36 results about "Centromere" patented technology

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 invention relates to the field of molecular cytogenetics and potato ploidy breeding, in particular to a potato ploidy identification method for marking and counting chromosome centromere based on a potato CENH3 antibody and a ploidy detection kit. According to the method, the chromosome centromere is marked by specifically recognizing the antibody of the potato centromere nucleosome core histone CENH3 and combining the immunofluorescence technology, so that the accurate counting of the chromosome centromere is realized at the single cell level, and the ploidy of potatoes is judged. The method comprises the following steps: preparing a leaf cell suspension, sequentially incubating a potato CENH3 antibody and a labeled secondary antibody after immobilization, and observing and counting by a microscope after redyeing. The method has the advantages of high species specificity, high throughput and low cost, is not limited by special material taking parts of root tips or shoot tips and cell division periods, can accurately identify the uploid and aneuploid of potatoes, and provides an efficient tool for potato germplasm resource evaluation and cross breeding.

The invention discloses a reference-level high-quality genome assembly method, which is characterized in that a compPoFi tool integrates a plurality of high-performance assembly tools, does not need expensive ONT sequencing, and can realize multi-species reference-level high-quality genome assembly only by adopting a second-generation Illumina short read length, a third-generation HiFi (Revio platform, average read length of 25kb) and Hi-C chromatin conformation capture sequencing. The sequencing cost is obviously reduced. In order to solve the problem of genome assembly with a high transposition element ratio, the average read length of a HiFi sequencing library is required to reach 25kb so as to cross most transposition elements. Under the standard, a developed compPoFi tool is utilized, the assembly of the high-quality chromosome scale reference genome of the field worst weed beckmannia syzigachne is completed for the first time, all telomere and centromere regions are identified, and the 2.8 G beckmannia syzigachne genome is assembled to the near telomere to telomere (T2T) level. The invention provides a more economical high-quality genome assembly scheme, and lays a research foundation for understanding rapid adaptation and evolution of weeds under environmental stress.

The invention discloses an annotation method for analyzing a genome centromere region structure, and belongs to the technical field of biological genes. And prerequisites are needed. The method comprises the following steps: firstly, analyzing repetitive monomers of a centromere sequence based on a heuristic strategy, and judging the centromere sequence; when the serial repetition units are identified, an adjacent matrix is obtained based on serial repetition unit information, the analysis problem of the HORs is converted into a graph theory problem of searching a specific structure in the adjacent matrix, and a sliding window strategy is combined to refine the structure analysis result of the HORs. Compared with the prior art, the method has the advantages that the length of the tandem repeat unit can be detected more accurately, and the defect that two continuous tandem repeat units are identified as a single tandem repeat unit by TRASH is effectively overcome. The method has an obvious efficiency advantage. When a human genome centromere area is analyzed, the method is 10 times faster than a current method while the precision is guaranteed.

The invention discloses a Rongchang pig T2T genome assembly method. The method comprises the following steps: 1) collecting and sequencing a sample; 2) genome investigation and assembly; 3) genome annotation; wherein in the sequencing step, three sequencing technical means, namely, a three-generation gene sequencing technology PacBio, Nanopore PromethION 48 short reading and chromatin conception capture (HiC), are adopted, and the Rongchang pig genome is subjected to sequencing and sequence splicing together. The Contig N50 value of the genome is nearly three times that of Sscrofa11.1, and the improvement is mainly embodied in a complex genome region (centromere and telomere regions), so that the genome becomes the most complete genome available at present.

The present application relates to the technical field of in-vitro diagnosis, and in particular to a cell detection kit for the abnormality of human chromosomes 3 and 10 and a use thereof. A probe set comprised in the kit uses a specific chromosome locus or a centromere as a target, or uses a combination of a plurality of specific chromosome loci or centromeres as a target, so that the kit can rapidly and effectively detect a variety of cancer samples comprising lung cancer, breast cancer, intestinal cancer, esophageal cancer, bladder cancer, liver cancer, gastric cancer, pancreatic cancer, ovarian cancer, cervical cancer or prostate cancer, and is suitable for cancer diagnosis and development and popularization of prognostic products.

Described herein are artificial centromeres and artificial chromosomes comprising the artificial centromeres and a cargo sequence, methods of designing and making such artificial centromeres and artificial chromosomes, cells comprising such artificial centromeres and artificial chromosomes, and methods of using such artificial centromeres and artificial chromosomes for stable passaging of artificial chromosomes and expression of cargo sequences in a mammalian cell.

