645 results about "Epigenetic Profile" patented technology

Provided herein are methods of identifying a methylation status of an analyte in a biological sample. Also provided herein are methods that combine identifying the methylation status with spatial technology to identify the location of a methylation status in a biological sample.

The present invention relates to the technical field of artificial intelligence for antenna array deployment, in particular to an intelligent arrangement method for array antenna elements and a clustering epigenetic optimization method. The intelligent arrangement method for array antenna elements comprises: performing encoding for a J_K array, and initializing an epigenetic algorithm so as to generate J+K genes. The present invention uses a clustering algorithm in machine learning to divide a population into sub-populations having different characteristics. Adaptive learning is performed on a portion of individuals in each type, and an epigenetics-based inheritance operation is performed on the basis of the fitness probability of population individuals. Then, minor random mutation operations are performed to generate a new sub-population. Algorithm hyperparameters such as population size and mutation probability participate in the evolution of individual genes, and adaptively change on the basis of evolutionary states. The invention solves the problems of low convergence speed and poor obtained results in optimization processes of current L-shaped array antenna system arrangement algorithms.

Platinum-acridines and analogs thereof as cytotoxic agents for cancer treatment. Also provided methods of using hMATE1 (SLC47A1) as a biomarker to identify tumors that are likely to respond to the agents, and epigenetically sensitizing tumor tissue to anticancer drugs targeting this membrane transporter.

The invention discloses a method for male biological age assessment and aging prediction based on DNA methylation data of peripheral blood. The method comprises the following steps: screening out DNA methylation sites related to male biological age and senescence by retrieving related literatures and research results; downloading DNA methylation chip sequencing data, and screening out male data; screening the modeling database and the DNA methylation sites to obtain a modeling sample and modeling sites; establishing an epigenetic clock model; comparing the epigenetic clock model with a traditional model, and performing model evaluation; carrying out biological age evaluation and aging prediction; according to the method, the regression models are established according to three methods based on screening of global male samples, few loci with top correlation ranking are selected from the regression models, few locus models are re-established to evaluate the age and the aging degree of people, and the method has the advantages of accurate male sample positioning, low prediction cost and convenience in later product popularization.

Some aspects of this disclosure provide compositions, methods, systems, and kits for controlling the activity of RNA-programmable endonucleases, such as Cas9, or for controlling the activity of proteins comprising a Cas9 variant fused to a functional effector domain, such as a nuclease, nickase, recombinase, deaminase, transcriptional activator, transcriptional repressor, or epigenetic modifying domain. For example, the inventive proteins provided comprise a ligand-dependent intein, the presence of which inhibits one or more activities of the protein (e.g., gRNA binding, enzymatic activity, target DNA binding). The binding of a ligand to the intein results in self-excision of the intein, restoring the activity of the protein.

The present invention provides a model or tool for predicting the editing efficiency of sgRNA in a CRISPR / Cas gene editing system, in particular a CRISPR / dCas epigenetic editing system, a training and prediction method thereof, and a related computer system, computer storage medium, and application. In particular, one or more sgRNA and target gene related epigenetic features are added to an input of the model.

The invention discloses an interpretable deep learning-based innate immune gene expression prediction method, which comprises the following steps of: 1, collecting and preprocessing a DNA (Deoxyribose Nucleic Acid) promoter sequence and epigenetic modification data, and dividing a preprocessed data set into a training set and an independent test set so as to verify the prediction performance of a model; 2, constructing a human innate immune gene expression prediction network based on residual connection, a convolutional neural network and an attention mechanism; 3, performing model training on a plurality of cell lines to obtain an optimal human innate immune gene expression prediction model, and evaluating the prediction effect of the model on the independent test set; and 4, carrying out post interpretability analysis on the model through an integral gradient method, and identifying a key motif which is most likely to influence gene expression. According to the method, DNA sequence information and epigenetic modification information are extracted more effectively, and a new tool is provided for deeply understanding a regulation mechanism of an innate immune gene and developing individualized medical treatment.

The invention provides a method for constructing a rice epigenetic recombinant inbred line, and belongs to the technical field of molecular biology and genetic breeding. According to the method for constructing the rice epigenetic recombination inbred line, a fertile rice DDM1 gene function weakening mutant is obtained through a CRISPR / Cas9 gene editing technology and hybridized with wild type rice with the same background to obtain F1, then the F1 and the wild type rice are subjected to backcrossing to obtain BC1F1, single-plant offspring selfing with the DDM1 genotype being the wild type is selected, selfing is conducted for multiple generations through a single-grain transmission method, and the rice epigenetic recombination inbred line is obtained. According to the present invention, the strain population with stable inheritance is constructed, such that the rice epigenetic recombinant inbred line is obtained, and has characteristics of rich phenotype, genetic and epigenetic variation so as to provide important population resources for batch identification and the like of important agronomic shape functional sites of rice.

