37 results about "Host genome" patented technology

Methods and compositions for modulating a target genome are disclosed. This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for inserting, altering, or deleting sequences of interest in a host genome.

The invention discloses a qualitative and quantitative detection method for the integrity of an AAV vector under multi-primer ITR design, and the detection method comprises the following steps: S1, designing a plurality of primers in a conserved region of an ITR sequence of the AAV vector, the length of the primers being 18-25bp, the Tm value being 55-65 DEG C, and the GC% being 40-60%; s2, carrying out validity inspection on the primer; s3, adopting a Multiplex LAM-PCR (Polymerase Chain Reaction) method, performing amplification and sequencing by using the primer to obtain a chimeric sequence of the ITR and the host genome screened by using a biological analysis method, namely obtaining information of an ITR breakpoint; s4, according to the information of the ITR breakpoints, carrying out statistics on the distribution condition of the ITR breakpoints in the ITR region to obtain a statistical table; and S5, obtaining a qualitative and quantitative result of the ITR fracture position according to the statistical table. According to the method, the number of chimeric sequences in each primer region is counted, and the ITR breakpoints are qualitatively judged and quantitatively analyzed, so that the integrity of the AAV vector is comprehensively evaluated.

The invention discloses an astragalus sinicus breeding genetic data mining system based on bioinformatics, and particularly relates to the technical field of data mining. The method comprises the following steps: acquiring and synchronizing original sequencing data of an astragalus sinicus host genome and a rhizobium symbiotic microorganism genome to generate a standardized genetic information data set; the method comprises the following steps: identifying sequence cross contamination sites between a host genome and a symbiotic microorganism genome, and eliminating genetic information interference of a microorganism source, so as to obtain purified host genome data without microorganism interference; analyzing the contribution degree of the microbial genome to the target character of the astragalus sinicus to obtain a microbial effect weight; integrating the purified host genome data and the microbial effect weight, constructing an astragalus sinicus character association analysis model, and positioning character association sites; and finally, screening candidate breeding markers based on character associated site information to obtain a precise breeding genetic marker set. According to the method, the accuracy and efficiency of milk vetch breeding are improved.

The invention discloses a method, a system, equipment and a medium for detecting an HPV (human papilloma virus) DNA (deoxyribonucleic acid) integration event, and relates to the technical field of gene detection. According to the method, HPV types and virus loads (Ct values) pre-screened by qPCR are used as natural identifiers to guide grouping and mixing of samples, and HPV integrated event detection and sample tracing are synchronously realized through single sequencing. Clinical verification shows that compared with qPCR, the comprehensive sensitivity reaches 97.1%, and the cost is reduced by 60%. And a built-in targeted retest mechanism improves the reliability of a detection result. The invention provides a novel, traceable, economical and feasible solution, is used for high-throughput HPV-host genome integration feature analysis, balances cost, expandability and clinical accuracy, and provides a high-throughput and low-cost solution for HPV-related cancer screening.

The application provides a quality control for detecting respiratory pathogen nucleic acid, which comprises any one or more of the following respiratory pathogens: coronavirus, influenza virus, adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, rhinovirus or / and Legionella pneumophila. The full-length genome sequence of the coronavirus is divided into 6 target fragments, each with a length of 4000-5500 bp. The quality control of the application covers all detection target sequences (or target points) of the coronavirus, has a wide coverage, comprehensively detects target points, and does not have the phenomenon of missed detection. The quality control of the application contains main respiratory pathogen infections, has a wide range, and uses real virus samples and lentivirus samples as raw materials, and has more accurate detection target points. The preparation of the coronavirus quality control of the application integrates the target gene sequence into the host genome through the lentivirus vector, knocks out the self-replication gene in the preparation process, and has a "self-inactivation" ability, so that the recombinant lentivirus cannot replicate in the target cells and infect other cells.

The application discloses circular RNA and application thereof in pigeon trichomonad vaccine. The circular RNA comprises a coding element capable of encoding recombinant pigeon trichomonad AP33 or AP65 protein. The coding element has a sequence shown in SEQ ID NO. 1 or SEQ ID NO. 2 or a conservatively variant sequence thereof. The circular RNA can induce protein expression and generate high-level antibodies in an animal body. When the circular RNA is applied to the pigeon trichomonad vaccine, the circular RNA does not contain infectious worm component, can be degraded into nucleotides in the body, cannot be integrated into a host genome, has no risk for pigeons, can stimulate pigeons to generate a stronger immune response, including humoral immunity and cellular immunity, and can effectively resist parasitic infection. Meanwhile, the vaccine has high stability, the vaccine of the application can be prepared on a large scale through a molecular technology, and production cost is low.

