241 results about "Chromatosome" patented technology

The present application provides methods and systems for detecting and quantifying chromosomal instability from histology images with machine-learning. Also described herein are methods for selecting treatments for a medical disease, by determining a chromosomal instability metric from histology images. The disclosed methods and systems may also be used to investigate disease progression and prognosis.

The invention relates to the technical field of biology, in particular to a molecular marker for accurately positioning centromere of chromosome of Chinese trumpet creeper, and the sequence of the molecular marker is as shown in SEQ ID NO.1 and SEQ ID NO.2. The method comprises the following steps: specifically enriching a DNA (Deoxyribose Nucleic Acid) sequence combined with a centromere specific histone CENH3 through a chromatin co-immunoprecipitation technology (ChIP), and sequencing the DNA sequence; sequencing data are analyzed to obtain a centromere sequence of the vicia villosa, and two specific repetitive sequences of the centromere of the vicia villosa are obtained after identification and optimization. Primers are designed according to the sequences, PCR amplification is carried out, amplification product sequences are marked, fluorescence in situ hybridization verification is carried out by analyzing a cytogenetics technology, it is proved that the primers are specifically distributed in a centromere area of vicia villosa, and the centromere specificity of the primers is proved. The marker can be used for genetic identification and accurate positioning of the centromere in genome research, and can also be used for cytological identification of the centromere and karyotype research such as chromosome counting and morphological analysis through centromere signal observation.

The present disclosure provides a Chinese Hamster Ovary (CHO) cell comprising one or more exogenous nucleotide sequences, wherein the one or more exogenous nucleotide sequences is inserted into a chromosomal locus of the CHO cell, wherein the chromosomal locus is located within contig NW_023276805.1 of chromosome X. Also provided herein are methods of producing a CHO cell capable of expressing a sequence of interest, methods of expressing a sequence of interest comprising culturing the CHO cell as described herein, and kits comprising the CHO cell as described herein.

The invention discloses a pichia pastoris engineering bacterium for synthesizing bakuchiol from de novo by converting methanol as well as construction and application of the pichia pastoris engineering bacterium. A heterologous p-coumaric acid synthesis pathway is introduced to neutral sites of different chromosomes of pichia pastoris, a high-yield p-coumaric acid strain is obtained through gene knockout, overexpression or heterologous expression of tyrosine and phenylalanine synthesis pathway key genes of a shikimic acid pathway, a heterologous bakuchiol biosynthesis pathway is introduced on the basis, and a high-yield p-coumaric acid strain is obtained. After overexpression of bakuchiol synthetase, endogenous overexpression or heterologous expression of MVA pathway key genes and exogenous acetyl coenzyme A supply pathway genes, methanol concentration optimization and bacterial strain His4 gene supplementation, the yield of bakuchiol is effectively increased to 91.2 mg / L and is increased by 59.8 times compared with that of an initial bacterial strain, and the yield of bakuchiol in a 15L fermentation tank reaches 692.8 mg / L. The method has the characteristics of high conversion efficiency, low production cost, convenience in preparation, wide industrial application prospect and the like.

The invention relates to a genome regulatory element analysis method based on deep learning. The method comprises the following steps: acquiring a genome DNA sequence and DNA shape information; on the basis of a shared hybrid neural network, transcription factor binding site features are extracted from a genome sequence, and binding specificity prediction is carried out aiming at the sequence level; aiming at the specificity of transcription factor binding, accurately positioning a transcription factor binding site on a nucleotide level by adopting a full convolutional neural network coupled with different models, and identifying a motif; for a chromosome three-dimensional genome, a chromatin ring is recognized in the three-dimensional whole genome based on a deep learning model, the relationship between the chromatin ring and regulatory elements in all cell lines is analyzed, and the chromatin ring represents cell type specificity and co-enrichment of transcription factor motifs among different cell lines and species. Compared with the prior art, the method has the advantages that the regulatory elements of the regulatory mechanism can be identified and analyzed by utilizing multiple information sources, and the accuracy of predicting the whole genome chromatin ring is effectively improved.