The invention belongs to the field of meat pigeon breeding, and particularly relates to miRNAs capable of serving as a trichomonad pigeon biomarker and application of the miRNAs. The invention provides application of miRNAs as a trichomonas pigeonae biomarker in preparation of a trichomonas pigeonae diagnostic reagent. According to the invention, high-throughput sequencing and bioinformatics analysis are simultaneously carried out on oral mucosa small RNA and transcriptome of a trichomonad infected positive individual and a healthy individual for the first time, so that an epigenetic molecular mechanism of oral mucosa tissue of a trichomonad infected regulation body is explained by mining a key significant difference miRNA-mRNA network.

The invention provides a beet genetic diversity analysis method based on whole genome re-sequencing. The method comprises the steps of PacBio HiFi library construction, computer sequencing, data information analysis, assembly quality evaluation and Hi-C auxiliary genome assembly. The invention further provides application, and the high-continuity beet reference genome is used for analyzing beet intraspecific genetic diversity and developing high-density molecular markers. According to the method, the high precision of HiFi, the super-long read length of Nanopore and Hi-C space interaction data are combined for the first time, the problems of repeated sequence and complex SV analysis are solved, and all-round breakthrough of genome continuity, annotation integrity, genetic diversity coverage and epigenetic integration is achieved.

The invention relates to the technical field of gene sequencing, in particular to a silkworm gene sequencing path optimization system and method based on a hybrid parallel genetic algorithm. According to the technical scheme, the method comprises the steps of data preprocessing and feature modeling, hybrid parallel genetic algorithm optimization, dynamic path planning and resource allocation and multi-omics verification and result output. Reference is provided for assembling path planning by recognizing the repeated area, local optimum is avoided by means of the hybrid parallel genetic algorithm, efficient assembling of the high-complexity repeated area is achieved, standardization processing is carried out on data, errors caused by data differences are reduced, and the accuracy of assembling path planning is improved. The multi-omics feedback correction module integrates transcriptome and epigenetic data, corrects an assembly result and inhibits error accumulation, and meanwhile, based on deep Q network model reinforcement learning and a dynamic resource scheduling module, assembly strategies and resource allocation are dynamically adjusted, efficient utilization of computing resources is achieved, and resource waste is reduced.

An epigenetic regulatory factor ZmULT1 related to corn grain size regulation and heat stress response and the use thereof, which solve the technical problems of how to increase the grain size and / or heat resistance and / or lodging resistance of corn. Use of a substance for reducing the content of the protein ZmULT1 or a substance for inhibiting the expression of the encoding gene of the protein ZmULT1, which use is any one of the following: P1, the use in increasing the grain size of corn; P2, the use in improving the heat resistance of corn; P3, the use in increasing the lodging resistance of corn; and P4, the use in plant breeding. The homozygous mutant strain with knockout of the ZmULT1 gene has a reduced plant height and an increased grain size, and exhibits significant heat stress resistance, this indicates that the research on the gene can further enrich the use of epigenetics in crops and is of important significance for improving the grain size, heat resistance and lodging resistance of corn.

The invention discloses a single-cell multi-modal data integration method based on an attention mechanism and a graph variation auto-encoder. The method comprises the following steps: step 1, pre-processing multi-modal data and constructing a cell relation graph; step 2, cross-modal adjacency matrix fusion based on multi-head attention; step 3, performing graph variation auto-encoder training and multi-objective optimization; 4, performing multi-target loss calculation and model joint optimization; and 5, carrying out low-dimensional embedding extraction and clustering analysis on the cells. According to the method, single-cell transcriptome and epigenetic group data are fused through a multi-head attention mechanism, and low-dimensional embedding representation of cells is learned by using a graph variation auto-encoder, so that efficient integration and clustering analysis of single-cell multi-modal data are realized.

Provided herein are epigenetic-modifying DNA-targeting systems, such as CRISPR-Cas / guide RNA (gRNA) systems, for the transcriptional repression of Hepatitis B viral (HBV) genes to promote a cellular phenotype that leads to the reduction of HBV infection. In some embodiments, the epigenetic-modifying DNA-targeting systems bind to or target a target site of at least one gene or regulatory element thereof in a Hepatitis B viral DNA sequence in cell. In some aspects, the provided systems relate to the transcriptional repression of one or more Hepatitis B viral gene and / or regulatory element thereof. In some aspects, also provided herein are methods and uses related to the provided compositions, for example in repressing Hepatitis B viral replication and expression in connection with Hepatitis B infections.

