35 results about "Genomic Segment" patented technology

The present disclosure encompasses a lipid nanoparticle (LNP) comprising a polypeptide comprising a nucleic acid sequence encoding an engineered meganuclease that binds and cleaves a recognition sequence within a Hepatitis B virus (HBV) genome. Further, the disclosure encompasses pharmaceutical compositions comprising the LNPs, and the use of such compositions for inactivating a pol gene of an HBV genome or an HBV genome fragment in a cell and treating HBV infections or diseases associated with HBV infections.

The application provides a human Helicobacter pylori detection method and kit based on the nature of four-strand DNA oxidoreductase. The method uses isothermal amplification technology, amplifies the genomic fragment containing the four-strand DNA sequence in the human Helicobacter pylori genome, and realizes rapid and visual detection of the human Helicobacter pylori by adding hematin and oxidoreductase substrate for color reaction.

Provided according to one aspect of the present disclosure is a composition for wound healing or tissue regeneration that comprises a genomic DNA fragment extracted from human placenta-derived mesenchymal stem cells and a placental growth factor and which exhibits excellent tissue regeneration ability. Provided according to another aspect of the present disclosure is a preparation method which enables the efficient, biocompatible, economical, and environmentally friendly production of a composition for wound healing or tissue regeneration having excellent tissue regeneration ability.

The application belongs to the technical field of biological information, and particularly relates to a method for locating ancestral haplotype genes for deep hybrid lines. In the application, the ancestral genotype of a sample to be analyzed is obtained, and then a genomic segment significantly associated with a phenotype is obtained. Then, whole genome analysis is performed. Compared with the prior art, the method for locating ancestral haplotype genes for deep hybrid lines can effectively reduce false positives, and can also be used for heterosis analysis, capture of dominant and epistatic effects between genetic markers and the like.

This invention discloses a chikungunya virus genome fragment armored RNA reference, its preparation method, and its application. The preparation process involves the following steps: (1) constructing the prokaryotic expression backbone vector pACYCAR; (2) cloning the CKV genome fragment CKA (nt17-2276); (3) constructing the prokaryotic expression vector pACYCAR-CKA; (4) inducing the expression of armored RNA; and (5) purifying the armored RNA. This invention solves the technical problems of high biosafety risk, poor stability, and insufficient gene fragment coverage in existing CKV nucleic acid detection references. It fills the gap in the lack of high-quality references for CKV detection.

A genome-wide R-loop detection method, in particular, a genome-wide R-loop detection method independent of affinity enrichment and a use. According to the genome-wide R-loop detection method, nucleases are used to perform enzyme digestion on genomic DNA fragments, and R-loop detection can be achieved by performing one-step enzyme digestion simply using a system of Nuclease P1, T5 exonuclease, and Lambda exonuclease. The whole R-loop detection process does not require affinity enrichment or labeling treatment. The method is not only simple and easy to operate, but also can avoid the loss of samples and fragments, thereby reducing the cost and risk of detection, and improving the applicability.

The application provides a porcine parvovirus detection method and kit based on the nature of four-strand DNA oxidoreductase. The method uses isothermal amplification technology to amplify the genomic fragment containing the four-strand DNA sequence in the porcine parvovirus genome, and realizes rapid and visual detection of porcine parvovirus by adding hematin and oxidoreductase substrate for color reaction.

Methods arc provided for making a plant genome having a desired nucleic acid sequence. One example method includes identifying genomic segments of a plant that include at least one desired nucleic acid sequence, using a trained neural network, which is biology-informed through first pre-training connections between a genetic data layer and at least one intermediate layer and second pre-training connection between the at least one intermediate layer and a phenotypic layer. The method also includes recombining the at least one at least one desired nucleic acid sequence with a second nucleic acid sequence to form a target plant genome.

A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.

The invention belongs to the field of biological products and the field of nucleic acid vaccines, and particularly relates to a virus (oropravirus)-like particle, preparation and application of the virus (oropravirus)-like particle as a vaccine. The virus-like particles are Oropers virus-like particles, and the virus-like particles contain proteins encoded by M genome segments of OROV strains or proteins encoded by gene segments of the M genome segments and N proteins of the OROV strains; wherein the corresponding sequence can also be a consistency sequence with the similarity of 75% with the corresponding sequence. Meanwhile, the particle VLP is used as a serum binding antibody of an antigen and an evaluation method of a T cell reaction, and the method can be used for detecting a serum lifting method after vaccine immunization. The invention further provides five nucleic acid vaccines for coding different functional domains of the OROV and combinations thereof, the immunogenicity and T cell reaction induced by the nucleic acid vaccines under different design strategies are displayed, strong body fluid and cell reaction is still kept 154 days after immunization, and it is proved that the nucleic acid vaccines can induce lasting and efficient immune reaction, and the immunogenicity and the T cell reaction are not influenced. The method can be used as a technical reserve and has huge clinical significance and application scenarios.

