Abstract: It is an object of this disclosure to provide systems, devices, and methods for the direct use of fluorescent reporters that measure multiaxial and dynamic shear flows that occur invitro or in vivo across a surface of interest, where shear flows canbe measured, quantified and/or correlated to physiological changes in cells or tissues in real time. In certain embodiments, this disclosure contemplates imaging or visualizing the shear field applied to a surface, e.g., a surface of cells or inner lining of a blood vessel, the lumen of pumping lymphatics, within the bile duct, vessels with significant leakage, inflamed endothelium, tumor vasculature, or other systems.

Abstract: Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

Abstract: Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: The present disclosure relates to methods and products associated with in vitro and in vivo protease activity measurements and enzyme profiling. Some aspects of the present disclosure relate to measuring remotely triggered protease activity. In particular, the disclosure relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence or absence of active enzymes associated with disease or conditions. The disclosure also relates to products, kits, and databases for use in the methods of the disclosure.

Abstract: CRISPR-based diagnostic methods and compositions are provided. One embodiment provides the use of DNA-barcoded antibodies or peptide-MHC (pMHC) tetramers (e.g., Kb-OVA257-264, Db-GP10025-33, Db-GP33-41) and CRISPR-Cas protein, and a guided DNA endonuclease, to achieve ultrasensitive detection of soluble and cell surface proteins. The disclosed embodiments can use type V: Cas12a; type VI: Cas13a, or Cas13b. Combining DNA encoding with CRISPR-Cas protein recognition is a sensitive system because barcodes can be isothermally amplified and Cas, for example Cas12a, enzymatically cleaves DNA reporters upon barcode detection, providing two rounds of amplification and enabling measurement of protein concentration by sample fluorescence or using by paper-based assays.

Abstract: The present disclosure relates to methods and products associated with in vitro and in vivo protease activity measurements and enzyme profiling. Some aspects of the present disclosure relate to measuring remotely triggered protease activity. In particular, the disclosure relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence or absence of active enzymes associated with disease or conditions. The disclosure also relates to products, kits, and databases for use in the methods of the disclosure.

Abstract: Disclosed herein are protease-based biological circuits for use in the diagnosis and treatment of disease and disorders characterized by aberrant protease signaling. An exemplary method of treating disease in a subject includes administering to the subject a plurality of therapeutic agent loaded-liposomes, wherein each of the liposomes comprises a different density of peptides surrounding the core and a different dose of the therapeutic agent, wherein the peptides comprise a cleavage site for a protease of interest, and wherein cleavage of the peptides open the liposome and release the therapeutic agent from within the liposome.

Abstract: Compositions and methods for pharmacodynamic monitoring of immunotherapy are provided herein. The compositions include an immunotherapeutic agent linked to protease substrates. Upon administration, the compositions target to sites of disease where proteases are upregulated during responsive immunotherapy and subsequently cleave the attached substrates. Cleavage fragments are detected in a sample from the body and detection of the fragments is indicative of an effect of the immunotherapeutic agent.

Abstract: An activity-based nanosensor composition for detecting protease activity comprising a cleavable detectable substrate and methods of use are disclosed.

Abstract: Disclosed herein are bacterial protease-activated prodrug compositions and methods of their use for the treatment and prevention of bacterial infection. Also disclosed are methods of reducing or eliminating defiant bacterial populations. An exemplary prodrug composition includes a cationic antimicrobial peptide conjugated to an anionic peptide with a protease cleavable linker substrate, wherein the antimicrobial peptide is inactive while it is in conjugation with the anionic peptide. Upon cleavage by the protease, the cationic AMP is released from the anionic peptide and can act upon bacteria. The protease is specific to the bacteria that are present in the sample or the subject, creating an auto-titrating mechanism wherein the AMP is released from the peptide only when there is bacteria present.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Methods and compositions for screening or diagnosis of liver disease are provided. The results may also indicate course and efficacy of treatment. The composition includes an activity sensor and a reporter releasably attached to the activity sensor. The method includes detecting the presence and/or amount of a reporter. The reporter is released from an activity sensor in the presence of diseased liver tissue but remains attached to the activity sensor in healthy tissue. The presence and/or amount of the reporter are used to characterize the liver disease. The liver disease may be nonalcoholic steatohepatitis (NASH) and results may further indicate staging of NASH.

Abstract: Methods and compositions for screening or diagnosis of liver disease are provided. The results may also indicate course and efficacy of treatment. The composition includes an activity sensor and a reporter releasably attached to the activity sensor. The method includes detecting the presence and/or amount of a reporter. The reporter is released from an activity sensor in the presence of diseased liver tissue but remains attached to the activity sensor in healthy tissue. The presence and/or amount of the reporter are used to characterize the liver disease. The liver disease may be nonalcoholic steatohepatitis (NASH) and results may further indicate staging of NASH.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Systems and methods for multiplexed cell sorting are provided herein. The disclosed cell sorting system is referred to as DNA gated sorting (DGS). An exemplary system provides a set of orthogonal sorting probes and release probes for sorting cells of one or more different cell types from a biological specimen.

Abstract: The present invention relates to methods and products associated with in vivo enzyme profiling. In particular, the invention relates to methods of in vivo processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. The invention also relates to products, kits, and databases for use in the methods of the invention.

Abstract: Embodiments of the present disclosure relate generally to compositions and methods for the design of remote controlled biological systems, and more specifically to synthetic bioswitches that provide the ability to non-invasively and remotely control the function and activity of live cells, such as for example and not limitation, the expression of biologically active proteins or biological therapeutics, and the manipulation of physiologic or genetic processes and/or protein expression in live cells, in vivo (including, e.g., at desired anatomical sites) or ex vivo.

Abstract: The disclosure provides methods and compositions to digitally profile biological activity by detecting the activity of at least two biomarkers using protease activity sensors or biocomparators.

Abstract: Methods of the present invention predict a physiological state of a subject. A composition comprising activity sensors is introduced into a body of a subject. The activity sensors comprise a plurality of reporters susceptible to cleavage when processed by the body during extracellular matrix remodeling. Cleavage may be indicative of enzymatic activity in the extracellular matrix. Signals detected by the activity sensors may be predictive of a physiological state. A sample is collected from the subject, and liberated reporters are detected in the sample. An onset of the physiological state of the subject, which may be a disease characterized by inflammation or atrophy, may be diagnosed based on the liberated reporters detected.