35 results about "Repeated sequence" patented technology

The invention discloses a divalent nucleic acid aptamer fluorescence detection method based on an exonuclease I auxiliary target circulation strategy, and belongs to the field of analysis and detection.The divalent nucleic acid aptamer is a repetitive sequence composed of two monovalent nucleic acid aptamers and can form double-stranded DNA through base complementary pairing with complementary strand cDNA of the divalent nucleic acid aptamer, and the divalent nucleic acid aptamer can be used for fluorescence detection of the divalent nucleic acid aptamer. The method comprises the following steps: taking a bivalent nucleic acid aptamer as a template, forming a DNA silver nanocluster (DNA-AgNCs) under the action of silver nitrate and sodium borohydride, and when the target okadaic acid exists, combining the bivalent nucleic acid aptamer with the target, so that cDNA can be replaced from double-stranded DNA by the target. Exonuclease I is added to perform enzyme digestion on the cDNA and the divalent nucleic acid aptamer, so that the fluorescence intensity of the DNA-AgNCs can be rapidly reduced. The content of the okadaic acid can be judged by detecting the change of the fluorescence intensity. The invention provides a simple, convenient, rapid, high-sensitivity and high-specificity detection method for okadaic acid detection based on a divalent nucleic acid aptamer for the first time.

The invention relates to the technical field of food safety detection, in particular to a food crop pathogenic mycotoxin detection method based on double signal amplification. The core of the method is a section of linear lock-type probe containing a mycotoxin specific nucleic acid aptamer, under the condition that target mycotoxin exists in a sample, the aptamer is combined with the mycotoxin, the probe is induced to generate conformational change, and the probe is closed into annular DNA under the catalysis of DNA ligase; then, the circular DNA is used as a template, isothermal rolling circle amplification is carried out through Phi29 DNA polymerase, and a long-chain DNA product containing a large number of repetitive sequences is generated; subsequently, the long-chain product is used as a molecular scaffold, and two kinds of gold nanoparticles of which the surfaces are modified with different complementary probes are cross-linked at the same time, so that the nanoparticles are quickly gathered, the color of the solution is changed from wine red to blue or purple, and convenient visual detection is realized. The method has the outstanding advantages of ultrahigh sensitivity, rapid detection and the like, and is suitable for on-site rapid screening of mycotoxin pollution.

This disclosure generally relates to super minimal transposon inverted repeat sequence (ITR) polynucleotides, compositions comprising the polynucleotides and methods of using compositions comprising the polynucleotides for the ex vivo and in vivo delivery of nucleic acids to cells, in particular, in vivo delivery of therapeutic genes to treat genetic disorders or diseases.

The application belongs to the technical field of biology, and discloses a kind of Myzus persicae densovirus, amplification and connector method and its application, Myzus persicae densovirus name is Myzus persicae densovirus 2, abbreviated as MpDV2, preserved in China typical culture preservation center, and the preservation number is V202281.The Myzus persicae densovirus MpDV2 provided in the application is a virus strain that has not been isolated and identified before and has pathogenicity to Myzus persicae, and the full-length sequence of the genome of the Myzus persicae densovirus MpDV2 (including the complete terminal inverted repeat sequence) is disclosed for the first time, and the influence of the virus infection on the growth and development of Myzus persicae and the population dynamics / growth.The Myzus persicae densovirus MpDV2 of the application significantly reduces the intrinsic growth rate (r), net reproduction rate (R0) and week-long growth rate (lambda) of Myzus persicae population, and prolongs the average generation time (T) of the population, and the MpDV2 infection has a significant influence on the growth and development of Myzus persicae and population growth.