Proteases of Group IV (+)ssRNA viruses were found to act on a human sequences in addition to the viral sequences. The identity of the cleavable human sequences is disclosed. Detection of these sequences can act as a diagnostic of infection. It is contemplated that these findings could be employed to facilitate post-translational silencing at the level of protein (e.g., removal of existing proteins), thus serving as a protein analog to CRISPR / Cas9 and RNAi / RISC, and further to enable sequence-specific silencing of host functions without the modification of the host genome.

The invention provides a genetic engineering strain, a construction method of the genetic engineering strain and application of the genetic engineering strain in biosynthesis of 5-hydroxytryptophan. According to the engineering bacterium, four key modules required by 5-HTP synthesis are sequentially introduced into a host genome in a genome integration mode through a CRISPR technology, and the four key modules comprise an aroGfbr-ppsA-tktA module for enhancing chorismate precursor supply, a trpEfbr-trpG module for catalyzing o-aminobenzoic acid generation, a salABCD gene cluster responsible for hydroxylating o-aminobenzoic acid into 5-hydroxy o-aminobenzoic acid, and a salABCD gene cluster responsible for hydroxylating 5-hydroxy o-aminobenzoic acid into 5-hydroxy o-aminobenzoic acid. And a trpDCBA module for converting the intermediate into the final product 5-HTP. The modules are respectively integrated into a plurality of non-essential gene regions, so that stable genetic expression is realized, and a complete metabolic pathway can be operated without plasmids or inducers. The strain can continuously accumulate 5-hydroxytryptophan (5-HTP) under a glucose fermentation condition, and has the advantages of simplicity and convenience in construction, high hereditary stability, low production cost, suitability for industrial-scale fermentation and the like.

The invention provides a multi-primer designed AAV vector ITR sequence integrity determination method, and belongs to the technical field of next-generation sequencing data analysis and application, and the method comprises the following steps: designing an AAV vector infection host cell with n primers in an ITR region, extracting intracellular fluid, and carrying out next-generation sequencing to obtain a primary Fastq file; the method comprises the following steps: carrying out coarse classification on sequences according to primer information, screening by using a biological information method to obtain a chimeric sequence, aligning one part of the chimeric sequence to a host genome, aligning the other part of the chimeric sequence to an AAV vector genome, and determining the junction of two sequences with different sources in the chimeric sequence as an ITR breakpoint; according to the samples, the primers and the sequence information corresponding to the ITR breakpoints, the distribution condition of the ITR breakpoints in the ITR area is counted, and a statistical table is obtained; and a qualitative and quantitative result of the ITR fracture position is obtained. According to the method, the integrity of the ITR region of the AAV vector sequence can be accurately qualitative and quantitative.

Methods and compositions for modulating a target genome are disclosed. This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for inserting, altering, or deleting sequences of interest in a host genome.

The invention relates to a method of treating a disease or disorder in a patient in need thereof that includes providing an active pharmaceutical ingredient (API) to the patient by administering more than one split-dose of the API over a pre-determined period of time. In embodiments of the invention, the API is an mRNA encoding an antigen. The attractiveness of mRNA as a vaccine modality is supported by several advantages. As a non-infectious agent that does not require incorporation into the host's genome to confer activity along with its well-defined chemical composition, mRNA is regarded as a relatively safe vaccine modality.

The application discloses a DNA polymerase III mutant and application thereof. The mutant contains an amino acid sequence shown in SEQ ID No. 1, and the mutant can be applied to improving the mutation frequency of a host strain genome. In the application, the Escherichia coli is used as a starting strain, a high-efficiency evolution auxiliary plasmid is introduced, and the mutation frequency of the host is improved; combined with competitive pressure directional screening of a tryptophan structural analog 5MT, finally, the Escherichia coli engineering strain with high yield of tryptophan is obtained. The auxiliary plasmid comprises a pBad24 plasmid vector skeleton and an engineered Escherichia coli DNA polymerase III danQ nucleotide fragment. The high-efficiency evolution auxiliary plasmid provided by the application can significantly improve the mutation rate of the host genome, combined with the directional screening of 5MT, the traditional mutagenesis cycle can be greatly shortened, the engineering strain with high yield of tryptophan can be efficiently screened, and the application has important application value.

