Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more target nucleic acids of interest in a sample. The compositions and methods allow one to control reaction kinetics of the cascade assay by two orders of magnitude via molecular design of one of the reaction components; further, varying molecular design also allows for quantification of target nucleic acids of interest over a large range of concentrations or discriminating between extremely low copy numbers of target nucleic acids of interest.

Abstract: RVDs with recognition preferences for 5mC, 5hmC and 6 mA and different binding properties to these epigenetic modifications are identified in this present invention. Methylation-dependent gene activation, efficient genome editing, targeted detection of 5hmC and other applications can be achieved by using these RVDs. The present invention therefore provides an isolated DNA binding polypeptide containing TALEs, a fusion protein, a polynucleotide, a vector comprising the polynucleotide and a host cell, and the use of the protein comprising TALE repeats domain in the preparation of a reagent for detecting a methylated base in a target sequence of a gene of interest, as well as a method for targeting and binding to a target sequence of a gene of interest in a cell.

Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more target nucleic acids of interest in a sample. The compositions and methods allow one to control reaction kinetics of the cascade assay by two orders of magnitude via molecular design of one of the reaction components; further, varying molecular design also allows for quantification of target nucleic acids of interest over a large range of concentrations or discriminating between extremely low copy numbers of target nucleic acids of interest.

Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more target nucleic acids of interest in a sample. The compositions and methods allow one to control reaction kinetics of the cascade assay by two orders of magnitude via molecular design of one of the reaction components; further, varying molecular design also allows for quantification of target nucleic acids of interest over a large range of concentrations or discriminating between extremely low copy numbers of target nucleic acids of interest.

Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more target nucleic acids of interest in a sample. The compositions and methods allow one to control reaction kinetics of the cascade assay by two orders of magnitude via molecular design of one of the reaction components; further, varying molecular design also allows for quantification of target nucleic acids of interest over a large range of concentrations or discriminating between extremely low copy numbers of target nucleic acids of interest.

Abstract: The present disclosure provides RNA-guided endonucleases, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided endonuclease of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided endonuclease of the present disclosure and a guide RNA.

Abstract: The technology described herein is directed to inducible and repressible polypeptides and polypeptide systems. In particular, described herein are split sequence-specific nucleases and split recombinases that are linked to drug-inducible or drug-repressible dimerization domains. In some embodiments, the polypeptides comprise sequestering domains and/or have their expression controlled by an inducible promoter. In multiple aspects described herein are polynucleotides, vectors, cells, and pharmaceutical compositions comprising said polypeptides or polypeptide systems. Also described herein are methods of using said polypeptide systems to modulate the expression of a target polypeptide or to treat a subject in need of a cell therapy.

Abstract: A cleavage-based real-time PCR assay method is provided. In general terms, the assay method includes subjecting a reaction mixture comprising a) PCR reagents for amplifying a nucleic acid target, and b) flap cleavage reagents for performing a flap cleavage assay on the amplified nucleic acid target to two sets of thermocycling conditions. No additional reagents are added to the reaction between said first and second sets of cycles and, in each cycle of the second set of cycles, cleavage of a flap probe is measured.

Abstract: The present invention provides, for example, a set of two polypeptides exhibiting the nuclease activity with dependence on light or in the presence of a drug, in which an N-terminal side fragment and a C-terminal side fragment of a Cas9 protein are bound to each of two polypeptides which form a dimer with dependence on light or in the presence of a drug.

Abstract: The present disclosure provides a composition comprising a site-specific nuclease domain capable of cleaving a target DNA sequence; and a sequence-specific DNA binding domain capable of specifically binding to a recognition DNA sequence, wherein the site-specific nuclease domain operably links to the sequence-specific DNA binding domain.

Abstract: Provided herein are materials and in planta methods for using haploid inducer lines containing a targeted endonuclease to generate transgenic or non-transgenic plants with targeted mutations and/or genomic modifications.