The invention belongs to the field of biosensing detection, and particularly relates to an ATP (adenosine triphosphate) nucleic acid aptamer based on m6A epigenetic base modification and application of the ATP nucleic acid aptamer. The invention provides a nucleic acid aptamer and a nucleic acid aptamer sensor. On the basis of recognition and binding specificity of a nucleic acid aptamer probe to a target, a single-point methylation closed switch type functional probe is constructed, and living cell and living body imaging detection of endogenous demethylase is realized. Taking ATP and an aptamer thereof as an example, m6A methylation modifies key sites of the aptamer so as to influence the binding stability between the aptamer and a ligand, after endogenous FTO demethylation, the aptamer recovers active sites, can be rapidly bound with ATP and is driven to allosteric to release fluorescence, and in-situ instant detection of FTO is realized.

The technology disclosed relates to detecting gene conservation and expression preservation. In particular, the technology disclosed relates to detecting gene conservation and epigenetic signals for a reference genetic sequence in comparison to a variant of the reference genetic sequence at base resolution through the generation of a plurality of alternative representations of the sequence in chromatin form which may represent evolutionary conservation, transcription initiation, or epigenetic signals, mapping the plurality of alternative chromatin sequences to a gene expression alterability classifier to generate a gene expression class prediction for the variant, and mapping the alternative chromatin sequence to a pathogenicity predictor to detect pathogenicity of variants.

The present disclosure relates to epigenetic editor compositions for gene activation and methods for epigenetic modification of target genes using the same. Aspects of the disclosure relate to compositions and methods comprising epigenetic editors for epigenetic modification of FOXP3, as well as nucleic acids and vectors encoding the same. Also disclosed are cells epigenetically modified by the epigenetic editors.

The invention relates to the fields of epigenetic regulation and tumor treatment, and aims to evaluate that the cell distribution of the mutant is consistent with that of H3 by constructing Bas-2B (H3K9R) and Bas-2B (H3K18R) stably transfected cell strains and analyzing the cell positioning condition of the H3K9R / H3K18R mutant through an immunofluorescence technique. According to the present invention, a Western blotting technology is adopted to detect the H3K9 / H3K18 lactic acid modification level of Bas-2B (H3K9R) and Bas-2B (H3K18R) cells compared to control cells so as to verify the influence of the H3K9R / H3K18R mutant on the H3K9 / H3K18 lactic acid modification; after Bas-2B (H3K9R), Bas-2B (H3K18R) cells and control cells of the Bas-2B (H3K9R) and the Bas-2B (H3K18R) cells are subjected to nickel compound exposure treatment, the influence of the H3K9R / H3K18R mutant on the nickel compound induced lung cancer is evaluated through a soft agar cloning formation experiment. An AGS cell line stably transfecting H2BK16R is constructed, and the cell localization condition of the H2BK16R mutant is analyzed through an immunofluorescence technology. According to the present invention, a Westernbloting technology is adopted to detect the lactic acid modification level of AGS (H2BK16R) cells so as to verify the influence of the H2BK16R mutant on the H2BK16 lactic acid modification; the influence of the H2BK16R on the malignant proliferation ability of the gastric cancer is researched through a soft agar clone formation experiment.

Provided is a gene ZmFIE2 for regulating maize kernel development, an encoded protein thereof, an InDel molecular marker, and a use thereof, aiming to solve the current technical problems of low maize haploid induction rate, long breeding cycle, and low maize yield. An InDel molecular marker for detecting ZmFIE2 mutants was screened out, and a primer for InDel molecular marker was designed, the InDel molecular marker and the primer thereof can be applied to the breeding of maize kernel size varieties and maize haploid or diploid lines. From the epigenetic level, it was found that ZmFIE2 regulates the development of maize embryo and endosperm, affects the accumulation of kernel storage materials, and affects the cell cycle process of endosperm cells, which has great value in improving maize yield. By using multiple created ZmFIE2 allele mutants, research has found that the loss of ZmFIE2 function can directly determine the division of endosperm cells and apomixis, which will provide new gene resources and new ways to achieve high-frequency haploid induction and heterosis fixation in maize.

The invention belongs to the technical field of biological analysis and evaluation, and particularly relates to a stem cell differentiation process multi-modal image fusion and intelligent evaluation method, which comprises a stem cell differentiation process multi-modal image fusion method: on the basis of constructing a multi-modal near-physiological mechanics microenvironment, carrying out image analysis by adopting the multi-modal image fusion method; an intelligent evaluation method for the stem cell differentiation process: developing an intelligent evaluation method based on deep learning driving on the basis of constructing a multi-modal near-physiological mechanical microenvironment, and revealing a mechanical-epigenetic regulation mechanism; the synergistic application of the two solves the core observation and regulation problems in stem cell differentiation research, and provides an industrialized intelligent platform for regenerative medicine. According to the method, the data integrity can be improved, the resolution limitation is broken through, the experiment process is accelerated, accurate mechanism analysis can be realized, automatic decision making is promoted, and the research and development cost is reduced.

