The present invention relates to systems and methods for screening natural products such as secondary metabolites produced by engineered microbial strains.

Provided herein are compositions and methods describing the generation and use of in vitro pro-organs using microparticle scaffolds.

The in vitro organoid model is a major technological breakthrough and an essential tool to study the basic biology of an organ system and for the development of various clinical applications for disease intervention. Organoids can self-renew and exhibit similarities in function as of their tissue of origin. Here, a step-by-step protocol is described to isolate region-specific progenitors from the human lung and generate 3D organoid cultures as an experimental and validation tool.

A system and method for searching published genomes utilizes a robust and sensitive model to identify peptides that may serve as protein toxins. The protein toxins include unique cysteine stabilized structures and may be referred to as sequential tri-disulfide peptides (STPs) or as non-sequential tri-disulfide peptides (NTPs). While the sequence variability of STPs is so great that there are severe limitations to searching using traditional sequence-based methods, the present system and method efficiently and accurately identifies STPs as well NTPs from published genome databases, or in any peptide sequence, including artificial sequences.

A method to evaluate the potential of cancer therapeutics to produce skin related side effects is disclosed. The method, which involves use of biological markers, can also be used to evaluate the efficacy of a composition in reducing the effects of cancer therapeutics on skin.

An extrudable hydrogel composition useful for making a three-dimensional organ construct includes a cross-linkable prepolymer, a post-deposition crosslinking group, optionally, an initiator that catalyzes the reaction between the prepolymer and said the crosslinking group; live cells (e.g., plant, animal, or microbial cells), optionally at least one one growth factor, and optionally water to balance. Methods of using the same and products so made are also described.

The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. More specifically, the field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout. Probe types other than antibodies and nucleic acids are also covered in the field of invention, including but not limited to carbohydrate-binding proteins (e.g., lectins), receptors and ligands. Finally, the field of the invention also encompasses multi-omic MSI procedures, where MSI of photocleavable mass-tag probes is combined with other modes of MSI, such as direct label-free MSI of endogenous biomolecules from the biospecimen (e.g., tissue), whereby said biomolecules can be intact or digested (e.g., chemically digested or by enzyme).

Microfluidic devices for modeling three-dimensional tissue structures and methods for making and using the same are described herein.

The present invention relates to a method of producing organoids, said method comprising or consisting of: (a) seeding a plurality of tissue-specific precursor cells into a container; (b) allowing to occur (i) aggregation of said cells; and (ii) maturation of the aggregate formed in (i) into a single organoid; wherein said method does not comprise embedding of said cells or said aggregates into a gel.

The invention relates to improved culture methods for expanding epithelial stem cells and obtaining organoids, to culture media involved in said methods, and to uses of said organoids.