Abstract: Methods and compositions of altering mitochondrial DNA of a eukaryotic cell are provided using one or more of a mitochondrial specific adeno-associated virus to deliver one or more nucleic acids encoding CRISPR system including a Cas9 protein or its nuclease inactive variant and a guide RNA into a mitochondria for expression within the mitochondria. The Cas9 system can cut, nick or regulate a target mitochondrial nucleic acid.

Abstract: The disclosure provides a method for detecting a target analyte in a biological sample including contacting the sample with one or more probe sets each comprising a primary probe and a linker, contacting the sample with an initiator sequence, contacting the sample with a plurality of fluorescent DNA hairpins, wherein the probe binds the target molecule, the linker connects the probe to the initiator sequence, and wherein the initiator sequence nucleates with the cognate hairpin and triggers self-assembly of tethered fluorescent amplification polymers, and detecting the target molecule by measuring fluorescent signal of the sample.

Abstract: A probiotic formulation is provided including one or more bacteria, bacterial strains or bacterial species of the genus Veillonella, genus Faecalibacterium, genus Phascolarctobacteria, genus Oscillospira, genus Ruminococcus, genus Bacteroides, genus Blautia, family Christensenellaceae, genus Dialister, or phylum cyanobacteria.

Abstract: Methods of volumetric imaging of a three-dimensional matrix of nucleic acids within a cell is provided. An automated apparatus for sequencing and volumetric imaging of a three-dimensional matrix of nucleic acids is provided.

Abstract: Novel methods for making high resolution oligonucleotide paints are provided. Novel, high resolution oligonucleotide paints are also provided.

Abstract: The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subjected to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: Methods for attaching barcodes to polypeptides are provided. Methods for detecting molecular interactions at the single molecule level are provided. Embodiments of the invention are directed to a ONA barcoded protein array technology for parallel protein interaction profiling on a single molecule basis. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Novel methods are described herein that measure protein interactions based on the statistical analysis of co-localized polonies arising from barcoding DNAs of interacting proteins.

Abstract: A method of altering a target nucleic acid sequence within a cell is provided including providing the cell with a donor nucleic acid, providing the cell with a single strand annealing protein, and providing the cell with a single strand DNA binding protein, wherein one or more or both of the single strand annealing protein and the single strand DNA binding protein is foreign to the cell, and wherein the donor nucleic acid is recombined into the target nucleic acid.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: Novel methods for making high resolution oligonucleotide paints are provided. Novel, high resolution oligonucleotide paints are also provided.

Abstract: Methods of volumetric imaging of a three-dimensional matrix of nucleic acids within a cell is provided. An automated apparatus for sequencing and volumetric imaging of a three-dimensional matrix of nucleic acids is provided.

Abstract: Methods and compositions of single tube preparation of sequencing libraries from a target DNA are provided. The methods include contacting the DNA with a composition comprising Cas9 endonuclease, a first and a second guide RNAs, a ligase, and sequencing adapters, subjecting the composition to thermal cycling to cleave the DNA at the sites flanking the regions of interest by the RNA guided endonuclease, and subjecting the composition to a temperature to allow ligation of the cleaved DNA fragments including the regions of interest with the sequencing adapters to generate the sequencing libraries.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: A probiotic formulation is provided including one or more bacteria, bacterial strains or bacterial species of the genus Veillonella, genus Faecalibacterium, genus Phascolarctobacteria, genus Oscillospira, genus Ruminococcus, genus Bacteroides, genus Blautia, family Christensenellaceae, genus Dialister, or phylum cyanobacteria.

Abstract: The present disclosure provides a number of targeted nucleic acid FISSEQ library construction methods. Targeted FISSEQ can exhibit several benefits, such as enhanced sensitivity and/or shorter assay time in the detection, identification, quantification, and/or determining the nucleotide sequence of the target species, relative to “random” or “whole-omic” detection via FISSEQ.