The invention provides an adaptive weight distribution chromosome stripe contrast enhancement method and system, and the method comprises the steps: firstly improving the significance of a chromosome stripe structure and an edge contour in a chromosome gray image through an edge enhancement convolution operator; carrying out chromosome monomer target detection and instance segmentation on the metaphase chromosome based on an instance segmentation network of deep learning to obtain a chromosome monomer ROI region; then, extracting a structure tensor response of the ROI region of the chromosome monomer, designing an adaptive enhancement weight of a histogram merging interval based on a normalized difference between a response value and global statistical information, and performing reconstruction and interpolation on a histogram of the image of the ROI region of the chromosome monomer; and finally, adaptively enhancing the contrast of the chromosome stripe through iterative histogram matching. According to the method, the original image texture structure is kept, and meanwhile, the definition and the distinguishability of chromosome stripes are effectively and adaptively improved.

The invention relates to a biological information data processing technology, in particular to a method for analyzing a single-cell Hi-C regulation scale chromatin band, which comprises the following steps: preprocessing single-cell Hi-C data to generate pseudo-batch Hi-C data; performing normalization processing on the pseudo batch Hi-C data to extract a Hi-C contact matrix of each chromosome; identifying and detecting false batch strips from the Hi-C contact matrix; projecting the pseudo batch strips to the original single cell Hi-C data to obtain single cell strips; and carrying out quantitative analysis on the single-cell strip in the original single-cell Hi-C data. According to the method, the regulation and control scale chromatin bands with definite endpoints and directivity can be stably identified, and a band set with remarkable statistics is output.

The present disclosure provides systems and methods for modulating the occurrence of chromosomal rearrangements, e.g., translocations, in a cell during genome editing. Embodiments are provided for reducing the occurrence of unwanted chromosomal rearrangements, and for increasing the occurrence of desired chromosomal rearrangements.

This invention is directed to a method of diagnosing bladder cancer in dogs.

The invention provides a method for identifying a structure variation linked haplotype, and particularly relates to a method for identifying an embryo structure variation linked haplotype. The method is independent of family information and is particularly suitable for identifying whether an embryo lacking family information carries a chromosomal structural variation in pre-transplantation screening and / or pre-natal screening, thereby implementing variation blocking. The invention also provides a detection product for implementing the method.

The invention relates to a method and a device for detecting chromosome uploidy. The method comprises the following steps: acquiring nanopore sequencing data of a detection sample; obtaining window division information of the reference genome; for each detection sample, determining a standard comparison sequence number of the detection sample in each window based on the nanopore sequencing data of the detection sample and the window division information; for each negative sample, eliminating discrete values in the standard alignment sequence number of each negative sample in each window, and correcting the standard alignment sequence number of each negative sample in each window to obtain a standard alignment sequence number baseline value of each window; and according to the standard comparison sequence number of the to-be-analyzed sample in each window and the corresponding standard comparison sequence number baseline value of each window, evaluating the chromosome uploidy condition of the to-be-analyzed sample. According to the method, the third-generation sequencing data is creatively applied to chromosome aneuploidy analysis through a new baseline data construction mode.

Methods of sequencing long chromosomal fragments using short read sequencing methods by using two separate transposase-based fragmentation steps.

Methods of assessing the percentage of total mRNA present encapsulated within lipid nanoparticles using the hypochromic shift of a phenothiazinium dye absorbance band are disclosed herein.

The present disclosure relates to Machado-Joseph disease (MJD), or spinocerebellar ataxia type 3 (SCA3), an autosomal dominantly inherited neurodegenerative disorder that is caused by an over-repetition of the polyglutamine-codifying region in the ataxin-3 (ATX7V3) gene. Expanded ATXN3 is prone to aggregate and disturbs diverse cellular systems, ultimately leading to cell dysfunction and death in specific neuronal populations. To date, no treatment able to reverse or stall MJD / SCA3 progression has been developed. Strategies based on the suppression of the deleterious gene products have demonstrated promising results in pre-clinical studies. Nonetheless, these strategies do not target the root cause of the disease, producing an incomplete and / or transient therapeutic effect in target cells or tissues. Recently, gene-based therapeutics, including the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) systems for gene edition, have been successfully used to permanently inactivate and correct disease-related genes, holding promise for the development of a definitive cure for inherited diseases.

The present disclosure relates to methods for detecting genomic abnormalities or variants, such as chromosomal abnormalities or structural variations, in cell populations, including engineered cell populations.

