69results about "Library member identification" patented technology

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

The present disclosure relates to methods and kits for analyzing a macromolecule. In some embodiments, the present disclosure relates to macromolecule analysis methods which employ barcoding and nucleic acid encoding of molecular recognition events. Also provided herein is a method and related kits for transferring information using a plurality of enzymes, including for performing a ligation, extension, and cleavage reaction with nucleic acid molecules associated with the macromolecule for analysis. In some embodiments, the macromolecule for analysis comprises a peptide, a polypeptide, or a protein.

The present disclosure provides methods, compositions, and systems for evolving virus-like particles (VLPs) having one or more desired properties such as increased production levels, increased cargo packaging efficiency, and / or increased transduction of particular target cell types of interest. The present disclosure also provides libraries for use in such methods, and methods for producing the libraries. Group specific antigen (gag) proteins comprising nucleocapsid protein variants evolved using the methods described herein are also provided herein. The present disclosure also provides VLPs comprising such gag proteins comprising nucleocapsid protein variants. Polynucleotides, vectors, cells, and kits useful for performing the methods described herein are also provided.

Methods for controlling non-systematic error in an amplification-based next generation sequencing (NGS) library preparation are described, which method includes using an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

The present application provides a method of producing a “liquid” array of ligand (such as glycan) modified bacteriophage where the ligand modification is encoded genetically within the bacteriophage genome. This method will allow for the determination of the ligand binding profile of biomacromolecules and cells. Furthermore the method allows the elucidation of ligand-protein interactions where ligand binding is co-operative and synergistic.

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

Disclosed is a fluorescently labeled peptide library useful for diagnosing multiple sclerosis. The fluorescently labeled peptide library comprising fluorescently labeled peptides represented by the following formula:wherein X1, X2, X3 and X4 are independently arbitrary amino acid residues, and the peptides are immobilized on a chip.

Micron scale biogeography is a major driver of physiology and ecology of complex microbial biofilm communities, which remains elusive largely due to the lack of tools for spatially resolved phylogenetic mapping. This disclosure provides methods, computer-readable storage devices and kits that allow highly multiplexed and spatially resolved imaging of microbial community spatial organization. The disclosure provides a highly-multiplexed approach to resolve the spatial structure of complex microbial community at high taxonomic resolution.

The disclosure relates to nucleic acid engineering and, more specifically, to synthetic RNA constructs and assembly methods that enable precise, site-specific inclusion of one or more RNA base modifications in a controlled and extendable sequence context suitable for long-read sequencing and quantitative benchmarking. Disclosed are methods of making a modular RNA construct. The methods may comprise annealing a modification loop bait RNA oligonucleotide with a hairpin RNA oligonucleotide, a modification loop RNA oligonucleotide, and a poly-A splint RNA oligonucleotide; and ligating the annealed oligonucleotides to form the modular RNA construct.

The present disclosure provides methods and compositions to develop AAV capsids with a desired characteristic compared to a natural AAV serotype. These capsids are useful, for example, for the delivery of genome engineering molecules and gene therapy molecules for the treatment of a subject in need thereof.

The present invention relates to methods and compositions for preparing a sample enriched for single stranded nucleic acids. The single stranded nucleic acids find use as templates for synthesizing Xpandomer copies of the nucleic acids. The Xpandomer copies may be passed through a nanopore sensor to determine the nucleic acid sequence of the nucleic acids. The methods include asymmetric PCR, amplicon immobilization melt, exonuclease-mediated partial or complete digestion of one or both strand of an amplicon and linear amplification.

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.

The present disclosure provides methods for non-invasive prenatal screening (NIPS) of fetal aneuploidies. The present methods are based on analyzing cell-free fetal DNA (cff DNA) found in a pregnant woman's circulation through the next generation sequencing (NGS) technology. Particularly, the present methods analyze the relative abundance of different fetal genomic fragments present in the maternal sample, where the fragments can be aligned to particular chromosomal locations of the fetal genome. The relative abundance information is indicative as to whether a particular chromosome is overrepresented or underrepresented in a fetal genome as compared to normal individuals, and thus can be used to detect fetal aneuploidy. Additionally, methods for increasing the positive predictive values (PPV) of NIPS by excluding false-positive detections are also provided.

The present invention provides a method for obtaining sequencing-based information from cells / nuclei, the method comprising (a) a first barcoding of cells and / or nuclei of a group of cells and / or nuclei comprising interacting cells with one or more group-specific barcode sequence(s) or a group-specific combination of one or more barcode sequence(s): (b) a second barcoding of nucleic acid molecules contained in and / or attached to individual cells and / or nuclei from said group of cells / nuclei with a cell / nucleus-specific barcode sequence; and (c) sequencing of the barcoded nucleic acid sequences.