The invention relates to the technical field of genome assembly, in particular to a medicinal plant genome assembly method and system based on high-throughput sequencing. The method comprises the following steps: acquiring a target sequencing sequence, and screening a function influence sequence; performing repetitive classification on the target sequencing sequence to obtain a non-repetitive sequence cluster and a repetitive sequence cluster, and dividing the repetitive sequence cluster into a functional repetitive sequence and a non-functional repetitive sequence; determining dynamic association strength by combining expression abundance of functional genes, content detection of medicinal components and base overlapping characteristics of adjacent sequences; constructing an association network; and according to the dynamic association strength in the association network, aiming at the functional association type repetitive sequence, the non-functional association type repetitive sequence and the adjacent non-repetitive sequence, respectively carrying out sequence splicing by adopting a differential assembly path to obtain a complete genome assembly result. According to the method, the problems of splicing errors, fragment breakage and redundancy caused by repeated sequences can be solved, and the assembly accuracy and integrity are remarkably improved.

The application belongs to the field of biological information visualization, and discloses a three-dimensional visualization functional gene browser and system based on Z series closed loop coding, which solves the problems of track disorder, arc winding, dependence on scaling and incomplete coding of existing tools. The application constructs Z series closed loop coding, packs genes and non-gene regions into Z0~ZN units, and adapts repeat sequences and ring chromosomes. L-X-Y three-dimensional coordinates are established, 65 standardized character libraries are constructed, and amino acids are labeled in a six-color degenerate system. Modular labeling is adopted, continuous functional elements are integrated into M modules, three types of background colors are used to classify levels, the trunk area and the independent labeling area are displayed separately, and tracks and arcs are abandoned. The system supports Z unit addressing, three-level interaction, module linkage, variation marking, Hi-C double-end alignment and reverse complementary strand switching, realizes full-link visualization from whole genome to single base, and is suitable for genomics and clinical variation analysis.

The invention discloses a dairy cow early embryo sex identification method, and belongs to the technical field of dairy cow breeding and breeding. The identification method comprises the following steps: (1) culturing a dairy cow embryo to an early blastocyst stage, starting to perform single-embryo single-droplet culture, and after culturing until a blastocyst cavity is formed, punching a blastocyst zona pellucida to promote the blastocyst to shrink and release blastocyst cavity liquid; (2) collecting blastocyst cavity liquid, and extracting embryo free DNA in the blastocyst cavity liquid; (3) by taking the free DNA as a template, designing a primer to amplify a specific repetitive sequence ChrY fragment of the bull Y chromosome; if the amplification product exists, the embryo is identified as a bull, and if the amplification product does not exist, the embryo is identified as a cow. The method can ensure that the embryo free DNA in the obtained blastocyst cavity fluid is only derived from the embryo, and can effectively avoid embryo injury. According to the method disclosed by the invention, the copy number of the amplified target area in the bull Y chromosome is more than 2000 times, a detection signal can be amplified, and the detection accuracy is improved.

A system and method for identification of target sites in a pathogenic genome and combating a pathogenic infection have been provided. The present disclosure utilizes the fact that a conserved stretch of nucleotide sequence in genomic neighborhood of genes important for bacteria can be targeted to disrupt the overall functioning of the pathogen. The method involves identification of nucleotide repeat sequences in the DNA. The method and system also involve administration of a cocktail comprising antimicrobial drugs, biofilm inhibitors and a construct. The genomic neighborhood or vicinity or ‘flanking genes’ refers to regions lying within a predefined number of genes to the identified conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome or within a distance of predefined number of bases with respect to the conserved stretch of nucleotide repeat sequence (or its reverse complement) on the candidate pathogen genome.

A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variants from next generation sequencing reads out of a pool of enriched genomic patient samples without suffering from next generation sequencing workflow biases such as those introduced by sequencing errors in particular in repeat patterns regions of the human genome such as homopolymers or heteropolymers. The variant calling module may estimate the probability distribution of the length of the repeat pattern for each patient sample and cross-analyze it against other samples in a single experimental pool to identify best-fit variant models for each pair of samples. The variant calling module may further group samples according to their matching best-fit variant models and identify which group of patient samples carries the wild type reference without the need for control data in the pool. The variant calling module may subsequently characterize the homozygous or heterozygous repeat patterns variants for each patient sample with improved specificity and accuracy even in the presence of next generation sequencing biases.