The invention relates to the technical field of molecular markers, in particular to a biomarker related to the lutein content character of sweet corn and application of the biomarker. Sweet corn selfing lines SHL01 and SHL03 are used as parents to construct an RIL population, the character data of the lutein content of the sweet corn kernels are detected through high performance liquid chromatography, QTL positioning is performed by using the character of the lutein content of the kernels, and an analysis result shows that a major QTL for regulating the lutein content of the kernels exists on a sixth chromosome of the corn, and the major QTL is used for regulating the lutein content of the kernels. The main effect QTL is located between the SNP loci Schr6: 82134355 and Schr6: 83130639, the phenotype contribution rate to the grain xanthophyll content is 27.14%, the molecular marker can be used for screening or auxiliary screening of sweet corn with relatively high xanthophyll content, the result is more accurate, a technical support is provided for molecular marker-assisted breeding, and the molecular marker has important significance for improving the taste quality of the sweet corn.

The invention provides an enhancer-promoter regulation and control network prediction model construction method, which comprises the following steps: S1, obtaining an original data set which comprises a plurality of enhancer-promoter pair data of a plurality of biological samples, and dividing the original data set into a plurality of subsets, dividing all enhancer promoter pairs on the same chromosome pair into the same subset; s2, the subsets are preprocessed, each subset comprises a plurality of data samples, and each data sample is an enhancer promoter pair, the feature vector of each data sample is a feature vector formed by splicing a sequence feature of a corresponding enhancer promoter pair, a distance feature between the enhancer promoter pairs and a chromatin open feature corresponding to the enhancer promoter pairs, and the tag of each data sample indicates whether interaction exists between the corresponding enhancer promoter pairs; and S3, iteratively constructing a plurality of symmetric decision trees to form a prediction model based on all the preprocessed subsets by adopting a category type feature gradient lifting mode.

Provided is an isolated human naive pluripotent stem cell (PSC), wherein: (i) when the naive PSC is a female PSC, then said naive female PSC has two unmethylated alleles of an X-inactive specific transcript (XIST) gene; and (ii) when said naive PSC is a male PSC, then said naive male PSC has an unmethylated allele of said XIST gene. Also provided is a culture medium which comprises an ERK1 / 2 inhibitor, a GSK3beta inhibitor, a p38 inhibitor, a JNK inhibitor, a STAT3 activator and at least one agent selected from the group consisting of: bFGF, TGFbeta 1, a PKC inhibitor, a ROCK inhibitor and a NOTCH inhibitor; or at least agent selected from the group consisting of: a TGFR inhibitor, a FGFR inhibitor, a PKC inhibitor, a ROCK inhibitor and a NOTCH inhibitor.

To provide proteins for enhancing proliferation and / or healing and / or inhibiting apoptosis of non-transformed tissue or non-transformed cells.SOLUTION: The present invention provides proteins comprising amino acid sequences encoded by nucleic acids derived from a human chromosomal region C19Orf10 termed Factor 1 and / or C19Orf63 termed Factor 2, or inhibitors thereof. Further provided is use of inhibitors of Factor 1 and Factor 2 for medical use, preferably for use in treating or preventing a disease in which angiogenesis contributes to disease development or progression.SELECTED DRAWING: None

The invention provides a method of karyotyping (for example for the detection of trisomy) a target cell to detect chromosomal imbalance therein, the method comprising: (a) interrogating closely adjacent biallelic SNPs across the chromosome of the target cell (b) comparing the result at (a) with the SNP haplotype of paternal and maternal chromosomes to assemble a notional haplotype of target cell chromosomes of paternal origin and of maternal origin (c) assessing the notional SNP haplotype of target cell chromosomes of paternal origin and of maternal origin to detect aneuploidy of the chromosome in the target cell. Also provided are related computer-implemented embodiments and systems.

The present invention discloses a transcriptome and genome accessibility dual-mode sequencing kit and method, which can simultaneously analyze the chromosome open region genome information and transcriptome information in a cell, and belongs to the field of single cell sequencing technology. The kit includes a transposase and a reverse transcription primer with a cell label 1, a first hybridization primer with a cell label 2, a second hybridization primer and a third hybridization primer with a cell label 3, and a variety of enzyme reagents; the method includes enzyme cutting, reverse transcription, terminal transferase tailing, connection, repair and amplification library and other steps. The present invention is based on a transposase with different cell marker sequences, random primers with different cell labels, connection primers and hybridization primers, to achieve hundreds of millions of molecular markers to mark single cells, and to perform ultra-high throughput transcriptome and genome accessibility sequencing, which has important application and promotion value.