The present disclosure provides a method for methylation analysis of genomic fragments.

This invention belongs to the field of biotechnology, specifically relating to a Cas9 nuclease and its uses. The Cas9 nuclease (Cas9-R780A) of this invention possesses Cas9 nuclease activity and is suitable for CRISPR / Cas9 systems. The Cas9 nuclease (Cas9-R780A) is obtained by mutating arginine at position 780 of the wild-type Cas9 nuclease to alanine. Using the Cas9 nuclease (Cas9-R780A) to cleave double-stranded DNA produces protruding breaks. Complementary bases to these protruding breaks can be added via ligation, enabling precise editing of specific locations within genomic DNA fragments.

This application provides a method and kit for detecting pathogenic microorganisms based on the properties of tetrastranded DNA oxidoreductase. The method utilizes isothermal amplification technology to amplify genomic fragments containing tetrastranded DNA / RNA sequences in the pathogenic microorganism genome, and then performs a colorimetric reaction by adding heme and oxidoreductase substrates, achieving rapid and visual detection of pathogenic microorganisms.

The invention discloses a sequencing library construction method and application of the sequencing library construction method in genome typing and high-density physical map construction. The method comprises the following steps: respectively connecting genome DNA fragments covering the whole genome of a target species to a cloning vector, then carrying out enzyme digestion by using restriction endonuclease, screening fragments of which the length is greater than the length of the cloning vector from the enzyme digestion fragments, and adding ligase to carry out catalytic connection to obtain a self-ligation product; carrying out PCR (Polymerase Chain Reaction) amplification by using the primer pair self-ligation product as a template, wherein an obtained PCR product is a genome sequencing library of the target species; in combination with a PacBio HiFi sequencing technology, the method provided by the invention omits the processes of BAC library construction and monoclonal selection, and the marker generation and genomic typing accuracy are significantly improved. The method can be applied to development of high-resolution bin markers of polyploidy species and genome assembly quality, and can promote breeding and improvement of polyploidy crops.

The invention discloses a chromosome outer circular DNA sequence identification method based on deep learning, and relates to the technical field of genome biological information, and the method comprises the following steps: obtaining a known chromosome outer circular DNA sequence as a positive sample; randomly selecting a genome segment as a negative sample, wherein the overlapping degree of the genome segment and any known chromosome outer circular DNA region is lower than 20% from the reference genome according to an equal length distribution and chromosome distribution principle; cleaning and standardizing the positive and negative samples, and dividing the positive and negative samples into a training set, a verification set and a test set; converting the positive and negative sample sequences into feature representation which can be processed by a neural network through a multi-modal coding strategy, and training a one-dimensional convolutional neural network architecture by using a training set; when the number of the training samples is insufficient, introducing a deep convolutional generative adversarial network to perform data enhancement; and processing a DNA sequence to be detected through a multi-modal coding strategy, inputting the processed DNA sequence to the trained model, outputting a probability score of existence of the circular DNA outside the chromosome, and completing classification judgment according to a preset threshold value.

The present disclosure provides a method for characterizing a genomic locus that can comprise providing a quantity of genomic DNA having a locus of interest therein; contacting the genomic DNA with a transposase, which transposase fragments the genomic DNA and appends transposon DNA on a terminus of the fragments, thereby creating tagmented DNA fragments; performing a PCR reaction utilizing (i) the tagmented DNA fragments; (ii) a first primer that anneals to a portion of the transposon DNA; and (iii) a second primer that anneals to a portion of the locus of interest; and sequencing a product of the PCR reaction.

The invention discloses a high-throughput transgene insertion site detection method based on a next-generation sequencing technology. The method is based on the sequencing library obtained by the construction method disclosed by the invention, and the construction method of the sequencing library comprises the following steps: (1) extracting a transgenic positive sample whole genome; (2) fragmenting the genome DNA, and purifying to obtain a first mixture; (3) carrying out PCR (Polymerase Chain Reaction) amplification on the first mixture by adopting a specific primer with a UMI sequence; (4) taking the purified first round of amplification product as a template, mixing the template with the primers ad1-F and ad1-R, and performing second round of amplification; and (5) uniformly mixing a certain amount of the second round of amplification products, taking the sample mixed product as a template, mixing the sample mixed product with the primers ad2-F and ad2-R, and carrying out third round of PCR amplification. The method provided by the invention overcomes the defects of low flux, low efficiency and high cost of the existing transgenic insertion site detection method, and realizes deep sequencing and analysis of the flanking sequence of the insertion site in combination with a next-generation sequencing technology.