The invention provides systems and methods for making sequencing libraries that are useful for quantitatively analyzing nucleic acids in a sample. Sample nucleic acids are randomly cleaved at, and PCR handled are attached to, a random cut site. The nucleic acid is amplified into a sequencing library in which a sequencing primer generates a sequence read from adjacent the random cut site. The sequence reads can be mapped to a reference, but they will also include a unique identifier sequence that comes from within the nucleic acid molecule being analyzed, i.e., an intrinsic molecular identifier (IMI). The IMI is unique for each molecule and can thus be used to deduplicate sequence reads originating from the same molecule.

Methods and systems for detecting MSI are provided. Also provided are methods for enriching human genomic DNA for microsatellite loci. Additionally, an oligonucleotide array for detecting MSI is provided. In some embodiments, the method for detecting MSI comprises detecting sequencing reads from a sample for a plurality of microsatellite loci; determining a metric for repeat length distribution (RLD) for each microsatellite locus; comparing the metric to a threshold value for the microsatellite locus; quantifying the number of microsatellite loci having an RLD metric exceeding the threshold value; and comparing the number of microsatellite loci having an RLD metric exceeding the threshold value to a microsatellite instability (MSI) proportion threshold.

To provide a method for identifying the presence of aneuploidy in the genome of a mammal.SOLUTION: Amplifying a plurality of chromosomal sequences in a cell-free DNA sample with a single primer pair complementary to the chromosomal sequences, wherein the primer pair amplifies a unique amplicon comprising short interspersed repeat sequences, determining at least a portion of the nucleic acid sequence of the plurality of amplicons to produce amplicon sequences, mapping the amplicon sequences to a reference genome, dividing the amplicon sequences into a plurality of genomic intervals, quantifying the number of reads for amplicon sequences mapped to the genomic intervals, and comparing the number of reads of amplicon sequences within a first genomic interval to: Comparing the number of reads of amplicon sequences in the one or more different genomic intervals, thereby identifying the presence of an aneuploidy in the genome of the mammal.SELECTED DRAWING: None

Disclosed is a method for identifying an evaluation target bacterium as a specific bacterial strain, the method comprising the following steps A and B: [step A] a step for performing PCR using a nucleic acid derived from the evaluation target bacterium as a template and using each of at least one set of primers that amplify a genome sequence specific to a bacterial species to which the specific bacterial strain belongs; and [step B] a step for performing PCR using a nucleic acid derived from the evaluation target bacterium as a template and using each of at least two sets of primers that amplify a repeating sequence present in the genome of the bacterial species to which the specific bacterial strain belongs.

The application provides a method for improving biological stress resistance by using a dotP gene, which comprises the following steps: transferring the dotP gene into a host organism, and making the host organism express the dotP gene; the host organism is a plant or a microorganism; the dotP gene encodes a protein (a) or (b): (a) a protein consisting of the amino acid sequence shown in SEQ ID NO. 2; (b) a protein derived from (a) by substituting, deleting or adding n amino acids in the amino acid sequence in (a) and having the activity of a quadruplet repeat sequence protein, wherein n is any integer between 1 and 4. By the technical scheme, the biological stress resistance of the plant or the microorganism is improved, and in particular, the dry resistance of the plant or the microorganism is improved.

The invention discloses insecticidal dsRNA synthesized according to PM as well as a synthesis method and application thereof, the gene sequence of the dsRNA is shown as SEQ ID NO: 1 or at least comprises a gene sequence with 90% of identity of the sequence shown as SEQ ID NO: 1, and after the dsRNA is introduced into a test insect body through micro-injection, it is found that the accumulated death rate can reach 100.00%, and the lethal effect is remarkable. According to the invention, a recombinant expression vector containing an inverted repeat sequence of the gene is constructed, and high-efficiency expression and accumulation of dsRNA are realized through IPTG induction in escherichia coli. After the dsRNA-containing engineering bacteria are mixed with flour, test insects are fed, and the accumulative fatality rate can reach 64.44%. A metal organic framework (MOF) material is used for loading the obtained dsRNA, the stability and delivery efficiency of the dsRNA can be further improved, the final death rate can reach 71.11% after a test insect compound is fed, and an effective means is provided for application of nucleic acid biopesticide in prevention and control of stored grain pests.