The invention provides improved methods for enriching targeted genomic regions of interest to be analyzed by multiplexed parallel sequencing. The methods of the invention utilize a pool of TArget Capture Sequences (TACS), wherein the pool comprises a plurality of TACS families, each member of a family binding to the same target sequence but with different start and / or stop positions on the sequence (i.e., staggered binding of the family members to the target sequence) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The methods of the invention can be used for a variety of clinical purposes, including non-invasive prenatal testing for chromosomal abnormalities, for example using a maternal blood sample or a sample of fetal cells, assessment of maternal and paternal carrier status for genetic disorders and detection of tumor biomarkers (e.g., liquid biopsy). Kits for carrying out the methods of the invention are also provided.

A method for detecting structural variations in chromosomes by labeling single-stranded chromatids with different colored probes is disclosed. The hybridization patterns of the labeled probes generate spectral profiles that enable high-resolution detection of structural variations, facilitating the distinction between benign and deleterious structural variations. Furthermore, the spectral profiles provide information about complex structural variations that may result from more than one rearrangement of chromosomal segments. The spectral profiles can be used to generate data tables, which can then be subjected to node analysis to identify structural features of interest.

It was discovered that by binding to CTCF which is important for maintaining chromosomal structures, hSATII RNA inhibits the function thereof, changes chromosome interaction, and induces transcription of inflammation-associated genes. It has also been discovered that cell death can be selectively induced in senescent cells and cancer cells by suppressing hSATII RNA expression. From the obtained results, it has been found that cancer treatment which targets senescent stromal cells and cancer cells can be performed with a substance that suppresses hSATII RNA or a substance that increases CTCF expression. In addition, cancer can be detected early by measuring the expression and activity of hSATII RNA and CTCF, and an epigenomic change of the hSATII DNA region. Thus, it is possible to provide a therapeutic drug for a cancer associated with cellular senescence, a method for screening thereof, and a test support method.

Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process.

Disclosed herein is a non-chromosomal dynamic activity system (ADAS) derived from a parent bacterial cell comprising at least one loss of genetic function in a lyase to increase the stability of the ADAS. Also disclosed are methods of blocking sporogenesis in a parent bacterial cell in combination with a lyase deletion or other loss-of-function mutation.

Compositions and methods related to transgenic glyphosate tolerant Brassica plants are provided. Specifically, the present invention provides Brassica plants having a DP-073496-4 event which imparts tolerance to glyphosate. The Brassica plant harboring the DP-073496-4 event at the recited chromosomal location comprises genomic / transgene junctions within SEQ ID NO: 2 or with genomic / transgene junctions as set forth in SEQ ID NO: 12 and / or 13. The characterization of the genomic insertion site of the event provides for an enhanced breeding efficiency and enables the use of molecular markers to track the transgene insert in the breeding populations and progeny thereof. Various methods and compositions for the identification, detection, and use of the event are provided.

Described herein are methods for making genetically modified cells by introducing combinations of genetic variants (designed or random) or constructs (genes or otherwise arbitrary DNA) into a population of cells, and for tracking each variant combination by sequentially building an array of barcodes at a common locus (chromosomal or plasmid), termed the barcode locus. Also described are the cells made by such methods.

The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

A multi-modal pan-cancer early prediction method is disclosed, comprising: collecting cfDNA samples of i cancer populations and healthy populations respectively and extracting methylation data; merging CpG sites based on the methylation data to obtain multiple methylation intervals, screening multiple candidate marker intervals from the multiple methylation intervals, and further screening the multiple candidate marker intervals; training a first prediction model using the multiple candidate marker intervals, training a second prediction model based on the fragmentation characteristics of the chromosomes extracted from the reference genome, and training a third prediction model by extracting the methylation entropy characteristics of the chromosomes; training a multi-modal pan-cancer early prediction model through the cancer population prediction values of the first prediction model, the second prediction model and the third prediction model, which can provide precise joint early screening for lung cancer, intestinal cancer, gastric cancer, liver cancer, esophageal cancer, thyroid cancer and ovarian cancer.