Analysis of cell-free DNA (cfDNA) fragment ends in patients with cancer provide a direct link between epigenetic changes and cfDNA fragmentation for non-invasive disease detection and treatment of patients.

Disclosed herein are methods and compositions for predicting tumor content e.g., tumor content in a sample and tumor burden of an individual. Generally, methods and compositions involve determining methylation statuses of two or more sequential CpG sites in one or more genomic locations using nucleic acids of the obtained sample. The methylation statuses of the two or more sequential CpG in genomic locations are used to distinguish between reads of nucleic acids that are likely derived from cancer and reads of other nucleic acids that are unlikely to be derived from cancer. Distinguishing reads that are likely derived from cancer enables the prediction of tumor content in a sample.

Disclosed herein are artificially synthesized nucleic acid constructs to guide an epigenetic modification for at least partially silencing or activating a target gene in an organism such as a plant or seed, and formulations thereof. Also disclosed are methods of applying such nucleic acid constructs to the plant or to the seed. Also disclosed are engineered seeds and plants obtained by the epigenetic modification.

Methods of predicting a chromatin state metric associated with a genomic region in a sample are provided. The methods comprise: receiving sequence data comprising genetic data and epigenetic data indicative of the presence of one or more epigenetic bases including methylated cytosine and hydroxymethylated cytosine at one or more genomic positions, the one or more epigenetic bases, the genetic data and epigenetic data obtained from a single assay; and predicting for each base or set of bases of the genomic region and using the sequence data associated with the genomic region, a value of the chromatin state metric, wherein the predicting is performed using a machine learning model.

The invention belongs to the technical field of biological detection, and particularly relates to a bisulfite-free detection kit for specific site 5-methylcytosine and a detection method thereof. According to the method, a TAPbeta treatment method is adopted, 5hmC is sealed through beta-GT, 5mC oxidation is carried out through TET, and 5mC is reduced into dihydrouracil (DHU) through pyridine borane, so that the apparent difference between 5mC and C and 5hmC is converted into single nucleotide polymorphism difference. In addition, a flow microsphere technology based on PNA-assisted click chemical connection starting is established to detect DNA methylation specific sites. A PNA clip is innovatively introduced into click chemical connection, and non-specific connection is inhibited. Target sequence enrichment, signal amplification and signal acquisition are carried out through surface-functionalized magnetic nanoparticles, and the detection sensitivity is improved to fM. The invention provides a new tool for high-specificity and high-sensitivity epigenetic marker detection.

Provided herein are epigenetic-modifying DNA-targeting systems, such as CRISPR-Cas / guide RNA (gRNA) systems, that bind to or target multiple genes or regulatory elements thereof, for instance in a T cell. In some aspects, the provided epigenetic-modifying DNA-targeting systems promote increased transcription of one or more first genes and promote repressed transcription of one or more second genes. In some aspects, the provided epigenetic-modifying DNA-targeting systems modulate a T cell function, such as a T cell phenotype or activity. Also provided herein are polynucleotides, vectors, cells, methods, and uses related to the provided epigenetic-modifying DNA-targeting systems, for example in modulating T cells, such as in connection with methods of adoptive T cell therapy.

The disclosure provides, in various embodiments, fusion proteins comprising a DNA-binding domain, a DNMT3A-binding domain, and a H3K4me0; and polynucleotides and vectors encoding one or more of the fusion proteins. The disclosure also provides, in various embodiments, gene-delivery systems, cells, compositions (e.g., pharmaceutical compositions) and kits comprising one or more of the fusion proteins polynucleotides, or vectors; methods of epigenetically modifying a genomic locus in a cell; and methods of treating a subject (e.g., a human) in need thereof.

Provided herein are methods related to detecting genetic and epigenetic information in a single workflow, as well as methods of treatment, uses, systems, and computer readable storage media related thereto. These methods allow, e.g., for detection of genetic variants and epigenetic modifications (e.g., methylation level) in a single workflow and / or from a single sample (e.g., a DNA sample).

Provided are methods for creating a diagnostic model for determining a disease of a subject, methods to identify disease-associated metaepigenomic biomarkers and methods to employ these biomarkers to accurately diagnose certain diseases from a tissue or liquid biopsy sample, based on epigenetic data from the subject's genome and microbial genomes contained within that subject

A method and device for predicting the bull semen quality. The method comprises: on the basis of the variation of methylation level values, using known methylation spectrum data of methylation sites of a bull sperm to select 83 methylation sites; on the basis of an elastic net regression algorithm, using the selected methylation sites to construct an epigenetic clock; and using the epigenetic clock to predict the age of a bull to be detected. The age of a bull can be predicted on the basis of an epigenetic clock, and the bull semen quality can be predicted on the basis of an epigenetic acceleration. The present invention can be applied to bull variety breeding and bull breeding.