The invention discloses a differential diagnosis and prognosis evaluation method for a pleural effusion microbiome based on metagenome sequencing and application, belongs to the technical field of bioinformatics, and discloses a method for analyzing the microbiome of a pleural effusion sample, and the method comprises the following steps: carrying out metagenome next-generation sequencing on an in-vitro pleural effusion sample to obtain a sequencing reading; performing bioinformatics analysis on the sequencing reading, and determining microorganism composition information of the pleural effusion sample based on a verification result; by establishing a unified mNGS experimental process and a parallel bioinformatics analysis path, two kinds of technical information of different dimensions, namely microbiome structural characteristics and host genome copy number variation (CNV), are synchronously output from single sequencing data, and the defect that microbiological analysis and genome analysis need to be carried out in batches in the prior art is overcome.

Methods and compositions for modulating a target genome are disclosed. This disclosure relates to novel compositions, systems and methods for altering a genome at one or more locations in a host cell, tissue or subject, in vivo or in vitro. In particular, the invention features compositions, systems and methods for inserting, altering, or deleting sequences of interest in a host genome.

The application discloses a biological information-based genetic data mining system for Astragalus sinicus breeding, and particularly relates to the technical field of data mining; the system is characterized in that: raw sequencing data of a host genome of Astragalus sinicus and a symbiotic microorganism genome of rhizobium is collected and synchronized to generate a standardized genetic information dataset; sequence cross-contamination sites between the host genome and the symbiotic microorganism genome are identified, and genetic information interference from the microorganism is removed to obtain purified host genome data free of microorganism interference; the contribution of the microorganism genome to target traits of Astragalus sinicus is analyzed to obtain a microorganism effect weight; the purified host genome data and the microorganism effect weight are integrated to construct a trait association analysis model of Astragalus sinicus and locate trait association sites; finally, candidate breeding markers are screened based on the trait association site information to obtain a precise breeding genetic marker set; the application improves the accuracy and efficiency of Astragalus sinicus breeding.

The invention discloses a targeted sequencing method for helicobacter pylori multi-site drug-resistant gene mutation detection, and relates to the technical field, and the targeted sequencing method comprises the following steps: obtaining a clinical gastric mucosa sample, extracting and purifying mixed DNA of genome DNA containing helicobacter pylori 23S rRNA, gyrA and pbp1 drug-resistant genes and host genome DNA, and introducing a competitive internal standard into the purified mixed DNA; taking the competitive internal standard and the mixed DNA as templates, and carrying out a first round of multiple PCR amplification by virtue of a composite primer system, so as to obtain a first amplification product; purifying the first amplification product, carrying out solution hybridization capture by using a probe library, and washing by using a washing solution at a specific temperature to obtain an enriched product; taking the captured enriched product as a template, carrying out a second round of PCR amplification by using a primer carrying a complete sequencing joint, and constructing a sequencing library; according to the invention, high-accuracy synchronous detection and complex sample applicability of the helicobacter pylori multi-site drug-resistant gene can be effectively realized.

According to some embodiments herein, methods and kits for labeling and analyzing nucleic acids are provided. In some embodiments, sequence-specific labeling is performed on polynucleotide sequences associated with a host genome, and the presence or absence of patterns characteristic of extragenomic sequences are determined.

The invention discloses a method and a device for mining virus small interfering RNA (Ribonucleic Acid) through multiple algorithms, and relates to the field of biological detection.The method comprises the following steps: removing linkers of input sequences through multiple linker removing algorithms, and merging and de-duplicating the obtained sequences to obtain linker-removed sequences; mapping the delinker sequence to a ribosome RNA database in a cascade mode through a plurality of mapping algorithms, and outputting a first incompletely mapped sequence; mapping the first incompletely-mapped sequence to a host genome by adopting a same mapping method, and outputting a second incompletely-mapped sequence; and mapping the second incompletely-mapped sequence to the viral genome through a plurality of mapping algorithms, and judging that the second incompletely-mapped sequence is from the viral sequence when the second incompletely-mapped sequence is mapped to the viral genome by any mapping algorithm in a way that the mismatched base number is less than or equal to 1. According to the method, the efficiency and the accuracy of mining the virus small interfering RNA from massive transcriptome data are remarkably improved.

