diagnosis and treatment of common variable immunodeficiency are disclosed.

Abstract: The present invention relates to biomarkers for chemoradioresistant subtypes of cervical cancer. In particular the present invention relates to a method for predicting a predisposition to a chemoradioresistant cervical cancer in a subject, a method for diagnosing a chemoradioresistant cervical cancer in a subject, a method for predicting the likelihood of recurrence of cervical cancer in a cervical cancer patient under treatment, and a method for predicting the prognosis for a patient with a chemoradioresistant cervical cancer.

Abstract: The invention relates generally to the field of the identification of DNA sequences, genes or chromosomes. Methods and composition to obtain Unique Sequence DNA probes are provided. Compositions comprises of and double stranded DNA containing Unique Sequences from which the repetitive sequences are eliminated according to the method described in this invention. The invention also relates to the preservation of cells that have been identified after immunomagnetic selection and fluorescent labeling in order to further interrogate the cells of interest. Furthermore the invention relates to genetic analysis of cells that have been identified after immunomagnetic selection and fluorescent labeling.

Abstract: The invention provides a high efficiency fluorescence in situ hybridization (FISH) method for detecting mutations on individual RNA transcripts, including both exonic and intronic RNA transcripts. In certain embodiments, the method is used to quantify allelic expression at the population and single cell level, and also to distinguish maternal chromosomes from paternal chromosomes in single cells.

Abstract: As described herein, the inventors have identified gene signatures which permit the identification of patients who will benefit from (e.g. have optimal outcomes) cytoreductive surgery as treatment for ovarian cancer. Accordingly, provided herein are methods of treatment, assays, and systems relating to ovarian cancer and the administration of cytoreductive surgery. In one aspect, the technology described herein relates to a method of treatment comprising, detecting, in a sample obtained from a subject in need of treatment for ovarian cancer, the level of activation of at least one pathway, and administering cytoreductive surgery to the subject if the level of activation is not increased relative to a reference level.

Abstract: The invention relates to methods for the diagnosis and prognosis of hepatic disorder and associated pathologies as well as of a solid proliferative disorder in a mammalian subject. More specifically, the methods of the invention are based on determining the expression, methylation of ARTS as well as histone trimethylation. The invention further provides therapeutic methods for treating said disorders.

Abstract: A method of estimating the amount of a methylated locus is provided. In certain embodiments the method comprises: digesting a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an MspJI family member to produce a population of fragments that are in the range of 20-40 nucleotides in length, ligating adaptor sequence A and adaptor sequence B to the respective ends of a target fragment of sequence X, and quantifying the amount of ligation products of formula A-X-B. A kit for performing the method is also provided.

Abstract: The present invention provides high-throughput methods of screening for members of a population comprising mutation(s) in one or more target sequence(s). The methods may comprise the steps of: pooling genomic DNA isolated from each member of said population; amplifying the one or more target sequence(s) in the pooled genomic DNA; pooling the amplification products of step (b) to create a library of amplification products; sequencing the amplified products by pair-end sequencing to produce paired-end reads for each sequencing reaction or obtaining paired-end sequence reads for the amplified products; merging the paired-end reads into composite read(s); mapping the composite read(s) to reference sequence(s) to identify mutation(s) in the one or more target sequence(s); and identifying member(s) of the population comprising one or more of the identified mutations in the target sequence(s). The invention further provides kits for use with the methods.

Abstract: Described herein are novel polynucleotides associated with viral infections. 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 viral infections.