Abstract: Provided herein are systems and methods for high-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.

Abstract: A method for detecting an analyte is described in which the simultaneously binding of two fusion proteins (i.e., a sandwich assay in solution) is used, bringing two halves of a split enzyme together to produce product, which is detected via a FRET-based biosensor. The method may incorporate an autocatalytic feedback loop that responds to enzymatic product by producing more product to provide ultrasensitive, bistable detection of analyte that is tunable over several orders of magnitude. This system is broadly applicable for protein and small molecule detection.

Abstract: The present disclosure provides a DNA-synthesis based recording system that, in combination with CRISPR-Cas9 or other CRISPR systems, can establish single-cell level connectivity for densely packed cells, for example in the brain.

Abstract: The present disclosure provides engineered bacteria for producing vanillin.

Abstract: The present disclosure relates generally to modified bacteria, such as E. coli, with modification in the expression of at least one gene encoding a type I and/or type II toxin-antitoxin (TA) system protein and/or at least one gene encoding a structural protein that modulates ribosomes and methods of using the disclosed bacteria for producing a biological compound of interest. The modifications of the bacteria result in enhanced bioproduction.

Abstract: Provided herein are systems and methods for using DNA polymerases to record information onto DNA for single cell high time-resolution recording and for high density data storage. The technology provides a DNA polymerase-based nano scale device that can be genetically encoded to record temporal information about the polymerase's environment into an extending single stand of DNA.

Abstract: Provided herein are compositions and systems comprising yeast-based biosensors (YBBs) and methods of use thereof. In particular, YBBs are provided for the detection and/or quantification of an analyte (e.g., peptide analyte) in a sample (e.g., a biological sample, environmental sample, etc.). In some embodiments, provided herein are diagnostic compositions, devices, and methods comprising yeast-based biosensors (YBBs) engineered to detect analytes (e.g., peptides (e.g., biomarker peptides, etc.), etc.). In some embodiments, YBBs comprise (a) recognition element (e.g., receptor (e.g., modified yeast receptor, etc.), etc.) on the exterior of the biosensor (e.g., for binding and or recognition of the analyte (e.g., peptide)), and (b) a reporter that signals binding or recognition of the analyte. In some embodiments, a recognition element is a cell surface receptor.

Abstract: Disclosed are systems, components, and methods for sensing a ligand in a cell or a reaction mixture. The disclosed systems, components, and methods may include and/or utilize a fusion protein comprising a ligand-binding protein and a DNA-binding protein. The fusion protein binds the ligand of the ligand-binding protein and modulates expression of a reporter gene operably linked to a promoter that is engineered to include specific binding sites for the DNA-binding protein. The difference in expression of the reporter gene in the presence of the ligand versus expression of the reporter gene in the absence of the ligand can be correlated to the concentration of the ligand in a reaction mixture.

Abstract: Disclosed are systems, components, and methods for sensing a ligand in a cell or a reaction mixture. The disclosed systems, components, and methods may include and/or utilize a fusion protein comprising a ligand-binding protein and a DNA-binding protein. The fusion protein binds the ligand of the ligand-binding protein and modulates expression of a reporter gene operably linked to a promoter that is engineered to include specific binding sites for the DNA-binding protein. The difference in expression of the reporter gene in the presence of the ligand versus expression of the reporter gene in the absence of the ligand can be correlated to the concentration of the ligand in a reaction mixture.

Abstract: Provided herein are systems and methods for high-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.

Abstract: Provided herein are compositions and systems comprising yeast-based biosensors (YBBs) and methods of use thereof. In particular, YBBs are provided for the detection and/or quantification of an analyte (e.g., peptide analyte) in a sample (e.g., a biological sample, environmental sample, etc.). In some embodiments, provided herein are diagnostic compositions, devices, and methods comprising yeast-based biosensors (YBBs) engineered to detect analytes (e.g., peptides (e.g., biomarker peptides, etc.), etc.). In some embodiments, YBBs comprise (a) recognition element (e.g., receptor (e.g., modified yeast receptor, etc.), etc.) on the exterior of the biosensor (e.g., for binding and or recognition of the analyte (e.g., peptide)), and (b) a reporter that signals binding or recognition of the analyte. In some embodiments, a recognition element is a cell surface receptor.