The invention discloses three tandem repeat PAV markers related to thousand seed weight of highland barley and application of the three tandem repeat PAV markers. The three PAV markers adopt an oligonucleotide probe sleeve # 8 as a probe, detection is carried out through chromosome fluorescence in situ hybridization in the mitosis metaphase of root tip cells, variations with repetitive sequence insertion fragments are respectively named as 1H-C, 3H-A and 6H-2, and types without insertion fragments are respectively named as 1H-D, 3H-B and 6H-1. Results show that the thousand seed weights of varieties containing 1H-C, 3H-A and 6H-2 are obviously higher than those of other polymorphic chromosomes respectively. The invention provides a cytological marker for thousand seed weight detection for highland barley breeding, and is beneficial to improving highland barley marker-assisted selective breeding efficiency. The influence of chromosome structure variation on the thousand seed weight of highland barley is disclosed, and important information is provided for mining environment adaptability genes and gene clusters.

Nucleic acid preparation and analysis techniques described. In an embodiment, techniques for generating tandem repeats include using adaptor sets having two types of adaptors with respective complementary regions present. When an adaptor of each type is present on end of a nucleic acid fragment, the complementary regions can bind to one another to generate tandem repeats of an insert, e.g., a fragment generated from a target nucleic acid.

A method for producing recombinant adeno-associated virus particle preparations (rAAVp) is reported herein, comprising the steps of culturing mammalian cells containing expression cassettes for non-adeno-associated virus genes, adeno-associated virus rep genes, adeno-associated virus cap genes, adeno-associated virus E1A genes, adeno-associated virus E1B genes, adeno-associated virus E2A genes, adeno-associated virus E4orf6, and adeno-associated virus VA RNA genes located between two AAV terminal inverted repeat sequences (ITRs), and producing rAAVp therefrom, wherein the culturing is performed at a pH value between pH 7.4 and pH 7.6. The yield of rAAVp produced by culturing at a pH value between pH 7.4 and pH 7.6 is higher than that of rAAVp produced by culturing at a pH value between pH 7.0 and pH 7.2, and the percentage of perfect particles is higher for rAAVp produced by culturing at a pH value between pH 7.4 and pH 7.6 than for rAAVp produced by culturing at a pH value between pH 7.0 and pH 7.2.

The invention discloses insecticidal dsRNA synthesized according to KCC as well as a synthesis method and application of the dsRNA. The gene sequence of the dsRNA is shown as SEQ ID NO: 1 or at least comprises a gene sequence with 90% of identity of the sequence shown as SEQ ID NO: 1. After the compound is introduced into the body of a test insect through a micro-injection method, the accumulated death rate can reach 98.33%, and the lethal effect is remarkable. According to the invention, a recombinant expression vector containing an inverted repeat sequence of the gene is constructed, and high-efficiency expression and accumulation of dsRNA are realized through IPTG induction in escherichia coli. After the dsRNA-containing engineering bacteria are mixed with flour, test insects are fed, and the accumulative fatality rate can reach 58.33%. A metal organic framework (MOF) material is used for loading the obtained dsRNA, the stability and delivery efficiency of the dsRNA can be further improved, the final death rate can reach 65.56% after a test insect compound is fed, and an effective means is provided for application of nucleic acid biopesticide in prevention and control of stored grain pests.

The application belongs to the technical field of genetic engineering, and specifically provides a recombinant human-like collagen polypeptide, a preparation method and application thereof. The recombinant human-like collagen polypeptide comprises a tandem repeat sequence at an N terminal and a C terminal sequence; the repeat sequence is shown as SEQ ID NO. 1; and the C terminal sequence is shown as SEQ ID NO. 2. The recombinant human-like collagen polypeptide provided in the application can correctly express active collagen with a triple helix structure in a prokaryotic expression system, greatly reducing the production cost of active human collagen and improving the production efficiency. The prepared recombinant human-like collagen polypeptide has better water retention capacity and anti-degradation capacity than natural human type I collagen, and shows a cell migration promoting effect superior to that of a commercial collagen product in a cell scratch experiment.

