Abstract: In accordance with the present invention, there are provided functionally modulated tool receptors which are useful for drug discovery and development. In certain aspects and embodiments as described herein, a sophisticated and powerful approach has been designed that allows the rapid development of enhanced receptors, while simultaneously exploring millions of possibilities for improved properties with respect to such properties as protein expression, homogeneity, stabilization, conformational and activation pathway selectivity, antigenicity, immunogenicity, and the like. Indeed, the new methodology described herein represents a breakthrough by leveraging a full range of combinatorial amino acid replacements, in multiple positions simultaneously, in order to generate modified membrane-spanning proteins.

Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Abstract: Described herein are methods, compositions, kits and systems for multiplexed detection of target molecules from a sample. In some embodiments, the methods, compositions, kits and systems can be used to perform multiplexed protein analysis of a sample (e.g., a sample comprising a small number of cells or a single-cell sample). In some embodiments, the same sample subjected to a multiplexed protein analysis using the methods, compositions, kits and systems described herein can also be subjected to a nucleic acid (e.g., RNAs, microRNAs, and/or DNA) analysis, thereby creating an integrated expression profiling from a limited amount of sample.

Abstract: The present invention includes, but is not limited to, methods, assays, and compositions for preparing libraries of nucleic acid molecules from biological samples, and for detecting and measuring the abundances of nucleic acid molecules, including RNA and DNA. The methods, assays, and compositions of the present invention provide in whole or in part for the detecting and measuring the abundances of nucleic acid molecules, and particularly but not limited to those nucleic acids that have structures that cannot be determined reliably by routine alignment to a reference sequence or concatenation of smaller sequences by matching homologous ends.

Abstract: An apparatus for analyzing individual cell composition in a heterogeneous cell population may include, in one embodiment, a deposition plate having an array of microwells disposed therein, and a cover plate substantially overlying the deposition plate. A pair of electrodes may be associated with one or more of the microwells, and may be configured to generate an electric field within the associated microwell.

Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Abstract: The disclosure relates to a method for constructing a plasma Deoxyribonucleic acid (DNA) sequencing library. The method includes: extracting a plasma DNA; making the plasma DNA ligate to a sequencing linker, and purifying a ligation product; performing Polymerase Chain Reaction (PCR) amplification for the purified ligation product, purifying the PCR amplification product, and obtaining the plasma DNA sequencing library, wherein, the method does not include the step of performing 5?-terminus phosphorylation for the plasma DNA.

Abstract: A high through-put screening method for identifying agents effective for inhibiting biofilm formation and/or killing established biofilm are disclosed. The method includes three tiers, and each tier includes three specific biological process assays. The tier levels are a primary screen, a confirmation screen, and a dose-response screen, and the biological process assays include as says for total bacterial growth, bacterial metabolic activity, and biofilm formation.

Abstract: Methods of clonal analysis of functional genomic assays are provided. Aspects of the invention include transducing a population of target cells with a packaged viral effector library made up of a plurality of effector construct subsets, wherein each effector construct subset of the library includes a plurality of effector constructs having a common effector cassette linked to a distinct clonal barcode. Inclusion of distinct clonal barcodes in the effector construct subset allows for determination of the clonal representation of an effector construct subset in transduced target cells that exhibit a specific phenotype. Aspects of the invention further include compositions, e.g., libraries and components thereof, which find use in practicing the methods.

Abstract: Patterned hydrogel arrays and methods of preparing patterned hydrogel arrays are disclosed. Advantageously, the methods used to prepare the patterned hydrogel arrays allow for controlling individual hydrogel spot conditions such as hydrogel spot modulus, hydrogel spot ligand identity and hydrogel spot ligand density, which allows for preparing a wide range of hydrogel spots in a single array format. Patterned hydrogel arrays can also be formed to include hydrogel-free pools surrounded by hydrogel. Additionally, the patterned hydrogel arrays of the present disclosure support the culture of a range of cell types. The patterned hydrogel arrays offer the ability to rapidly screen substrate components for influencing cell attachment, spreading, proliferation, migration, and differentiation.

Abstract: The present disclosure provides a method of identifying a peptide antigen, including contacting an antibody-comprising composition to a peptide microarray having an array surface and a plurality of feature pairs disposed thereon. Each of the feature pairs includes a first feature of wild-type peptides having a defined sequence and a second feature of mutant peptides having the defined sequence with a single amino acid mutation. Each of the wild-type peptides and the mutant peptides has an array-coupled terminus coupled to the array surface and an opposing free terminus, and the position of the amino acid mutation in the mutant peptides is located closer to the array-coupled terminus of the mutant peptides than the free terminus. The method further includes detecting binding of an antibody in the antibody-comprising composition to at least one of the feature pairs on the peptide microarray, and identifying feature pairs exhibiting differential binding.

Abstract: Theranostics platforms for identifying drugs and nutraceuticals for treatment of rare disease are described. The platforms comprise (a) a cell-phenotype image-enhancing instrument; (b) a drug/nutraceutical library; and (c) a computer-implemented system for analyzing a response of an optically-visible rare-disease cell phenotype to a drug or nutraceutical from the drug/nutraceutical library.

Abstract: Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Abstract: A method of data interpretation from a multiplex cancer assay is described. The aggregate normalized score from the assay is transformed to a quantitative risk score quantifying a human subject's increased risk for the presence of cancer as compared to the known prevalence of the cancer in the population before testing the subject.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: A method is provided for characterizing a lipofilling agent causing increased lipofilling activity in adipose tissue from a target body area. Such a method can include obtaining a plurality of distinct preadipocyte cultures taken from a plurality of distinct body areas of an individual, exposing the plurality of distinct preadipocyte cultures to a plurality of potential lipofilling agents, culturing the plurality of distinct preadipocyte cultures through differentiation to form a plurality of distinct adipocyte cultures, measuring a degree of lipofilling activity of adipocytes from each of the plurality of distinct adipocyte cultures, and quantifying the measured lipofilling activity across the plurality of distinct adipocyte cultures to identify a lipofilling agent causing increased lipofilling activity in adipose tissue from the target body area as compared to adipose tissue in the non-target body area.

Abstract: The present invention provides a formulation to link protein to a solid support that comprises one or more proteins, Oligo-dT and one or more non-volatile, water-soluble protein solvents, solutes or combination thereof in an aqueous solution. Further provided is a method of attaching a protein to a surface of a substrate. The formulations provided herein are contacted onto the substrate surface, printed thereon and air dried. The substrate surface is irradiated with UV light to induce thymidine photochemical crosslinking via the thymidine moieties of the Oligo-dT.

Abstract: Microarray compositions suitable for analysis by one or several spectrographic methods are disclosed. In an embodiment, a microarray composition includes a three-dimensional solid support and a plurality of reactive microbeads positioned on the solid support in spatially distinct and addressable locations.

Abstract: The present invention provides compositions comprising randomized in-frame fusion polynucleotides and methods for introducing them into a host organism to identify desirable phenotypic changes that disrupt or alter existing genetic or biochemical mechanisms or pathways, thus creating novel characteristics of the transformed organism. Methods for using the compositions for increasing diversity within populations of organisms are also presented.

Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids as well as new methods for fluorescent in situ sequencing (FISSEQ) in a new process referred to herein as “expansion sequencing” (ExSEQ).