463 results about "Epigenetic Profile" patented technology

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.

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 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.

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.

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.

This invention provides a method for hypertension risk assessment, relating to the field of epigenetic detection technology. It includes: performing event alignment and residual modeling on a qualified signal set to establish a base probability at the locus level and forming baseline features through neighborhood consistency screening; constructing a tunneling sensitization model and contextual attention, fusing discriminative and generative evidence to obtain enhanced features; quantifying IGF2BP3 and aligning and fusing it with the enhanced features; constructing an IGF2BP3-mediated metabolic network based on this, performing time-series modeling and stability assessment, and extracting final-state features; fusing the final-state risk vector with multi-gene scores to complete adaptive grading and compliant report generation. This method is robust, interpretable, and easy to deploy.

The invention relates to the technical field of genes, in particular to preparation of a Trmt61a enzyme activity deleted zebrafish model, and the Trmt61a enzyme activity deleted zebrafish model is used for preparing a zebrafish strain which stably inherits trmt61aD181A-P2A-EGFP knock-in zebrafish strain. According to the invention, trmt61a D181A mutation site specificity is introduced into a zebra fish genome by using a CRISPR / Cas9 technology, and a zebra fish model with Trmt61a catalytic activity deficiency and tRNA m1A modification level significantly reduced is obtained. The zebrafish model fills the existing research blank, provides an available in-vivo research model for biological development regulation mechanism research related to tRNA m1A epigenetic modification and pathological mechanism analysis of diseases (such as malignant tumors and hematopoietic dysfunction), and can be directly used for exploring the core effect of the epigenetic modification in development and diseases.

Disclosed are methods and compositions for gene-specific epigenetic editing involving contacting a gene or gene promoter with a gene-specific fusion complex containing a DNA demethylase enzyme. The methods include demethylating one or more nucleotides within the gene, promoter, or anticipated regulatory region, resulting in epigenetic editing of the gene, nucleotides, regulatory motif, or promoter. This demethylation process serves to test the mechanistic significance of gene demethylation or enhance the transcriptional responsiveness of the gene.

This invention belongs to the field of plant genetic engineering technology, specifically relating to the application of H3K27me3 in regulating the cotton response to potassium chloride stress. By integrating CUT & Tag chromatin analysis and RNA-seq, this invention demonstrates that potassium chloride stress induces a reduction in H3K27me3 deposition across the entire genome, accompanied by characteristic stress phenotypes in cotton seedlings. Inhibition of H3K27me3 using RDS 3434 significantly improved KCl-induced physiological damage, confirming the functional correlation between this epigenetic marker and stress tolerance. Furthermore, virus-induced gene silencing confirmed that genes associated with H3K27me3 are important components of the cotton ion stress response network. Therefore, this invention elucidates the epigenetic landscape regulating adaptation to potassium chloride stress.

Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer`s disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolor fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque- associated microglia during neurodegeneration. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration.

The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample: the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample: the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxy methylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcy tosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample. Compositions, kits, and related methods are also provided, including an embodiment in which truncated sequencing adapters are used in conjunction with barcoded PCR primers.

The present disclosure is directed to compositions and methods for increasing expression of target genes in a cell, e.g., using an expression activator that comprises a targeting moiety that binds a target gene and an effector domain comprising an epigenetic activating domain. Systems comprising two or more expression activators are also disclosed.

The invention includes improved methods and compositions for reduction of a C5-C6 double bond of a cytosine. In particular, the improved methods and compositions for reduction of a C5-C6 double bond of a cytosine is via enzymatic means, not via chemical means. In particular, the disclosure is directed to methods of converting 5,6-dihydro-fC (fC) and / or 5,6-dihydro-caC to 5,6-dihydro-U (DHU). In particular, the disclosure is directed to methods of converting 5fC and / or 5caC to DHU. In addition, the disclosure is directed to methods for detection of epigenetic cytosine modification, particularly cytosine methylation, using ene reductases to reduce the C5-C6 double bond of cytosine.

The invention belongs to the technical field of biology, and particularly relates to a construction method of epigenome edited zebrafish, sgRNA of a targeted zebrafish runx2b gene promoter region and application of the sgRNA. The invention provides a construction method of epigenome edited zebrafish, which comprises the step of carrying out methylation editing by using a CRISPR / dCas9-methyltransferase system targeting runx2b gene promoter region, thereby inhibiting runx2b gene expression and reducing intermuscular bone formation. According to the method, the expression level of the runx2b gene is accurately regulated and controlled through an epigenetic editing technology on the premise that a DNA sequence is not changed, and formation of fish intermuscular bones is effectively reduced. The zebra fish F0 treated by the method represents that the runx2b mRNA expression level is obviously reduced, and the intermuscular bones of the eleventh to sixteenth sarcomedo regions of adult F0 generation fish are obviously shorter than those of a control group, and the shortening range reaches 23.3% to 38.8%. Besides, the method provides theoretical basis and technical support for improving fish economic traits by accurately regulating and controlling the expression mode of the key economic trait gene and simultaneously keeping the integrity of genome DNA (Deoxyribose Nucleic Acid).

The present invention relates generally to compositions, systems and methods for modulating hepatitis B virus (HBV) by targeting gene repression. In particular, the present invention provides an epigenetically modified DNA targeting system, such as a CRISPR-Cas / guide RNA (gRNA) system, for transcriptional repression of hepatitis B virus genes to promote cell phenotypes that lead to reduced HBV infection. In some embodiments, the epigenetically modified DNA targeting systems of the present invention bind to or target a target site of at least one gene in the hepatitis B virus DNA sequence or a regulatory element thereof in a cell. In some aspects, the systems provided herein relate to transcriptional repression of one or more hepatitis B virus genes and / or regulatory elements thereof. In some aspects, the invention also provides methods and uses associated with the provided compositions, such as in repression of hepatitis B virus replication and expression associated with hepatitis B infection.

The invention discloses a recombinant genetically engineered bacterium for producing a micafungin precursor FR901379 and an application of the recombinant genetically engineered bacterium. The recombinant genetically engineered bacterium for producing the micafungin precursor FR901379 is obtained by performing overexpression on an epigenetic modification factor in a phomopsis sheathing genome and performing screening to obtain the recombinant genetically engineered bacterium for producing the micafungin precursor FR901379. The epigenetic modification factor comprises a histone methyltransferase (Dot 1), a histone methyltransferase (Set2) or a histone deacetylase (Rpd3). The yield of FR901379 produced by the engineering strain is increased by 40% compared with that of an original strain. The method disclosed by the invention has the characteristics of simplicity and convenience in operation, high transformation efficiency and good genetic stability.

The invention discloses a mycoplasma pneumonia infection severity and complication marker and application thereof in preparation of a mycoplasma pneumonia infection diagnostic kit, and belongs to the field of epigenetics and microbiology. In the invention, it is studied that the editing levels of six RNA editing sites of five genes in the severe side and the control side of an MPP patient are obviously different, namely CCRL2: chr3: 46408483, CCNI: chr4: 77058527, CTSS: chr1: 150732881 / 150732032, IRAK3: chr12: 66194142 and LYN: chr8: 56010885, the five different genes are associated with the severe degree and complications of MPP, and the RNA editing combination has very high accuracy in diagnosing the severity and complications of MPP.