The present disclosure is directed to a streamlined sample preparation process, VERA (Viral Enrichment by Reducing Artifacts), to tilt total genomic material in favor of DNA / RNA viral genomes. This reduction of host genomic artifacts can be completed in <8 hours from sample acquisition. Using a rapid library preparation protocol (˜1.5 minutes) and real-time nanopore sequencing, potential viral contamination, for example RNA viral contamination, can be identified in less than one workday from sample acquisition.

The invention discloses an automatic body fluid sample pathogen and host genome nucleic acid synchronous extraction method. The method comprises the following steps: S1, mixing a large-volume body fluid sample with a lysis buffer solution Buffer LA containing chaotropic salt and protease K, and carrying out lysis to release nucleic acid; s2, amino-modified magnetic beads are added, nucleic acid is captured through electrostatic interaction, after room-temperature combination, magnetic separation is conducted, supernatant is abandoned, and the amino-modified magnetic beads are reserved; s3, eluting nucleic acid on the amino-modified magnetic beads, and performing magnetic separation to retain eluent; s4, adding a protective agent Buffer GTN, isopropanol and ion exchange magnetic beads into the eluent, uniformly mixing and combining, performing magnetic separation, discarding supernatant, and retaining the ion exchange magnetic beads; s5, washing the ion exchange magnetic beads, drying, and eluting with Buffer EB1 to obtain whole nucleic acid; according to the method, large-volume, high-efficiency and high-purity nucleic acid synchronous extraction is realized through a double-magnetic-bead staged capturing and cracking-protective agent combination technology.

The invention belongs to the technical field of biological information, and discloses an integration site analysis method based on multi-primer design, which comprises the following steps: inserting primers at a plurality of positions of an AAV vector sequence to form a multi-primer vector; integrating the multi-primer vector into a host genome, and capturing a sequence of an integration site through primer amplification; sequencing is conducted on the sequence where the integration site is located, and sequencing data is obtained; and sequencing data redundancy elimination processing: eliminating sequencing result redundancy caused by multi-primer amplification through a multi-primer sequencing data redundancy elimination signal generation algorithm to obtain an accurate integration site detection result. By designing the primers at multiple positions, the problem that the sequence of the integration site cannot be effectively captured under the condition that the AAV vector is integrated into the host genome in an incomplete sequence in the experiment process can be solved.

There is provided a method for removing host nucleic acid from a biological sample, the method comprising the steps of: a) contacting the sample with an excess amount of a saponin-containing formulation so as to sufficiently react the host in the sample with the saponin-containing formulation; b) adding at least one saponin inhibitor in order to inhibit the activity of excess saponin; and c) adding at least one nucleic acid digestive enzyme to allow removal of the host nucleic acid. Also provided are methods for detecting microorganisms in a biological sample, kits for host nucleic acid removal of a biological sample or kits for detecting microorganisms in a biological sample, and uses thereof. The provided method does not need to calculate or consider the concentration of host cells in a sample, can reduce the loss of microorganisms, and ensures the effect of removing the host genome.

The invention discloses a transcription factor decoy short-chain DNA-Max protein complex and application thereof in preparation of a medicine for inhibiting colorectal cancer, and relates to the technical field of biology. The DNA-Max protein complex is composed of TCF / LEF TFD DNA and a Max protein complex, and the TCF / LEF TFD DNA is a transcription factor decoy short-chain DNA and can block combination of a TCF / LEF transcription factor and a downstream gene promoter of an original Wnt signal channel, so that the Wnt signal channel is blocked, tumor growth is inhibited, and the DNA-Max protein complex cannot be integrated to a host genome and is high in safety; the short-chain DNA sequence has a specific binding site with a delivery protein Max, and a targeted recognition protein for a colon cancer cell marker is added on the basis, so that the off-target risk is small, and a drug DNA molecule can be safely and efficiently delivered into a cell nucleus of a colon cancer cell in a targeted manner to play a role; the protein compound is natural macromolecules, does not contain other chemical elements, can be metabolized and absorbed by an organism, has small toxic and side effects, and can be applied to preparation of medicines for inhibiting colorectal cancer.

The application provides an IBS micro-ecological transplantation intelligent prediction method and system based on multi-omics driving, and relates to the field of biomedical technology. The method comprises the following steps: establishing a multi-omics data fusion subsystem to collect target patient metagenome, metabolome, host genome and clinical phenotype group data; inputting the data into a bacterial flora-metabolite joint network analysis model to construct an interaction network and extract features; generating a correlation matrix based on the features and host genome data and calculating an index; combining the clinical phenotype data and the index to generate an index through a dynamic response algorithm; and using a transfer learning framework to jointly model and output a therapeutic effect prediction result. The system comprises data acquisition, network analysis, correlation calculation, dynamic response and joint modeling modules. The application integrates multi-omics data, accurately mines the relationship between flora and host, realizes intelligent prediction of micro-ecological transplantation efficacy, provides strong support for IBS personalized treatment, and has data processing and security guarantee measures.