Abstract: The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

Abstract: The present invention provides CD20-binding proteins that bind to and rapidly internalize in a CD20-mediated fashion from a cell surface location to the interior of the cell. CD20-binding proteins of the invention comprise a CD20 binding region and a Shiga toxin effector region. Certain of the disclosed CD20-binding proteins kill cells that express CD20 on their surface. Further, the presently disclosed CD20-binding proteins can comprise additional exogenous materials, such as, e.g., antigens, and are capable of targeted delivery of these additional exogenous materials into the interior of CD20 expressing cells. These CD20-binding proteins have uses in methods such as, e.g.

Abstract: This disclosure provides various TcBuster transposases and transposons, systems, and methods of use.

Abstract: Engineered transcriptional activator-like effectors (TALEs) are versatile tools for genome manipulation with applications in research and clinical contexts. One current drawback of TALEs is that the 5? nucleotide of the target is specific for thymine (T). TALE domains with alternative 5? nucleotide specificities could expand the scope of DNA target sequences that can be bound by TALEs. Another drawback of TALEs is their tendency to bind and cleave off-target sequence, which hampers their clinical application and renders applications requiring high-fidelity binding unfeasible. This disclosure provides methods and strategies for the continuous evolution of proteins comprising DNA-binding domains, e.g., TALE domains. In some aspects, this disclosure provides methods and strategies for evolving such proteins under positive selection for a desired DNA-binding activity and/or under negative selection against one or more undesired (e.g., off-target) DNA-binding activities.

Abstract: Provided are an adaptor element in a bubble shape, a method of constructing a sequencing library with such an adapter element. The adaptor element is a hybrid formed with a long-chain nucleic acid A and a short-chain nucleic acid B. The hybrid is in the bubble shape with paired regions at two terminals and a non-paired region in the middle.

Abstract: The present invention relates to polypeptides, nucleotides encoding the polypeptide, as well as methods of producing the polypeptides. The present invention also relates to detergent composition comprising polypeptides, a laundering method and the use of polypeptides.

Abstract: Proteases are enzymes which hydrolyze protein enzymes, eliminating their activity. The present invention exploits the hydrolyzing activity of proteases including proteinase K, endoproteinase LysC and/or trypsin to control the activity of restriction enzymes and/or eliminate or reduce production of unwanted DNA or RNA fragments (known as star activity).

Abstract: A peptide with anti-inflammatory activity is described, wherein the peptide comprises at least one amino acid sequence among SEQ ID NO: 2 to SEQ ID NO: 179, the peptide has above 80% homology of amino acid sequence with above-mentioned sequences, or the peptide is the fragment of the above-mentioned peptides. The peptides that have at least one amino acid sequence of SEQ ID NO: 2 to SEQ ID NO: 179 shows outstanding efficacy in both suppressing inflammation and in prophylactic means. Therefore, the composition comprising those peptides can be used as anti-inflammatory pharmaceutical compositions or as cosmetic compositions, in turn, treating and preventing a variety of different types of inflammatory diseases.

Abstract: Disclosed herein are synthetic nucleic acids comprising a nucleic acid sequence that encodes a codon-Adapted Nuclear Argonaute protein (ANAGO) that is a species-specific to a eukaryote, and compositions comprising ANAGO and donor molecules for use in homologous recombination directed targeted gene editing in the eukaryote.

Abstract: The present invention relates in general to cellular analysis tools and more particularly to methods and systems for detecting or determining cyclic nucleotide concentrations and related pathway activation in samples. Samples containing cyclic nucleotides may be contacted with a cyclic nucleotide-dependent protein kinase (e.g., cAMP- and cGMP-dependent protein kinases) and a detection system that includes a substrate capable of being phosphorylated by the cyclic nucleotide-dependent protein kinase. The activity of cyclic nucleotide related cell signaling pathways may be measured based on detecting the activity of the cyclic nucleotide-dependent protein kinase.

Abstract: Simple ?-hairpin peptides in linear and cyclic form that specifically bind to HIV-1 Trans-Activation Response element (HIV-1 TAR), as well as compositions and use thereof are described.