Crimean-Congo hemorrhagic fever (CCHF) virus replicon particles (VRP) are described. These VRP are capable of undergoing a single round of virus replication, but are unable to produce new particles or spread to neighboring cells due to the lack of the glycoprotein-encoding M genome segment. In some instances, the VRP contains one or more mutations in the viral ovarian tumor domain protease encoded by the L genome segment or heterologous antigens within its S genome segment. These VRP are shown to elicit a protective immune response against lethal CCHF virus challenge in an animal model.

Provided herein are Beta vulgaris plants resistant to Cercospora. Also provided herein are methods for identifying Cercospora resistant Beta vulgaris plants, methods for providing Cercospora resistant Beta vulgaris plants and means for identifying Cercospora resistant Beta vulgaris plants. Specifically, provided herein are Cercospora-resistant Beta vulgaris plants including a first Cercospora resistance providing genomic fragment on chromosome 4, wherein said first Cercospora resistance providing genomic fragment includes at least one sequence from the group consisting of SEQ ID Nos. 1, 3, 5, 7, 9, 11, 13, and 15.

The invention relates to a method for detecting cell gene editing efficiency through a CRISPR / Cas9 in-vitro shearing method and application, and the method comprises the following steps: (1) after CRISPR / Cas9 gene edits cells, INDEL is formed on a genome to cause gene silencing; (2) extracting genome DNA (Deoxyribose Nucleic Acid), and carrying out PCR (Polymerase Chain Reaction) to amplify a target genome segment containing INDEL; (3) cutting the fragment obtained by PCR amplification in the step (2) by using RNP formed by Cas9 protein and sgRNA; (4) carrying out agarose gel electrophoresis on a cutting product obtained in the step (3); and (5) carrying out quantitative analysis on the electrophoretic band in the step (4) through ImageJ software to obtain the gene editing efficiency. The scheme provided by the invention has high detection precision, is very suitable for multiple occasions, such as screening of electrical conversion conditions, screening of substrate concentration, optimization of an electrical conversion process and the like, and has the characteristics of high efficiency, rapidness, accuracy and the like.

Provided herein are spinach plants resistant to Peronospora farinosa and Stemphylium vesicarium, and spinach plants additionally resistant to Cucumber Mosaic Virus (CMV). Also provided herein are genomic fragments providing the present resistances and use thereof for identifying spinach resistant to Peronospora farinosa and Stemphylium vesicarium, and spinach plants additionally resistant to Cucumber Mosaic Virus (CMV). Provided herein are a spinach plant resistant to Peronospora farinosa and Stemphylium vesicarium: including a genomic fragment of Spinacia tetrandra located on chromosome 4 between positions 8255074 and 8620598 of the spinach reference genome, the genomic fragment of Spinacia tetrandra lacking a lethal factor and providing Peronospora farinosa resistance and including a genomic fragment located on chromosome 3 and between positions 1177586 and 1271037 of the spinach reference genome providing Stemphylium vesicarium resistance.

The application belongs to the field of molecular biology, and particularly relates to a method for efficiently constructing large fragment deletion of zebrafish helt gene and application. The method for efficiently constructing large fragment deletion of zebrafish helt gene is applied to constructing an animal model for treating and drug screening of Alzheimer disease caused by large fragment deletion of genome. The application also provides a method for efficiently constructing large fragment deletion of zebrafish helt gene. Through design of a target and a primer, a mutant with large fragment deletion of zebrafish helt gene is obtained. The CRISPR / Cas system is used to perform genome large fragment deletion in a zebrafish helt gene cluster. The length of the deleted genome fragment ranges from 1.4 kb, and the average efficiency reaches more than 60%, which greatly improves the efficiency of genome large fragment deletion.

Provided herein are constructs comprising an NS genomic segment lacking the coding sequence for NS1 and recombinant Influenza A viruses comprising an NS genomic segment lacking the coding sequence for NS1. Also, provided herein are constructs comprising an NS genomic segment lacking the coding sequence for NS 1 and a transgene. Also, provided herein are recombinant Influenza A viruses comprising NS genomic segment lacking the coding sequence for NS 1 and a transgene. Further, provided herein are compositions comprising such recombinant Influenza A viruses and uses of such recombinant Influenza A viruses (e.g., as vaccines).

