Abstract: Methods and compositions for performing highly sensitive in vitro assays to define substrate preferences and off-target sites of nucleic-acid binding, modifying, and cleaving agents.

Abstract: Methods and compositions are provided for transferring a genetic circuit from one prokaryotic cell (“donor cell”) to another prokaryotic cell (“recipient cell” or “target cell”). The genetic circuit contains a nucleic acid of interest under the transcriptional control of a repressor binding sequence. The nucleic acid sequence of interest may encode a protein or RNA of interest.

Abstract: The present disclosure provides a method for analyzing nucleic acid sequences. The method can comprise determining, by a computer system, a base trace by trimming a Sanger sequencing trace of a plurality of nucleic acid molecules from a sample based on a first target sequence and a second target sequence. Each of the first and second target sequences can be in the plurality of nucleic acid molecules or can be in the complement of sequence of the plurality of nucleic acid molecules.

Abstract: Provided, in an aspect, is a gene therapy vector, such as for treating retinitis pigmentosa. In an embodiment, a target specific optimization design is performed on a PROM1 gene coding sequence to obtain a nucleotide sequence particularly suitable for efficiently expressing a PROM1 protein in a mammalian cell, and a recombinant AAV virus for expressing a normal human PROM1 protein is constructed. Compared with a coding sequence which is not optimized, the expression level of the optimized PROM1 coding sequence (SEQ ID NO.:1) is increased more than three times. The sequence is particularly suitable for expression in a mammalian cell.

Abstract: The present disclosure relates to a replication deficient oncolytic viral vector or replication capable group B oncolytic adenovirus selected from the group consisting of Ad11 and enadenotucirev, wherein the virus encodes an antibody or a binding fragment thereof for expression on the surface of a cancer cell, wherein said antibody or binding fragment is specific to a CD3 protein of a T-cell receptor complex (TCR), wherein the virus does not encode a B7 protein or an active fragment thereof, pharmaceutical compositions comprising the same, and use of any one of the same in treatment, particularly in the treatment of cancer.

Abstract: Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers.

Abstract: The present disclosure relates to compositions of matter and assay methods used to detect one or more non-nucleic acid targets of interest in a sample. The compositions and methods provide signal boost upon detection of non-nucleic acid targets of interest in less than one minute and in some instances instantaneously at ambient temperatures down to 25° C. or less, allow for massive multiplexing, high accuracy, minimal non-specific signal generation, and are easily reprogrammable.

Abstract: A method for sequencing a target polynucleotide includes detecting a first series of nucleotide incorporations complementary to at least a portion of the target polynucleotide. The first series of nucleotide incorporations forms a first complementary polynucleotide. The target nucleotide is secured to a substrate disposed in a sequencing zone of an assembly. The method further includes moving the substrate to which the target nucleotide is secured to a templating zone of the assembly; removing the first complementary polynucleotide when the substrate is disposed at the templating zone of the assembly, the target polynucleotide remaining secured to the substrate; following the removing, moving the substrate to which the target polynucleotide is secured to the sequencing zone; and detecting a second series of nucleotide incorporations complementary to at least a portion of the target polynucleotide, the second series of nucleotide incorporations forming a second complementary polynucleotide.

Abstract: The purpose of the present invention is to provide, for translation in a cell-free translation system, a novel translation system capable of synthesizing a peptide having therein consecutive non-proteinogenic amino acids. The present invention provides a tRNA containing the base sequence represented by SEQ ID NO: 1 and encoding a non-proteinogenic amino acid.

Abstract: The present disclosure provides for endonuclease enzymes as well as methods of using such enzymes or variants thereof.

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 invention provides a non-naturally occurring composition comprising a CRISPR nuclease comprising a sequence having at least 95% identity to the amino acid sequence selected from the group consisting of SEQ ID NOs: 1-8 or a nucleic acid molecule comprising a sequence encoding the CRISPR nuclease.

Abstract: Disclosed herein are methods, compositions, and kits for engineering proteins using error-prone orthogonal replication (epOrthoRep) and yeast surface display (YSD).

Abstract: Expressing guide nucleic acids (e.g., gRNA) from the same oligonucleotide that contains donor sequence permits the high efficiency, simultaneous transformation of a population of cells with both substrates. Using oligonucleotide chip array technology, one can construct thousands of oligonucleotides with customized gRNA and donor sequence in a cost effective manner. In combination, one can efficiently modify endogenous and exogenous genes.

Abstract: Methods are provided herein for assembling at least two nucleic acids using a sequence specific nuclease agent (e.g., a gRNA-Cas complex) to create end sequences having complementarity and subsequently assembling the overlapping complementary sequences. The nuclease agent (e.g., a gRNA-Cas complex) can create double strand breaks in dsDNA in order to create overlapping end sequences or can create nicks on each strand to produce complementary overhanging end sequences. Assembly using the method described herein can assemble any nucleic acids having overlapping sequences or can use a joiner oligo to assemble sequences without complementary ends.

Abstract: It is to provide an immunocompetent cell that expresses regulatory factors of immunocompetent cell immune function and possesses all of proliferative potential, viability, and the ability to accumulate a T cell, and an expression vector of regulatory factors of immune function for generating the immunocompetent cell. An immunocompetent cell expressing a cell surface molecule specifically recognizing a cancer antigen, interleukin 7 (IL-7), and CCL19 is generated. Preferably, the cell surface molecule specifically recognizing a cancer antigen is T cell receptor specifically recognizing the cancer antigen, and the immunocompetent cell is a T cell.

Abstract: This disclosure relates to compositions and methods for three-dimensional spatial profiling of analytes in a biological sample. The methods include use of a hydrogel comprising one or more polymers that include a phenol moiety, an azide moiety, or an alkyne moiety.

Abstract: The present disclosure relates to recombinant adeno-associated vims (rAAV) delivery of a neurotrophin 3 (NT-3) polynucleotide. The disclosure provides rAAV and methods of using the rAAV for NT-3 gene therapy to improve muscle strength, stimulate muscle growth and to treat muscle wasting disorders, such as muscular dystrophy and Charcot-Marie-Tooth neuropathy.

Abstract: Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.

Abstract: IN The present invention relates to a method for the recombinant production of DNA single stranded molecules, comprising the steps of (1) providing a pseudogene nucleic acid; (2) integrating the pseudogene nucleic acid into a vector, transforming bacterial cells with said vector and producing a precursor ssDNA from said vector under bacterial culture conditions; (3) isolating the precursor ssDNA from the bacterial culture; (4) digesting the precursor ss DNA under reaction conditions where self-cleaving DNA sequences become active; and (5) separating and obtaining the target single stranded DNA oligo- or polynucleotide(s). The method of the present invention is suitable for the mass production of DNA single stranded molecules. The present invention further relates to the use of the target single stranded DNA oligo- or polynucleotide(s), in particular in DNA nanotechnology, or as research tools.