Abstract: The present invention provides improved DNA polymerases, in particular, type A DNA polymerases, that may be better suited for applications in recombinant DNA technologies. Among other things, the present invention provides modified DNA polymerases derived from directed evolution experiments designed to select mutations that confer advantageous phenotypes under conditions used in industrial or research applications.

Abstract: Methods of making mutant Cas9 proteins are described.

Abstract: Fusion polypeptides having a heterologous 5?-3? exonuclease domain linked to a polymerase that does not naturally have 5?-3? exonuclease activity, as well as methods of their use are provided. Other aspects are also disclosed.

Abstract: The disclosure concerns a detergent composition comprising one or more anionic surfactants; an enzyme selected from the group consisting of: a protease, a lipase, a cutinase, an amylase, a carbohydrase, a cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xylanase, and an oxidase; and a deoxyribonuclease (DNase), as well as methods for washing a textile.

Abstract: Compositions and methods for using programmable DNA binding proteins to increase the efficiency and/or specificity of targeted genome modification or to facilitate the detection of specific genomic loci in eukaryotic cells.

Abstract: Methods for screening pancrelipase for RNA virus contamination comprise removing free viral RNA from the pancrelipase, denaturing any viruses in the pancrelipase to release encapsidated RNA into the pancrelipase milieu, and detecting this released RNA. Removal of free viral RNA may comprise treating pancrelipase with RNase and DNase or precipitating the protein fraction of pancrelipase with a salt that precipitates the protein fraction while leaving nucleic acids such as RNA in solution. Pancrelipase substantially devoid of free nucleic acid is also provided.

Abstract: Apparatus and methods for size selecting nucleic acid molecules having wide range of applications including the production of DNA libraries for sequencing technologies. An automated high throughput system for size selection of multiple nucleic acid samples that uses imaging technique to detect the progress of a target fraction and feedback from the imaging to control electrophoresis. Predictive algorithms for timed nucleic acid extractions are generated to provide size selected nucleic acid molecules of required size ranges.

Abstract: Disclosed herein are compounds, compositions and methods for modulating the expression of LMNA in a cell, tissue or animal. Also provided are methods of target validation. Also provided are uses of disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders. Further provided are methods of identifying cis splicing regulatory elements of a selected mRNA using the disclosed compounds.

Abstract: The present invention is concerned with nuclease fusion proteins and various uses thereof. Specifically, it relates to a polynucleotide encoding a polypeptide comprising (i) a first module comprising at least a first DNA binding domain derived from a homing endonuclease, (ii) a linker, and (iii) a second module comprising at least a second DNA binding domain and a cleavage domain derived from a restriction endonuclease, wherein the polypeptide functionally interacts only with DNA comprising a DNA recognition site for the first DNA binding domain and a DNA recognition site for the second DNA binding domain, and wherein the cleavage domain cleaves DNA within a specific DNA cleavage site upon binding of the polypeptide. Further contemplated are a vector and a non-human transgenic organism comprising the polynucleotide as well as a polypeptide encoded by the polynucleotide of the invention.

Abstract: Compositions for inhibition of RNA Polymerase I include peptides of Rpa43. Methods of production and use thereof are also disclosed.

Abstract: Methods for increasing specificity of RNA-guided genome editing, e.g., editing using CRISPR/Cas9 systems.

Abstract: A processing method to trim ends of DNA fragments, exposing the internal DNA part to give original DNA sequence information enabling application of next generation sequencing for DNA samples to be amplified by DOP-PCR or other primer dependent amplification methods. Specifically, nucleic acids are amplified using primers comprising a recognition site for a restriction enzyme, for example Bpml or Mmel. Primer sequences are removed by cleavage with the restriction enzyme.

Abstract: The present invention provides methods for modulating expression of endogenous cellular genes using recombinant zinc finger proteins.

Abstract: Disclosed herein are engineered cleavage half-domains; fusion polypeptides comprising these engineered cleavage half-domains; polynucleotides encoding the engineered cleavage half-domains and fusion proteins; and cells comprising said polynucleotides and/or fusion proteins. Also described are methods of using these polypeptides and polynucleotides, for example for targeted cleavage of a genomic sequence.

