38 results about "Cellular resolution" patented technology

The present invention relates generally to methods for single-cell nucleic acid profiling, and nucleic acids useful in those methods. For example, it concerns using barcode sequences to track individual nucleic acids at single-cell resolution, utilizing template switching and sequencing reactions to generate the nucleic acid profiles. These methods and compositions are also applicable to other starting materials, such as cell and tissue lysates or extracted / purified RNA.

Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.

A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.

The invention provides, inter alia, automated medical methods and apparatus that test PD effluent in a flow path (e.g., with an APD system or CAPD setup) to detect, for example, the onset of peritonitis, based on optical characteristics of the effluent resolved at cellular scales of distance. For example, according to one aspect of the invention, an APD machine includes, in an effluent flow path, apparatus for early stage peritonitis detection comprising an illumination source and a detector. The source is arranged to illuminate peritoneal effluent in a chamber that forms part of the flow path, and the detector is arranged to detect illuminant scattered by the effluent. The detector detects that reflected or scattered illuminant at a cellular scale of resolution, e.g., on a scale such that separate cellular-sized biological (or other) components in the effluent can be distinguished from one another based on scattering events detected by the detector.

This invention describes a device for optical stimulation of cells and other biological structures. It has an ability to target multiple cells and / or multiple sub-cellular targets. The stimulation optical pattern on each cell can be independently controlled with individual frequencies. The light sensitivity of the cells can be imparted as a result of genetic expression of surface and / or subsurface proteins, chemical modification of existing proteins, or via the release of caged entities which in turn act to stimulate the cell through chemical means. The embodiment is capable of functioning on neurons but can also be used for other cells. It can perform optimal stimulation with sub-cellular resolutions, record the activity of the targeted cells and perform processing to ensure calibration.

Imaging techniques. Radiation is directed from a source onto a sample using an endoscope having cellular or subcellular resolution. The endoscope includes one or more fibers. The fibers have a proximate end and a distal end, and the distal end is lensless. A focal plane of the endoscope is substantially at a tip of the distal end. Radiation from the sample is directed onto a detector to diagnose or monitor the sample.

An optical device is described that may be used as a microscope system for real-time, three-dimensional optical imaging. The device includes a miniature, fiber optic, intra-vital probe microscope that uses a dual-axes confocal architecture to allow for vertical scanning perpendicular to a surface of the sample (e.g., a tissue surface). The optical device can use off-axis illumination and collection of light to achieve sub-cellular resolution with deep tissue penetration. The optical device may be used as part of an integrated molecular imaging strategy using fluorescence-labeled peptides to detect cell surface targets that are up-regulated by the epithelium and / or endothelium of colon and breast tumors in small animal models of cancer.

Novel methods and devices including modified endoscopes that employ fiber optic technology and multiple extrinsic optical sensors for enablement of simultaneous determination of change rates of biological analytes in vivo with single-cell resolution. The devices employ dynamic oscillatory actuation to determine the gradient of analytes of interest along one or multiple directions with respect to the cell. The change rate or flux of the analyte of interest can be easily determined by applying the first Fick's law that relates the flux with the concentration gradient. The dual operation mode of the device markedly increases measurement sensitivity and accuracy.

Systems and methods for in situ laser lysis for analysis of biological tissue (live, fixed, frozen or otherwise preserved) at single cell resolution in 3D. For example, a system and method for lysing individual cells in situ, including the steps of capturing a tissue sample comprising a cellular content, subjecting the tissue sample to a stream of continuous fluid flow, lysing a selected area of the tissue sample with a laser, thereby releasing at least a portion of the cellular content from the tissue sample, recovering at least one target molecule from the cellular content in the stream, and processing at least one target molecule is provided. The system collects cellular contents, performs highly multiplexed (RT-qPCR or RNA-seq), and sequentially (cell-by-cell) reconstructs a 3D spatial map of mRNA expression of the tissue with a large number of genes. A 3D spatial map of the DNA, RNA, and / or proteins can be generated for each cell in the tissue.

Systems for measuring protein translation and methods for measuring overall translation activity in viable cells or subcellular compartments is disclosed. The methods identify general ribosomal activity, if desired at sub-cellular resolution, thereby providing a signal indicating the rate of any of the steps of protein synthesis selected from initiation, elongation, termination or recycling. The translation system can be used to identify translation modulators in high-throughput-screening (HTS).

The invention relates to bioinformatics, in particular to a receptor-ligand system analysis method influencing intercellular communication. The invention provides an analysis method which comprises the following steps: carrying out primary clustering analysis on cells according to provided gene expression quantitative data; carrying out differential gene expression analysis on the provided cell population; screening the provided differential genes; providing enriched pathways and / or biological processes according to the provided relationship pairs of ligands and receptors; and / or, according tothe provided differential genes and the provided relationship pairs of the ligands and the receptors, providing the inter-cell population communication relationship corresponding to the relationshippairs of the ligands and the receptors. The analysis method provided by the invention is based on single cell sequencing instead of traditional RNA-seq, can deeply understand transcriptome under single cell resolution, can deeply understand tumor heterogeneity, and can further construct a prognosis risk model in combination with an external common data set.

Imaging techniques. Radiation is directed from a source onto a sample using an endoscope having cellular or subcellular resolution. The endoscope includes one or more fibers. The fibers have a proximate end and a distal end, and the distal end is lensless. A focal plane of the endoscope is substantially at a tip of the distal end. Radiation from the sample is directed onto a detector to diagnose or monitor the sample.

