Abstract: Disclosed herein are methods and compositions for targeted cleavage of a genomic sequence, targeted alteration of a genomic sequence, and targeted recombination between a genomic region and an exogenous polynucleotide homologous to the genomic region. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain and polynucleotides encoding same. Methods for targeted cleavage include introduction of such fusion proteins, or polynucleotides encoding same, into a cell. Methods for targeted recombination additionally include introduction of an exogenous polynucleotide homologous to a genomic region into cells comprising the disclosed fusion proteins.

Abstract: The invention relates to methods of altering expression of a genomic locus of interest or specifically targeting a genomic locus of interest in an animal cell, which may involve contacting the genomic locus with a non-naturally occurring or engineered composition that includes a deoxyribonucleic acid (DNA) binding polypeptide having a N-terminal capping region, a DNA binding domain comprising at least five or more Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and a C-terminal capping region, wherein the polypeptide includes at least one or more effector domains, and wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to the DNA of the genomic locus.

Abstract: The invention provides compositions and methods for regulating intracellular osmolarity in cells, e.g., in cultured cells, including in cultured cells in bioreactors. The invention provides nucleic acids comprising at least one osmo-responsive transcriptional regulatory element (OR-TRE), and cells, vectors, products of manufacture, artificial organs or implants and the like containing an osmo-responsive transcriptional regulatory element (OR-TRE).

Abstract: The present disclosure provides reagents and methods for molecular proximity detection of specific endogenous nucleic acids in situ using RNA-guided nucleic acid binding proteins.

Abstract: The present invention provides a method of designing an optimized gene which comprises altering a nucleotide sequence of a target protein gene, so that only preferential codons with high frequency of use in human cells are selected and a GC content of not less than 60% is achieved. A gene design method which involves the feature “only preferential codons with high frequency of use are selected and a GC content of not less than 60% is achieved” can be established as a general rule for preparing proteins with high expression level, in order to obtain chemically synthesized genes for proteins capable of high-level expression in eukaryotes.

Abstract: Provided herein, in some embodiments, are nucleic acid-based tools that may be used for high-throughput functional genomics studies as well as for the generation of knockout (gene inactivation or deletion) or knockin (gene activation or insertion) cell lines. Tools of the present disclosure include an “activatable reporter cassette,” a guide RNA construct and a nuclease that can be used together, for example, to modify and isolate targeted cells of interest.

Abstract: The present invention relates to a fusion protein comprising a Cas9 domain and a Spo11 domain, as well as the use of this protein to induce targeted meiotic recombinations in a eukaryotic cell.

Abstract: The present invention provides systems and methods for identifying, isolating, and/or characterizing microRNAs, their targets, and microRNA response elements, and for predicting their biological function.

Abstract: TRPV4 activation increases vascular permeability and can be triggered by both chemical and mechanical cues. This activation of TRPV4 can contribute to a number of pathological conditions, e.g., edema, inflammation, hypertension, and/or hyperalgesia. Described herein are methods and compositions relating to inhibition of mechanically-induced TRPV4 activation, e.g., for the treatment of pulmonary edema, edema, inflammation, hypertension, and/or hyperalgesia.

Abstract: Disclosed herein are methods and compositions for modulating expression of a PD1 gene.

Abstract: The invention concerns the field of cell culture technology. It concerns RNA having a specific sequence, expression vectors encoding the RNA, production host cell lines comprising the RNA, and methods of producing recombinant biopharmaceutical products using engineered host cell with altered levels of the RNAs, such as small non-coding RNAs, preferably microRNAs (miRNAs). The invention also relates to engineered host cells with altered levels in one or more of the RNAs. Those cell lines have improved secretion and/or growth characteristics in comparison to control cell lines.

Abstract: Provided herein is a method for making an cDNA library, comprising adding an affinity tag-labeled GMP to the 5? end of targeted RNA species in a sample by optionally decapping followed by incubating the sample with an affinity tag-labeled GTP and a capping enzyme, enriching for RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag, reverse transcribing the enriched RNA to produce a population of cDNAs, and adding a tail to the 3? end of the population of cDNAs using a terminal transferase, to produce an cDNA library.

Abstract: The present invention relates to a method for the generation of compact Transcription Activator-Like Effector Nucleases (TALENS) that can efficiently target and process double-stranded DNA. More specifically, the present invention concerns a method for the creation of TALENs that consist of a single TALE DNA binding domain fused to at least one catalytic domain such that the active entity is composed of a single polypeptide chain for simple and efficient vectorization and does not require dimerization to target a specific single double-stranded DNA target sequence of interest and process DNA nearby the DNA target sequence. The present invention also relates to compact TALENs, vectors, compositions and kits used to implement the method.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: The present invention relates to methods to determine the identity of one or more organisms present in a sample (if these are already reported in a taxonomic database) or the identity of the closest related organism reported in a taxonomic database. The present invention does this by comparing a data set acquired by analyzing at least one component of the biological sample to a database, so as to match each component of the analyzed content of the sample to one or more taxon(s) and then collating the phylogenetic distance between each taxa and the taxon with the highest number of matches in the data set. A deconvolution function is then generated for the taxon with the highest number of matches, based on a correlation curve between the number of matches per taxon (Y axis) and the phylogenetic distance (X axis), the outcome of this function providing the identity of the organism or the closest known organism to it.

Abstract: Engineered CRISPR from Prevotella and Francisella 1 (Cpf1) nucleases with altered and improved target specificity and their use in genomic engineering, epigenomic engineering, genome targeting, genome editing, and in vitro diagnostics.

Abstract: Disclosed herein are methods and devices for using digital isothermal amplification to detect subtle responses to environmental stimuli, such as detecting antibiotic susceptibility using digital quantification of DNA replication and/or chromosome segregation.

Abstract: The disclosure relates to the identification, cloning, and expression of a genetic locus within a Listeria monocytogenes genome that encodes a phage tail-like bacteriocin (PTLB), termed a monocin. Also provided are non-natural monocins, which have been engineered to have altered bactericidal specificity. Nucleic acid molecules encoding natural or non-natural monocins, vector constructs containing such nucleic acids operably linked to a heterologous promoter, producer cells containing such vectors, the encoded monocins, as well as methods of making and using such monocins are described.

Abstract: Described herein is a method that generally includes infecting a host cell with a rescue adenovirus, wherein the rescue adenovirus genome comprises a loxP site and encodes at least one marker, and wherein the host cell comprises a library of polynucleotides that complement the adenovirus genome marker and encode a detectable polypeptide; incubating the infected host cell under conditions effective to permit recombination between the adenovirus genome and one or more of the library polynucleotides and the production of recombinant adenovirus particles comprising at least on detectable polypeptide; and detecting the at least one detectable polypeptide. Also described are adenovirus libraries constructed using such a method.

Abstract: The present invention provides an assay that identifies genes required for telomerase-dependent telomere elongation by measuring the de novo telomere addition at a single chromosome.