The invention discloses a baculovirus expression vector as well as a construction method and application thereof. The vector takes pFastBacDual as a skeleton, 2-9 repetitive BS sequence modification promoters are connected in series to the downstream of a polh promoter, an extremely advanced transcription factor VLF-1 gene is introduced, and the two components synergistically enhance the transcriptional activity. According to the invention, three types of recombinant vectors pBSX-eGFP, pBSX-eV and pBSX-GV are constructed, and the optimal combination is determined as overexpression of two repeated BS sequences and VLF-1, so that the expression quantity of the target protein can be increased. The vector construction process is standardized, enzyme cutting sites such as BamHI and EcoRI are reserved, and high-expression protein can be obtained after Sf9 cells are transfected and cultured for 4-5 days. The recombinant protein expression efficiency of a baculovirus expression system is improved, the advantages of correct folding and post-translational modification of the recombinant protein are reserved, and the method is suitable for large-scale industrial recombinant protein production scenes such as biopharmacy and vaccine research and development and has important application value.

To provide the use of a host modifying (HM) CRISPR / Cas system for inhibiting bacterial population growth or altering the relative proportions of subpopulations in a mixed bacterial population.SOLUTION: (I) a nucleic acid sequence encoding a Cas nuclease; (ii) a host cell target sequence and an engineered host modifying (HM) CRISPR array comprising a spacer sequence and repeats encoding a HM-crRNA comprising a sequence that hybridises to the host cell target sequence to guide Cas to the host cell target and modify the target sequence; (iii) a tracrRNA sequence or DNA sequence expressing same; (iv) a nucleic acid vector that is divided between the host cell and a nucleic acid vector that transforms the host cell; Whereby the HM-crRNA guides the Cas to the target and modifies the host CRISPR / Cas system in the host cell; wherein the target sequence is modified by the Cas, whereby the host cell is killed or host cell proliferation is reduced.SELECTED DRAWING: Figure 12

The present application relates to the fluorescence marker for identifying the centromere region of the chromosome of P. wallichii and its application, belongs to the technical field of molecular cytogenetics, the fluorescence marker probe is named HS-CHTZ5, the probe belongs to the centromere region repeat sequence of P. wallichii, can be combined with the centromere of P. wallichii chromosome and show fluorescence signal, and the centromere segment of P. wallichii chromosome is identified.The fluorescence marker provided by the present application can be used as a beneficial supplement to the prior art, and through in situ hybridization, the efficient identification of the centromere region of the chromosome of P. wallichii is realized, and the present application has important significance for cytogenetic map construction, chromosome karyotype analysis and different genus and species chromosome relationship analysis.

The invention discloses a transposon insertion site identification method based on high-throughput sequencing and application. A transposon with high copy and high sequence consistency is obtained through genome repetitive sequence analysis, restriction enzyme for library construction is determined through enzyme cutting site analysis, and a transposon terminal enriched library is constructed through the steps of genome DNA enzyme cutting, joint connection, PCR amplification and the like. Flanking sequence information of the transposon insertion site is obtained through high-throughput sequencing, the position of the insertion site on a genome is positioned through comparison with a reference genome, primers at the two ends of the insertion site are designed for identification of the insertion site, and therefore the high-throughput sequencing-based transposon insertion site identification method is established. According to the invention, the transposon terminal enriched library can be effectively constructed. Through high-throughput sequencing and bioinformatics analysis, high-throughput identification of transposon insertion sites can be realized.

The invention provides a paternity test method and system based on an SNP (Single Nucleotide Polymorphism) marker combination, and relates to the technical field of biological detection.The method comprises the following steps: respectively performing library construction and sequencing on samples of a detected object and a suspicious object to obtain original sequencing data of the samples; the method comprises the following steps: splitting original sequencing data to respectively obtain individual sample data of a detected object and a suspicious object; performing quality control filtering on individual sample data to remove low-quality sequencing data so as to obtain quality-controlled data; comparing the quality-controlled data with a human reference genome to obtain sequence comparison data; and performing de-duplication processing on the sequence comparison data to eliminate repeated sequences, thereby obtaining de-duplicated data. The scientificity and reliability of paternity test are improved.