Described herein are methods for identifying immune cell-specific antigens and compositions for use in the methods.

The present invention provides to an improved high-throughput system and method for generated and screening of genetic variants by combinatorial modifications. Also provided are optimized SpCas9 enzyme variants produced by this system.

Provided herein are, inter alia, peptides, nucleic acids, and methods of identifying and uses thereof. The peptides provided herein can, inter alia, be used as therapeutics. The peptides provided herein are, inter alia, useful for treating cancer in a subject in need thereof. Also provided herein are, inter alia, methods for screening genes or proteins encoded by genes for inhibitory or stimulatory activity in a cell.

A method for characterizing proteins, including steps of (a) detecting a plurality of proteins, wherein individual proteins of the plurality are associated with unique identifiers, wherein the detecting distinguishes the identities of the individual proteins and the unique identifiers associated with the individual proteins; (b) digesting the proteins to form peptides, wherein the peptides from each protein are associated with the unique identifiers for the respective individual protein; (c) detecting the peptides and associated unique identifiers, wherein the detecting distinguishes characteristics of individual peptides, and wherein the detecting distinguishes unique identifiers associated with the individual peptides; and (d) correlating characteristics detected in step (c) with individual proteins detected in step (a) based on the unique identifiers associated with the individual proteins and the peptides.

Provided herein are methods and compositions related to nucleic acid barcoding. In some aspects, provided herein are methods and compositions for writing, storing, reading, and resetting data, for example, using photocrosslinking and / or a substrate or compressible hydrogel.

The present disclosure provides methods for non-invasive prenatal screening (NIPS) of fetal aneuploidies. The present methods are based on analyzing cell-free fetal DNA (cff DNA) found in a pregnant woman's circulation through the next generation sequencing (NGS) technology. Particularly, the present methods analyze the relative abundance of different fetal genomic fragments present in the maternal sample, where the fragments can be aligned to particular chromosomal locations of the fetal genome. The relative abundance information is indicative as to whether a particular chromosome is overrepresented or underrepresented in a fetal genome as compared to normal individuals, and thus can be used to detect fetal aneuploidy. Additionally, methods for increasing the positive predictive values (PPV) of NIPS by excluding false-positive detections are also provided.

Provided herein are methods of differentiating cells in a cell population that includes detecting fluorescent signals emitted by at least one set of fluorescent barcoding proteins in the cell population to produce a first detected fluorescent signal data set, in which a first subset of the cells in the cell population each comprise a first fluorescent barcoding protein that comprises at least one copy of a first fluorescent protein (FP), or a functional portion thereof, and at least one copy of a second FP, or a functional portion thereof, and in which the first and second FPs, or the functional portions thereof, differ from one another. The methods also include identifying the first fluorescent barcoding protein in the first subset of the cells in the cell population using the first detected fluorescent signal data set. Related methods, compositions, kits, systems, and computer readable media are also provided.

To provide macromolecule analysis employing nucleic acid encoding.SOLUTION: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed. There remains a need in the art for improved techniques relating to macromolecule sequencing and / or analysis, with applications to protein sequencing and / or analysis, as well as to products, methods and kits for accomplishing the same. There is a need for proteomics technology that is highly-parallelized, accurate, sensitive, and high-throughput. The present disclosure fulfills these and other needs.SELECTED DRAWING: None

The present disclosure relates to systems and methods for screening proteins (e.g., libraries of protein variants). In particular, the present disclosure provides systems and methods for generating DNA-encoded protein libraries on hydrogel beads using particle-templated emulsification.

To provide specific polypeptides and methods for cleaving a DNA molecule at a target site using the polypeptides.SOLUTION: The invention provides a polypeptide comprising a specific amino acid sequence where a residue corresponding to residue 1003 of a specific sequence is substituted and a residue corresponding to residue 661 of the specific sequence is substituted. The invention provides such a polypeptide where the residue corresponding to residue 1003 of the specific sequence is substituted with histidine and the residue corresponding to residue 661 of the specific sequence is substituted with alanine. A method for cleaving a DNA molecule at a target site is provided which comprises bringing the DNA molecule comprising the target DNA site into contact with the polypeptide and a short guide RNA (sgRNA) that specifically binds the target DNA site, thereby causing the DNA molecule to be cleaved at the target DNA site.SELECTED DRAWING: Figure 1a