Abstract: The subject of the invention is the ribonuclease which cleaves RNA strand in DNA-RNA hybrids, wherein ribonuclease comprises fusion protein comprising catalytic domain of RNase HI (RNase HI) or derivative thereof with a zinc finger DNA-RNA hybrid binding domain, and wherein the zinc finger binding domain has the ability to bind to specific sequences in the DNA-RNA hybrid. The invention also relates to new methods for determination of the sequence preference of DNA-RNA hybrid binding protein(s) or its domain(s) and allows determining the sequence recognized by sequence specific binding protein in the DNA-RNA hybrid.

Abstract: The invention includes methods and apparatus for separating heteroduplexed nucleic acids from homoduplexed nucleic acids having similar sequences and being at a much higher concentration. The heteroduplexed nucleic acids may be separated through the application of a time varying driving field and a time-varying mobility field to a sample of heteroduplexed and homoduplexed nucleic acids in a separation medium. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

Abstract: The purpose of the present invention is to provide a nuclease that secretes natural nonpathogenic microorganisms extracellularly, has higher specific activity than conventional nucleases, and is useful in nucleolytic degradation on an industrial scale. This purpose is achieved with an extracellularly secreted nuclease derived from Streptomyces bacteria, the nuclease having specific activity equal to or greater than the specific activity of Benzonase® when supplied to double-stranded DNA for 30 minutes at 37° C. in 20 mM Tris/HCl (pH 8.5) containing 1 mM MgCl2 and 1 mM CaCl2 after purification, using double-stranded DNA, single-stranded DNA, and RNA as substrates.

Abstract: Disclosed herein are methods and compositions for generating a single-stranded break in a target sequence, which facilitates targeted integration of one or more exogenous sequences.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.

Abstract: The present invention relates to polypeptide fragments comprising an amino-terminal fragment of the PA subunit of a viral RNA-dependent RNA polymerase or variants thereof possessing endonuclease activity, wherein said PA subunit is from a virus belonging to the Orthomyxoviridae family. This invention also relates to (i) crystals of the polypeptide fragments which are suitable for structure determination of said polypeptide fragments using X-ray crystallography and (ii) computational methods using the structural coordinates of said polypeptide to screen for and design compounds that modulate, preferably inhibit the endonucleolytically active site within the polypeptide fragment. In addition, this invention relates to methods identifying compounds that bind to the PA polypeptide fragments possessing endonuclease activity and preferably inhibit said endonucleolytic activity, preferably in a high throughput setting.

Abstract: The present invention relates to the use of ribonucleases (RNases) in the treatment or prevention of disease.

Abstract: Methods are provided for engineering non-naturally occurring proteins comprising artificial pH-sensitive conformational switches that respond to a change in pH by causing a global unfolding of the proteins. Non-naturally occurring proteins comprising artificial pH-sensitive conformational switches that respond to a change in pH by causing a global unfolding of the proteins are also provided.

Abstract: The invention provides for engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors with additional functional domains. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.

Abstract: The present invention provides new zinc finger proteins and zinc finger nuclease (ZFNs) that find particular using in repairing the cystic fibrosis transmembrane conductance regulator (CFTR) gene.

Abstract: The present invention provides autonomous replication sequences (ARSs) isolated from Nannochloropsis that support the replication of episomal DNA molecules (EDMs) in eukaryotic cells. The ARSs and EDMs provided herein can be used for expressing genes in organisms including algae and heterokonts.

Abstract: The invention provides for engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors with additional functional domains. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.

Abstract: The present invention relates to lower eukaryotic host cells having modified oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar and sugar nucleotide transporters to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified lipid-linked oligosaccharides are created or selected. N-glycans made in the engineered host cells exhibit GnTIV, GnTV, GnT VI or GnTIX activity, which produce multiantennary N-glycan structures and may be modified further by heterologous expression of one or more enzymes, e.g., glycosyltransferases, sugar, sugar nucleotide transporters, to yield human-like glycoproteins. For the production of therapeutic proteins, this method may be adapted to engineer cell lines in which any desired glycosylation structure may be obtained.