Provided herein are methods for increasing plant cell transformation efficiency. These methods include exposing the plant cells to a liquid medium containing a surfactant. Following exposure to the surfactant-containing medium, the cells can become more amenable to transformation and may be genetically transformed using methods known in the art. Exposure of the cells to the surfactant-containing medium prior to transformation can increase plant transformation efficiency when compared to transformation efficiency of cells not exposed to the surfactant-containing medium.

The invention relates to methods, kits, and compositions for reducing the level of or eliminating a nucleic acid vector in situ. The invention encompasses compositions and methods for selectively eradicating nucleic acid vectors in the microbiota using packaged phagemids. The microbiota can be intestinal and the packaged phagemids can be administered orally. The phagemid encodes a nuclease or other enzyme that genetically modifies the nucleic acid vector so that the nucleic acid vector can be inactivated or eliminated.

A method for producing genetically engineered immune cells, e.g. T cells, or iPSCs which uses an RNA-scaffold mediated base editing system. The method enables precise modifications to be made to the genome whilst minimizing the possibility of off-target effects, making the method particularly suitable for therapeutic applications.

In alternative embodiments, provided are compositions, including recombinant expression systems and vectors, products of manufacture and kits, and methods, for remotely-controlled and non-invasive manipulation of intracellular nucleic acid expression, genetic processes, function and activity in live cells such as T cells in vivo, for example, activating, adding functions or changing or adding specificities for immune cells, for monitoring physiologic processes, for the correction of pathological processes and for the control of therapeutic outcomes. In alternative embodiments, provided are blue-light-mediated light-inducible nuclear translocation and dimerization (LINTAD) systems for gene regulation to control cell activation based on the integration of light-sensitive LOV2-based nuclear localization, light-induced active transportation via the biLINuS motif, and CRY2-CIB1 dimerization that feature high spatiotemporal control to control or alter cell activities in vivo, for example, to limit CAR T cell activity to the tumor site for immunotherapy applications.

The disclosure provides, e.g., compositions and methods for modulating a host response to a Gene Writer system. In some embodiments, modulation of the host response results in increased integration of a heterologous nucleic acid sequence of interest into a target genome. In some embodiments, modulation of the host response results in an increased stability, e.g., maintenance of an insertion or expression thereof. In some embodiments, modulation of the host response results in decreased cytotoxicity.

The present invention belongs to the field of genetic engineering. Specifically, the present invention relates to a directed evolution method based on geminivirus. More specifically, the present invention relates to a directed evolution method for in vivo screening of a genetic element in a plant cell by using primary and secondary replicons of geminivirus.

The present disclosure provides methods, systems, and kits for processing nucleic acid molecules. A method may comprise providing a template nucleic acid fragment (e.g., within a cell, cell bead, or cell nucleus) within a partition (e.g., a droplet or well) and subjecting the template nucleic acid fragment to one or more processes including a barcoding process and a single primer extension or amplification process. The processed template nucleic acid fragment may then be recovered from the partition and subjected to further amplification to provide material for subsequent sequencing analysis. The methods provided herein may permit simultaneous processing and analysis of both DNA and RNA molecules originating from the same cell, cell bead, or cell nucleus.

The invention relates to methods of enriching for target nucleic acid molecules, More particularly, the methods of enriching for target nucleic acid molecules comprise binding target nucleic acid molecules in a sample with one or more first target endonucleases that are specific to a first locus of a target region of the target nucleic acid molecules, separating the target nucleic acid molecules from nontarget nucleic acid molecules in the sample, and binding the separated target nucleic acid molecules with one or more second target endonucleases that are specific to a second locus of the target region of the target nucleic acid molecules, and uses thereof.

Biodegradable particles for delivering a nucleic acid encoding gene-editing factors or a nucleic acid associated with a therapeutic protein to a cell, and compositions, methods, systems, and kits for gene editing in vivo or ex vivo or gene therapy for treating retinal eye diseases are disclosed.

The present disclosure relates to cells modified by a Cas12i polypeptide, methods of modifying the cells, processes for characterizing the modified cells, compositions and formulations comprising the modified cells, and uses of the compositions and formulations comprising the modified cells.