The invention features methods of identifying and validating affinity reagents, such as antibodies. The methods of the invention generally involve screening an antibody library by, for example, phage display on bacteria (e.g., E. coli) to identify particular antibody clones capable of binding a desired target polypeptide. Clones identified in this way can then be validated using yeast 2-hybrid. In some instances, antibodies identified by their capacity to binding a partial antigen can be validated by their capacity to bind to the full-length antigen. Validated clones can be further screened by additional rounds of phage display and/or yeast 2-hybrid. Between each round, additional variants of particular antibody clones can be generated and screened to identify variants that demonstrate higher binding affinity to the target of interest.

Disclosed are new nucleic acid base-editing systems comprising fusion proteins comprising a) an RNA-programmable nucleic acid recognition module or other suitable nucleic acid recognition module, b) a light inducible reactive oxygen generator. Further disclosed are methods and kits to modify or mutagenize a target DNA region in prokaryotic or eukaryotic cells or organisms.

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.

Characterization of the binding dynamics at the interface between any two proteins that specifically interact plays a role in myriad biomedical applications. The methods disclosed herein provide for the high-throughput characterization of the specific interaction at the interface between two protein binding partners and the identification of functionally significant mutations of one or both protein binding partners. For example, the methods disclosed herein may be useful for epitope and paratope mapping of an antibody-antigen pair, which is useful for the discovery and development of novel therapies, vaccines, diagnostics, among other biomedical applications.

The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample may comprise hybridizing a probe molecule to a target region of a nucleic acid molecule (e.g., a ribonucleic acid (RNA) molecule), barcoding the probe-nucleic acid molecule complex, and performing extension, denaturation, and amplification processes. A method for processing a sample may comprise hybridizing first and second probes to adjacent or non-adjacent target regions of a nucleic acid molecule (e.g., an RNA molecule), linking the first and second probes to provide a probe-linked nucleic acid molecule, and barcoding the probe-linked nucleic acid molecule. One or more processes of the methods described herein may be performed within a partition, such as a droplet or well. One or more processes of the methods described herein may be performed on a cell, such as a permeabilized cell.

Disclosed herein are insulin resistance reporters for use in quantifying insulin response in biological cells. These biological cells may be stem cell compositions or derivatives thereof comprising the insulin resistance reporter. The stem cell derivatives include but are not limited to insulin responsive cells, tissues, or organoids, such as pancreatic, brain, adipose, muscle, or liver cells, or tissues or organoids thereof. Also disclosed herein are methods of using said insulin resistance reporters and cells with these insulin resistance reporters as models to examine insulin resistance and screening for compounds that are potentially useful for the treatment of diseases or disorders associated with insulin resistance. The cells comprising an insulin resistance reporter may be hepatic cells or liver organoid compositions, which can be used in investigating hepatic insulin resistance, for example, as a result of non-alcoholic fatty liver disease or steatohepatitis.

Methods for detection of molecular interactions, such as protein/protein or small molecule/protein interactions, are described.

Methods for detection of molecular interactions, such as protein/protein or small molecule/protein interactions, are described.

Disclosed herein, in some embodiments, non-naturally occurring proteins (e.g., non-naturally occurring modified proteins) that may be useful in the treatment of bacterial and viral infections, including SARS-CoV-2 infection, host cells comprising the same, and methods of treating bacterial and viral infections including SARS-CoV-2 infection. Also provided herein are host cells comprising fusion proteins for split intein-based selection of peptides that bind a target protein, methods of using the same, and methods of identifying peptides that bind a target protein.

The present disclosure provides synthetic modular polypeptide libraries and nucleic acids encoding such synthetic modular polypeptide libraries. Also provided are methods of making synthetic modular polypeptide libraries and nucleic acids encoding synthetic modular polypeptide libraries. Methods of screening a synthetic modular polypeptide library to identify a selected phenotype associated with a member of a synthetic modular polypeptide library are also provided where such methods find use in both in vitro and in vivo assays.