The invention discloses a centromere sequence extraction and chromosome classification method and a related device, and belongs to the technical field of bioinformatics. The method comprises the following steps: acquiring a second-generation sequencing sequence data file and a corresponding reference genome sequence file, and segmenting the second-generation sequencing sequence data file into N sub-files according to a set parallel thread count; creating N parallel thread units, extracting feature vectors of the sequencing sequences in the N sub-files by adopting a DNA sequence feature extraction model, inputting the feature vectors into a pre-constructed centromere sequence recognition model, and screening out candidate centromere sequences; and converting each candidate centromere sequence into a feature vector by using the DNA sequence feature extraction model, and inputting the feature vector into a pre-constructed chromosome classification model to obtain a chromosome attribution result. According to the method, by combining data parallel preprocessing, machine learning and a deep learning model, the centromere region sequence can be identified in large-scale massive next-generation sequencing data, and the chromosome to which the centromere region sequence belongs can be further predicted.

The invention belongs to the technical field of biological information, and discloses a plant centromere identification and boundary defining method, which specifically comprises the following steps: carrying out quality control on CENH3 ChIP-seq original sequencing data; comparing the reads after quality control to a target plant reference genome, calculating the average coverage or ChIP signal of each bin according to a preset window after file conversion, and generating a CENH3 distribution curve; identifying a CENH3 binding peak region by using signal enrichment analysis software; and selecting a section of which the continuous strength is higher than a preset threshold value as a core centromere, extending towards two sides at a fixed step length until the signal strength is lower than the preset threshold value, determining the starting and ending positions of the boundary, and outputting. According to the plant centromere recognition and boundary defining method, automation and repeatable recognition of a centromere area are achieved, the boundary resolution and accuracy are improved, the method is suitable for double plants, and a reliable tool is provided for chromosome structure research and crop breeding.

The present application relates to the technical field of in-vitro diagnosis, and in particular to a cell detection kit for the abnormality of human chromosomes 3 and 10 and a use thereof. A probe set comprised in the kit uses a specific chromosome locus or a centromere as a target, or uses a combination of a plurality of specific chromosome loci or centromeres as a target, so that the kit can rapidly and effectively detect a variety of cancer samples comprising lung cancer, breast cancer, intestinal cancer, esophageal cancer, bladder cancer, liver cancer, gastric cancer, pancreatic cancer, ovarian cancer, cervical cancer or prostate cancer, and is suitable for cancer diagnosis and development and popularization of prognostic products.

The disclosure provides for methods of constructing synthetic chromosomes including the steps of providing host cells with an endogenous chromosome, transforming a cloning vector and a cloning cassette into the host cells, excising target genomic nucleic acids from the endogenous chromosome, recombining the excised target genomic nucleic acids with the cloning cassette via homologous recombination to form heterologous vectors comprising cloned sequences, extracting the heterologous vectors containing the cloned sequences from the host cells, digesting the heterologous vectors with a restriction endonuclease to release the cloned sequences from the heterologous vectors to provide released cloned sequences, and introducing the released cloned sequences, a centromere cassette, and a yeast artificial chromosomes or bacterial artificial chromosomes into a second host cell, such that the released cloned sequences, the centromere cassette, and the YAC or BAC recombine with one another via homologous recombination to produce the synthetic chromosome.

The invention relates to the technical field of biology, in particular to antigen polypeptide of mandulapalka functional centromere histone CENH3 and application of the antigen polypeptide. The amino acid sequence of the antigen polypeptide is shown as SEQ ID No: 3. The polypeptide is used for conventionally immunizing New Zealand white rabbits to prepare antiserum and an anti-CENH3 protein antibody subjected to antigen affinity purification. The verification proves that the antibody is effective and reliable, and the functional centromere of the cyperus esculentus can be accurately identified. The method has a wide application prospect in the research fields of molecular cytogenetics, genomics, epimics and the like of cyperus esculentus.

Compositions and methods for deleting a target DNA sequence from a target DNA molecule are provided. The disclosed GRAND-Del system employs a pair of pegRNAs that target nearby genomic sites and have mutually complementary sequences to jointly form a template for inserting an exogenous sequence into a target DNA molecule to replace a target DNA sequence to be deleted. The deleted chromosomal DNA sequence can be degraded, randomly inserted (resulting in random transposon), or inserted at a target location, such as at different locations of the same chromosome or in different chromosomes (resulting in targeted transposon) or in centromere-containing plasmids (resulting in the production of artificial chromosomes).