The invention discloses a bacterium multi-target non-specific genome engineering method and application thereof, and relates to the field of gene engineering. According to the invention, the MTI system is successfully expanded from eukaryotic cells to a prokaryotic bacterium system for the first time, the dependence on a long-segment specific attachment site (attB) is thoroughly eliminated in mechanism, and any pre-modified specific sequence does not need to be carried out on a host genome, so that real host-independent editing is realized. On the basis, a set of genome engineering platform which is simple and convenient to operate and universal is constructed, the platform supports stable integration of multi-copy and large-fragment DNA and is successfully applied to various bacteria including gram-positive bacteria and gram-negative bacteria, and the operable host range of genome engineering is greatly expanded.

Provided herein are methods of site-specific integration of a heterologous sequence into a host genome (e.g., by administering a recombinant adeno-associated virus (rAAV) to a host cell in the presence of a Rep protein), and methods for treating diseases and disorders by delivering an rAAV that comprises a nucleic acid vector comprising a Rep protein. Also provided herein are methods and compositions for producing rAAV particles with improved titer and transduction efficiencies.

The invention provides a CAR (chimeric antigen receptor) integration site detection method based on multiple amplification and long-read-long sequencing, and belongs to the technical field of cell and gene therapy, and the method comprises the following steps: carrying out PCR (polymerase chain reaction) amplification on sample DNA (deoxyribonucleic acid) by using a CAR specific primer to obtain an initial library; primarily screening the amplified fragments in the initial library, and reserving the amplified fragments with the length of more than or equal to 500bp to obtain a primarily selected library; performing third-generation sequencing on the amplified fragments in the primary selection library to obtain Raw FASTQ; further screening the amplified fragments in the Raw FASTQ, and retaining the amplified fragments simultaneously containing a CAR non-human primer binding region and an HA sequence to obtain a secondary selection library; and detecting the precise integration site of the CAR in the host genome. The method solves the technical problem that a traditional detection method is difficult to break through interference of a CAR homologous sequence, and provides safety guarantee for clinical transformation of gene editing cell therapy products such as CAR-T and the like.

The present invention relates to the field of biotechnology. More precisely, a genetic construct and method for producing a transgenic plant event, especially a sugarcane event {Saccharum spp.), which is resistant to infestation by the Diatraea saccharalis pest, popularly known as a pest, ordinary borer, reed borer or just borer is described. The invention describes the event, the methods for event identification as well as the insertion detection method based on the unique region of intersection between the insert and the host genome and the flanking regions that characterize it.

The application discloses an avian leukosis virus fluorescent quantitative PCR detection kit based on a pol gene and application thereof. The application is based on a fluorescent quantitative PCR technology, and specific primers and a TaqMan probe aiming at a pol gene conservative region of avian leukosis virus are designed to realize specific amplification and detection of virus nucleic acid. The core improvement of the application is that after nucleic acid is extracted from animal tissue, plasma and other samples, a DNA enzyme is added to perform digestion treatment, and residual host genome DNA in the sample is specifically degraded, so that a false positive problem caused by amplification of an endogenous pol gene is completely eliminated, and the specificity and accuracy of detection are obviously improved.

This invention discloses a method and apparatus for mining viral micro-interference RNA using multiple algorithms, relating to the field of biological detection. The method includes: removing adapters from an input sequence using multiple adapter removal algorithms, merging and deduplicating the resulting sequences to obtain an adapter-removed sequence; mapping the adapter-removed sequence to a ribosomal RNA database using multiple mapping algorithms in a cascaded manner, outputting a first incompletely mapped sequence; mapping the first incompletely mapped sequence to a host genome using the same mapping method, outputting a second incompletely mapped sequence; mapping the second incompletely mapped sequence to a viral genome using multiple mapping algorithms. If the second incompletely mapped sequence is mapped to the viral genome by any mapping algorithm with a mismatch number ≤ 1, it is determined to originate from a viral sequence. This invention significantly improves the efficiency and accuracy of mining viral micro-interference RNA from massive transcriptome data.