A multiplex assay for nucleic acid detection includes a substrate, a sample, and a fluorophore-labeled oligonucleotide. The substrate has a plurality of physically separated assay locations, each of which includes a nucleotide-targeting enzyme configured to cleave nucleic acids, a guide ribonucleic acid (gRNA), and a quencher-labeled oligonucleotide. A portion of the sample is distributed to each assay location. The gRNA recognizes target nucleic acid in the sample, thereby activating the nucleotide-targeting enzyme to cleave nucleic acids, including the quencher-labeled oligonucleotide. The fluorophore-labeled oligonucleotide is subsequently added to each assay location, which facilitates identification of a presence of the target nucleic acid in the sample via detection of unquenched light emitted by the fluorophore in one or more of the plurality of assay locations.

Provided are RNA recognition complexes that include an RNA-targeting agent; and a coronavirus-derived protein. In some embodiments, the RNA recognition complex further includes a linker. In some embodiments, the RNA-targeting agent includes CRISPR/Cas9 components (e.g., a Cas9 protein, a Cas 13b protein, or a Cas 13d protein). Also provided herein are methods of upregulating gene expression of a target RNA that include delivering a RNA recognition complex into a cell, wherein the RNA recognition complex comprises a RNA-targeting agent, and a coronavirus-derived protein, and wherein the RNA recognition complex binds to the target RNA and upregulates gene expression of the target RNA in the cell.

Provided herein are methods and materials for treating or reducing the risk of obesity and/or conditions associated with obesity (e.g., type 2 diabetes or hyperinsulinemia). For example, provided herein are methods and materials for inhibiting RalA to treat obesity and/or conditions associated with obesity in a subject in need thereof. In some cases, the subject has elevated expression of RalA compared to a healthy individual.

The disclosure provides, in various embodiments, compositions, such as polypeptides, polynucleotides, gene editing systems, small molecules, vectors or host cells, that comprise and/or modulate expression or activity of immune regulation-associated proteins, such as cytokines. The disclosure also provides, in various embodiments, methods of treating inflammation, aging, senescence, fibrosis, autoimmunity, cancer, an infection, and/or an immunological disease using an agent that comprises and/or modulates expression or activity of an immune regulation-associated protein, and methods of identifying said agent.

The disclosure provides nucleic acid constructs comprising a transmembrane reporter cassette encoding an affinity tag, a transmembrane (TM) domain and a fluorescent reporter protein. In embodiments, the nucleic acid constructs are inserted in a safe harbor locus or an immunoglobulin constant domain locus of in a cell of a non-human mammal. In embodiments, when the transmembrane reporter cassette is expressed in the cell, the affinity tag is displayed on a surface of the cell while the fluorescent reporter protein is located inside the cell membrane. The presence of the affinity tag and the fluorescent reporter protein allow for identification, sorting and/or isolation of cells expressing the nucleic acid constructs. The disclosure also provides embodiments of methods of modifying cells and non-human organisms with the nucleic acid constructs, along with embodiments of cells and non-human organisms produced using the disclosed methods.

The disclosure provides modified plant viruses designed for delivering a nucleotide of interest into mammalian cells. The modified plant viruses include a plant virus nucleotide sequence (e.g. fragment) that is capable of transfecting a mammalian cell when that mammalian cell expresses a receptor for the modified plant virus. Accordingly, the disclosure also provides receptors for the modified plant viruses as well as methods of using the receptor or the modified plant virus and receptor.

The disclosure provides polypeptides, polynucleotides, compositions, kits and methods useful for modulating RNA molecules including degrading disease-causing RNA(s) or stabilizing RNA(s) to treat diseases.

Disclosed are methods and kits for eliminating cancer cells and treating cancers by targeting neo splice sites or cryptic exons of oncogenic gene fusions.

Aspects herein concern cdtR mutations that can lead to reduced or absent virulence in C. difficile bacteria. Disclosed are compositions and methods using the cdtR mutants to treat or prevent C. difficile infections or diseases caused by C. difficile. Also disclosed are methods for detecting or determining C. difficile virulence based on mutation status of the cdtR gene in C. difficile.

The present application relates to a method of predicting possible off-targets in a gene editing process (for example, genome editing process) using a gene editing system.