The present invention relates to the technical fields of bioinformatics and molecular cytogenetics, and particularly relates to a method and application for chromosome centromere counting based on Nuf2 antibody. The present invention comprises the following steps: performing chromosome centromere counting on the Nuf2 antibody and the centromere-specific protein Nuf2 through an immunofluorescence reaction, so as to directly observe the number of chromosome centromeres, and thus efficiently and rapidly determine the number of chromosomes. In addition, in view of the high conservation of the centromere-specific protein Nuf2 in eukaryotes, the present invention also provides the application of this method in identifying the ploidy of plants. The operation is simple, the cost is low, the efficiency of ploidy identification is significantly improved, and a general technical platform is provided for genetic breeding.

The invention discloses a peanut chromosome centromere specific molecular marker and application thereof, particularly relates to the technical field of molecular cytogenetics, and aims to solve the technical problem that peanut chromosome centromere is difficult to accurately recognize in the prior art. According to the specific molecular marker of the peanut chromosome centromere, the molecular marker comprises CentAh106 or CentAh342; the nucleotide sequence of the CentAh106 is as shown in SEQ ID NO. 1, and the nucleotide sequence of the CentAh342 is as shown in SEQ ID NO. 2.

The invention discloses an identification method of a sequence participating in potato centromere relocation, and belongs to the technical field of plant heredity and molecular biology. According to the method, T2T-level genome data and CENH3 ChIP-seq data of different haplotypes of potatoes are integrated, sequence screening, annotation and function prediction are carried out by utilizing a bioinformatics analysis tool, and a satellite DNA sequence which is 2-3Kbp in length, is highly conserved in the same haplotype and can be specifically combined with CENH3 protein is identified. The sequence can induce CENH3 to deposit in a non-native centromere area, so that functional relocation of centromere is realized, and a core molecular element and a technical support are provided for artificial centromere construction, plant chromosome engineering and accurate genome operation. The method solves the problems that in the prior art, a functional sequence for clearly inducing centromere relocation is lacked, a CENH3 targeted recruitment mechanism model is not established and the like, and has a wide application prospect.

The invention relates to a breast cancer HER2 gene and muscle epithelium marker synchronous detection fluorescence double-staining kit and a method thereof. The double-staining kit comprises a HER2 gene specific fluorescence labeling probe and a CEP17 centromere probe; an anti-CK5 / 6 antibody and a corresponding fluorescently-labeled secondary antibody; the EDTA buffer solution is used for antigen repair; the invention discloses a dyeing buffer solution capable of ensuring double dyeing compatibility. The method is suitable for accurate detection of breast cancer samples with limited infiltration components in a dark field, synchronous analysis of HER2 genes and myoepithelium markers on the same slice is realized, the problems of inaccurate positioning, low efficiency, specimen waste, treatment delay and the like in the existing FISH detection technology are solved, and the method has the advantages of improving the detection accuracy, improving the efficiency, reducing tissue consumption, reducing the cost and the like. And the clinical application potential is improved.

The present application belongs to the field of biotechnology and medicine, and relates to a centromere binding protein Cbf1, a coding gene thereof and application. Specifically, the present application provides a Cryptococcus virulence related protein, which is a centromere binding protein Cbf1. Meanwhile, the present application also provides application of the centromere binding protein Cbf1 in preparation of a medicine, CBF1 Gene knockout leads to reduction of tolerance of the strain to 37 DEG C, oxidation and cell wall pressure, and reduction of melanin production, so that the protein can be used as a drug target and applied to research and development of a new drug for treating diseases caused by Cryptococcus.

The invention discloses a crop centromere automatic identification method, and belongs to the field of crop centromere identification, and the method comprises the steps: constructing a training set according to a verified CENH3 binding region sequence and a random non-centromere region sequence; extracting multi-dimensional features of the DNA sequence according to the training set; training a CNN-RNN hybrid model according to the multi-dimensional features and obtaining a prediction model used for identifying centromere; and identifying the target genome sequence according to the prediction model to obtain a candidate centromere region. The method does not depend on repetitive sequences any more, and directly utilizes the CENH3 binding characteristics, so that the prediction accuracy is improved. And cross-species application can be realized, so that the general applicability of centromere region identification is improved.