The application belongs to the technical field of biology and particularly relates to a Cas9 nuclease and use. The Cas9 nuclease (Cas9-F916P) has Cas9 nuclease activity, is suitable for a CRISPR / Cas9 system, and is obtained by mutating a wild-type Cas9 nuclease at the 916th phenylalanine into proline. The Cas9 nuclease (Cas9-F916P) can cut DNA double strands to produce overhanging break ends, and complementary bases to the overhanging break ends can be added in a way of leveling connection, so that precise editing of a specific position of a genomic DNA fragment can be realized.

The rate of evolution may be estimated for any length of genomic fragments (or amino acid sequences) from a single codon (or amino acid position) to the entire genome or protein. Under the condition that a target genome reference sequence at initial time and each genome specific sequence of one or more target strains within a certain time period after the initial time are given, some genome fragments can be selected; a genetic differentiation parameter for a reference sequence fragment may then be calculated based on the genetic distance between the fragment and a corresponding fragment in each strain-specific sequence. Based on the genetic differentiation parameters, the evolution rate or evolution stability parameter of the fragment may be calculated and applied to the design of antiviral therapy or antiviral vaccines and / or the estimation of tumor growth.

The application provides an African swine fever virus detection method and kit based on the properties of four-strand DNA oxidoreductase. The method uses isothermal amplification technology to amplify the genomic fragment containing the four-strand DNA sequence in the African swine fever virus genome, and realizes rapid and visual detection of the African swine fever virus by adding hematin and oxidoreductase substrate for color development.

Methods and compositions for maintaining DNA contiguity for sequencing is provided. For example, fragments of genomic DNA can be provided that are reacted with an adapter-loaded tagmentase such that the DNA fragments comprise breakpoints in the fragments and an inserted adaptor at the break points, wherein the tagmentase binds the breakpoints to form linked DNA segments in the form of DNA segment-first adaptor tagmentase second adaptor-(DNA segment-first adaptor tagmentase second adaptor)n-DNA segment, where n is any integer and “-” indicates a covalent linkage. The method allows for maintaining contiguity of sequences such that sequences on the same haplotype can be determined and associated with each other.

The application discloses a method for rapidly screening high-purity Gastrodia elata and a primer composition used in the method. The application aims to solve the technical problem of how to screen or assist in screening high-purity Gastrodia elata varieties. The application provides a reagent for identifying a RFLP molecular marker site of Gastrodia elata, and identifies or assists in identifying the purity of Gastrodia elata varieties by detecting the genotypes of the RFLP molecular marker site of the Gastrodia elata to be tested. After the PCR products of the RFLP sites of the genomic DNA fragments of different Gastrodia elata varieties are cut and subjected to gel electrophoresis, different numbers of bands can be obtained, and the purity of the RFLP sites of the genomic DNA fragments of the Gastrodia elata varieties is selected to be equal to or greater than 95%, thereby obtaining a high-purity Gastrodia elata variety. The composition for detecting the RFLP molecular marker sites in the genomes of the Gastrodia elata and other substances (such as substances for detecting other single nucleotide polymorphisms or genotypes of molecular markers related to the purity of Gastrodia elata) are combined to prepare a product for identifying high-purity Gastrodia elata varieties.

The present application relates to Pichinde viruses with rearrangements of their open reading frames (“ORF”) in their genomes. In particular, described herein is a modified Pichinde virus genomic segment, wherein the Pichinde virus genomic segment is engineered to carry a viral ORF in a position other than the wild-type position of the ORF. Also described herein are trisegmented Pichinde virus particles comprising one L segment and two S segments or two L segments and one S segment. The Pichinde virus, described herein may be suitable for vaccines and / or treatment of diseases and / or for the use in immunotherapies.

The application discloses an enzyme composition for low-preference DNA fragmentation and a reaction solution thereof. The enzyme composition comprises an endonuclease, a nucleotide kinase and a DNA polymerase, the endonuclease comprises any one of DNase I, heat-stable high-salt-tolerant endonuclease HL-SAN or endonuclease IV or a combination of at least two of them, the nucleotide kinase comprises T4 polynucleotide kinase, and the DNA polymerase comprises any one of Taq DNA polymerase, a Klenow fragment of DNA polymerase I or T4 DNA polymerase or a combination of at least two of them. The application develops a one-tube method for genome fragmentation, end repair and A-tailing module, including an enzyme composition and a reaction solution thereof. In view of the problems and deficiencies of the current enzyme library construction, the components are optimized and explored, and a suitable connection module is combined, so that the finally obtained product has low preference, the output library has higher uniformity, and has a wide application prospect in second-generation sequencing.