Polymer substrates including adhesion layers for activating the surface of the substrate are provided, thereby allowing the substrate to react with organic, inorganic, metallic and / or organometallic materials. The surface of the polymer substrate is coated with a metal oxide layer that is subjected to conditions adequate to form an oxide adhesion layer. Combining deposition techniques for formation of functionalized polymer surfaces with photolithographic techniques enables spatial control of RGD presentation at the polymer surfaces are achieved with sub-cellular resolution. Surface patterning enables control of cell adhesion location at the surface of the polymer and influences cell shape. Metallization of polymers as described herein provides a means to prepare metal-based electrical circuitry on a variety of flexible substrates.

Systems for measuring protein translation and methods for measuring overall translation activity in viable cells or subcellular compartments is disclosed. The methods identify general ribosomal activity, if desired at sub-cellular resolution, thereby providing a signal indicating the rate of any of the steps of protein synthesis selected from initiation, elongation, termination or recycling. The translation system can be used to identify translation modulators in high-throughput-screening (HTS).

Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.

The present invention provides high-throughput functional genomic methods for determining gene and protein function in a cellular context. Also provided are methods for identifying chemical modulators of gene and protein / enzyme activity. Assays are generated in concert with screening in an iterative process which expands the scope of biological coverage with each iteration and which uses image-based analysis to yield data at sub-cellular resolution.

The invention discloses an optical device of a flexible implantable nerve photoelectrode, which is arranged on a flexible polymer substrate and includes: an input grating, a waveguide and an output grating, the input grating is a parallel grating for coupling incident light, and the input of the waveguide The end of the waveguide is coupled to the input grating, the output end of the waveguide is coupled to the output grating, and the output grating is a focusing grating, which is used to couple and focus light on the recording electrode to provide optical stimulation with single-cell resolution. The invention also discloses the design and preparation method of the optical device. The optical device of the flexible implantable neural photoelectrode provided by the present invention provides single-cell resolution optical stimulation and in-situ recording through the design of the waveguide and grating; the small size of the device can reduce implant damage, and it has low loss and high Coupling and strong focusing; its high integration is conducive to the realization of multi-channel, high-density nerve stimulation and recording; the use of flexible polymer substrates can reduce the formation of nerve scars and achieve long-term stable work in vivo.

The invention discloses an optical device of a flexible implantable neural photoelectrode. The optical device is arranged on a flexible polymer substrate and comprises an input grating, a waveguide and an output grating, wherein the input grating is a parallel grating and is used for coupling incident light; the input end of the waveguide is coupled with the input grating; the output end of the waveguide is coupled with the output grating; and the output grating is a focusing grating and is used for optically coupling and focusing light to irradiate above a recording electrode and providing photostimulation with single cell resolution. The invention also discloses a design and preparation method of the optical device. The optical device of the flexible implantable neural photoelectrode, provided by the invention, has the advantages that photostimulation and in-situ recording with single cell resolution are provided through design of the waveguide and the gratings; the device is small in size, so that implantation damage can be reduced, and the device is low in loss, high in coupling and strong in focusing; the high integration level of the device is beneficial to realizing multichannel and high-density nerve stimulation and recording; and by adopting the flexible polymer substrate, formation of nerve scars can be reduced, and long-term in-vivo stable work is realized.

The invention relates to a method for identifying and screening human embryo bone marrow-derived mesenchymal stem cells, a related detection agent combination, a kit and related application. According to the invention, human embryo BM karyocytes (BMNC) are comprehensively screened by single cell resolution, scRNA-seq analysis is carried out by using two complementary strategies (STRT and 10X genomics), and LIFR + PDGFRB + is identified as a specific marker of MSC. The invention also finds that the hematopoietic microenvironment can be effectively reconstructed in vivo by using the LIFR, the PDGFRB and the CD45-CD31-CD235a-MSC. The invention also identifies a monopotent bone progenitor cell subset for expressing the TM4SF1 + CD44 + CD73 + CD45-CD31-CD235a-, and the monopotent bone progenitor cell subset has osteogenic potential. Therefore, the invention identifies two types of human embryo bone marrow MSCs, and the invention deepens the understanding of the human embryo bone marrow derived MSCs and further promotes the understanding of the clinical application of the MSCs.

Apparatus and methods for mechanical cell lysis with single cell resolution which requires very low applied pressure. The device can be handheld, simple to operate, requires no external power except for hand-applied pressure via a syringe, and is applicable to all cell types including yeast and bacterial cells. The device is also capable of mechanically lysing a single cell. A single cell is selected from a biological sample of interest. The single cell is lysed by application of mechanical stress in a single cell lysing apparatus having a trap structure for deterministically capturing the cell and a stress raiser that cooperates with a source of mechanical stress so as to apply sufficient force to rupture a cell. The stress raiser can be a properly designed edge of the trap or it can be a lithographically produced structure such as a nanoblade or a nanopillar.

In one aspect, a method of sorting cells in a flow cytometry system is disclosed, which includes illuminating a cell with radiation having at least two optical frequencies shifted from one another bya radiofrequency to elicit fluorescent radiation from the cell, detecting the fluorescent radiation to generate temporal fluorescence data, and processing the temporal fluorescence data to arrive at asorting decision regarding the cell without generating an image (i.e., a pixel-by-pixel image) of the cell based on the fluorescence data. In other words, while the fluorescence data can contain image data that would allow generating a pixel-by-pixel fluorescence intensity map, the method arrives at the sorting decision without generating such a map. In some cases, the sorting decision can be made with a latency less than about 100 microseconds. In some embodiments, the above method of sorting cells can have a sub-cellular resolution, e.g., the sorting decision can be based on characteristicsof a component of the cell. In some embodiments in which more than two frequency-shifted optical frequencies are employed, a single radiofrequency shift is employed to separate the optical frequencies while in other such embodiments a plurality of different radiofrequency shifts are employed.