The invention discloses a yarrowia lipolytica expression vector and application thereof, and particularly discloses a nucleic acid molecule C-M6, and the DNA sequence of the nucleic acid molecule C-M6 is SEQ ID NO: 23; the invention also discloses a vector containing the nucleic acid molecule, the vector comprises the following elements: centromere, an autonomous replication sequence, a resistance gene, a promoter, a selection marker gene and a terminator, and the centromere is the nucleic acid molecule in claim 1. The nucleic acid molecule provided by the invention is used as a centromere in a yeast carrier, and compared with a traditional carrier carrying ARS and a carrier carrying a wild type centromere sequence, the constructed yeast carrier has higher stability and can be used for expressing target protein to obtain higher protein expression yield.

The present invention concerns DNA motifs for identifying, isolating and assembling the nucleotide sequence of a chromosome centromere. In particular, these motifs are designed for the identification, isolation, and assembly of the nucleotide sequence of a chromosome's centromere. Additionally, the invention encompasses methods for validating these sequences within any human genome. The primary application of these DNA motifs and methods lies in their ability to facilitate the detailed characterization and analysis of centromeres and chromosomes. This innovation stands to make significant contributions to the fields of genomic research and diagnostic genetics, offering a novel approach to centromere study and genome assembly.

The invention discloses a preparation method of chromosomes of tiny insects trichogramma dendrolimus, and belongs to the technical field of chromosome preparation. Comprising the following steps: (1) preparing a pre-pupa material: selecting corcyra cephalonica eggs parasitized by trichogramma dendrolimus for 4-8 days, and cutting out a trichogramma dendrolimus pre-pupa; (2) pretreatment: pretreating the pre-pupa material in a colchicine solution; (3) low-permeability treatment: carrying out low-permeability treatment on the pretreated material in a low-permeability solution; and (4) fixing, uncovering, dyeing and sealing the material subjected to the low-permeability treatment. The invention provides a simpler trichogramma dendrolimus chromosome slide preparation method, chromosome slides with clear forms can be prepared in batches, the dispersion degree of chromosomes is large, the length, centromere position, arm ratio and other characteristics of the chromosomes can be observed more clearly, the chromosome characteristics are determined through karyotype analysis, and the chromosome slide preparation method is suitable for large-scale production. And a foundation is laid for cell level research and genomics deep research of trichogramma dendrolimus.

The invention relates to a centromere sequence alignment method based on phylogenetic information and pairing editing distance, and belongs to the technical field of centromere sequence alignment. According to the algorithm provided by the invention, a collinearity relation is constructed by utilizing phylogenetic information of a satellite sequence and a pairing editing distance. According to the method, firstly, a conservative selection mode is adopted, and an editing distance (ED) threshold value is gradually increased until a collinear framework between two sequences covers more than 20% of the total number of monomers or 100 monomers; according to the method, an ordered chain with the highest comprehensive score is identified through DAGchainer software according to sequence homology and genome coordinates by integrating the physical distance between adjacent elements, the sequence and the E value score of BLAST, and a collinear satellite region is constructed. Then, a sliding window strategy is adopted, 20 collinear satellite pairs serve as a window, sub collinear satellite areas are recognized, and therefore the analysis precision is effectively improved, and local satellite collinear pairs are supplemented by widening an editing distance (ED) threshold value.

This invention belongs to the field of genomics and bioinformatics technology, specifically relating to a method for multidimensional quality assessment of telomere-to-telomere genomes. The method includes the following steps: preprocessing the genome data to be assessed to obtain preprocessed data; quantitatively assessing multiple core features of the preprocessed data, including accuracy, completeness, continuity, and region specificity; the region specificity includes telomere identification, centromere identification, and collinearity with a reference genome; calculating a comprehensive score based on the weighted results of the quantitative assessment of the core features, and using the comprehensive score to determine the quality of the genome to be assessed. This assessment method is specifically adapted to the core features of T2T genomes, taking into account continuity, completeness, accuracy, and region specificity, thus solving the problem that traditional methods cannot assess T2T-specific features.

The present disclosure discloses a breeding method and use of a blue-grained two-line hybrid wheat system. The present disclosure creates alien translocated chromosomes (T4AgL (Ba-containing fragment)-4BL (fragment near centromere).4thS and T4AgL (Ba-containing fragment)-4BL (fragment near centromere).4thS (Rf-containing fragment)) and alien translocated telosomes (T4AgL (Ba-containing fragment)-4thS (Rf-containing fragment), T4thS (Rf-containing fragment)-4AgL (Ba-containing fragment). and T4thS (Rf-containing fragment)-4AgL (Ba-containing fragment)-4BL (fragment near centromere).) of a blue-grained gene Ba and an alien restoring gene Rf, which exhibit xenia and dose-response and can lead to complete recovery of a recessive genetic male sterility (GMS) gene ms1. In this way, the present disclosure completes the improvement of a blue-grained two-line hybrid wheat system.

The invention discloses a design method and application of a pig chromosome end centromere probe, and belongs to the technical field of molecular biology. According to the invention, a bioinformatics means is utilized to screen out a sequence with high repetition frequency and strong specificity from preliminary searching, comparison and screening, a probe specifically combined with pig chromosome end centromere is screened out, and the nucleotide sequence of the probe is shown as SEQ ID NO.1. According to the invention, an in-situ fluorescence hybridization prefabricated reagent is developed by using a porcine primary cell line and an immortalized cell line, and the result shows that the probe can be well combined with the current DNA region. The design method of the pig chromosome centromere probe can be generally used for designing most probes, the developed pig chromosome end centromere probe is good in specificity, good in hybridization effect and high in detection accuracy, and a new view angle and method are provided for deeply researching pig chromosome rearrangement and translocation.

The invention discloses a method for rapidly identifying chromosome ploidy of a cucumber horticultural variety. The method mainly comprises the following steps: preparing cucumber somatic cell interphase nuclear flakes; preparing a 5S rDNA (ribosomal deoxyribonucleic acid) probe / centromere sequence (Type-III) probe; and carrying out FISH hybridization. FISH hybridization signals of the 5S rDNA probe / centromere sequence (Type-III) probe are very stable in the whole cell cycle of the cucumber and are convenient to count, so that the chromosome ploidy of the cucumber variety can be accurately identified no matter whether the cell is in an interphase or a division phase. The invention provides a rapid and accurate identification method for chromosome ploidy identification of cucumber haploids or some growing point materials difficult to obtain root tips and the like.

Described herein are artificial centromeres and artificial chromosomes comprising the artificial centromeres and a cargo sequence, methods of designing and making such artificial centromeres and artificial chromosomes, cells comprising such artificial centromeres and artificial chromosomes, and methods of using such artificial centromeres and artificial chromosomes for stable passaging of artificial chromosomes and expression of cargo sequences in a mammalian cell.

The invention discloses a genome assembly method, system and device based on a perl language and a storage medium. The method comprises the steps that a high-precision long-Reads interaction intensity two-dimensional matrix NormalForceMatrix is obtained; the two-dimensional matrix NormalForceMatrix is split, and a clustering result with high precision and long Reads is obtained; and according to the clustering result of the high-precision long Reads, assembling to obtain final results AD and STD. According to the method, a series of bioinformatics means are adopted, sequences measured by single chromosomes are classified into a class group, and the influence of other chromosome repetitive sequences (mainly from telomeres and centromeres) is reduced, so that the assembly complexity of each chromosome is reduced, and the assembly efficiency is improved. The continuity (reflected in the average length of the assembled sequence) of a single chromosome sequence can be effectively improved, and then a genome map with better assembly quality is obtained.

The invention discloses an in-vivo protein-DNA interaction analysis method based on methylated DNA immunoprecipitation, and belongs to the technical field of molecular biology. According to the method, an instantaneous protein binding event is recorded as stable 6mA, MeIP captures interaction which cannot be detected by ChIP, and meanwhile, the sequence background limitation of DamID is avoided. The compatibility with qPCR and sequencing enables the experiment scale to be flexibly adjusted, and the simple implementation of the method enables the method to be very suitable for researching related proteins interacting with chromatin in organisms lacking endogenous DNA methylation. The invention also discloses the transient but critical localization of a kinase at the centromere, and emphasizes the necessity of capturing a dynamic chromatin event for understanding genome regulation. The MeIP technology can be applied to a mammalian cell system, and a powerful tool is provided for researching instantaneous chromatin regulation events in higher eukaryotes.