The invention relates to the field of tumor molecular diagnosis, in particular to a method for noninvasive prediction of breast cancer molecular typing and application thereof. Specifically, the invention provides a construction method of a non-invasive prediction model for breast cancer molecular typing by taking the signal intensity of an LTR repetitive sequence region as one of extracted cfDNA features, and provides application of the model in non-invasive prediction of breast cancer molecular typing, so that non-invasive detection of different types of breast cancer is realized, and the non-invasive prediction of breast cancer molecular typing is realized. The method is especially suitable for patient groups needing dynamic monitoring or difficult to obtain tumor tissues.

This invention discloses a recombinant *Escherichia coli* strain that synergistically enhances the synthesis efficiency of β-elemene based on liquid-liquid phase separation, temporal regulation, and dynamic multi-enzyme assembly, and its application in β-elemene biosynthesis. In the recombinant *E. coli* strain, a stable covalent dual-enzyme complex of IspA and GAS is first constructed using a SnoopTag / SnoopCatcher system, and the upstream key enzyme IDI is further introduced. Simultaneously, the RGGRGG repeat sequence, capable of forming membrane-free droplets, is used as a phase separation scaffold, with an SH3 ligand fused to its N-terminus. The SH3 domain is then linked to the C-terminus of both the IspA-GAS enzyme complex and IDI. Through the specific interaction of the SH3 ligand / SH3 domain, the key enzyme is directionally recruited and spatially enriched into the aggregates. A temporal regulation strategy is also introduced: the expression of the IspA-GAS enzyme complex and IDI is first induced by IPTG, followed by delayed induction of RGGRGG aggregate expression, thus recruiting the already formed enzyme complex into the aggregates. This invention not only reduces the amount of glycerol used and improves the glycerol conversion rate, but also increases the yield of β-elemene.

The present invention relates to methods of amplifying DNA comprising: a)providing a DNA template molecule comprising at least one inhibitory region; and b) amplifying the DNA template molecule to generate an amplified DNA product, wherein the DNA template molecule is amplified in the presence of at least one type of single-stranded nucleic acid (ssNA) molecule, which cannot be extended by a polymerase, and wherein the at least one type of ssNA molecule anneals to the at least one inhibitory region and improves the amplification. The ssNA molecule may be random oligonucleotides and the inhibitory regions may be a homopolymeric region, e.g. poly A, a region with a high GC content, a repeated sequence; or a sequence that is prone to forming an inhibitory structure. The invention also relates to adaptor-ligated DNA products that may be produced by the methods.

This invention discloses a breeding method for long-spike, low-amylose-content rice. The method includes: hybridization using long-spike, large-grain Yiyang Dahe rice as the female parent and low-amylose-content japonica rice as the male parent; backcrossing the F1 generation seeds with the female parent once; planting for three consecutive generations; and performing molecular marker detection on the BC1F4 individual plant lines. Wx This invention involves inserting repetitive sequences into genes, designing dominant marker W1 and / or co-dominant marker W2 to detect the inserted repetitive sequences, and determining whether the corresponding BC1F4 line has a glutinous phenotype. The progeny lines obtained by planting glutinous BC1F4 single plants through multiple generations exhibit non-segregating phenotypes. This invention solves the problem of existing technologies failing to improve the amylose content of Dahu rice and thus being unsuitable for producing high-quality Yiyang rice cakes. By combining traditional hybridization-backcrossing methods with RVA viscosity detection, molecular marker-assisted selection, and phenotypic identification breeding techniques, a new Bai Ruyu Dahu rice variety with long spikes, large grains, disease resistance, and low amylose content can be rapidly and accurately bred.

The application discloses a screening method for identifying nucleotide fragments of close relatives of microorganisms, which comprises the following steps: cutting the whole gene sequence of a target microorganism into small nucleic acid fragments containing overlapping regions by using an electronic cutting technology; comparing the fasta file of the small nucleic acid fragments with the NCBI NT database; obtaining a hit table I, deleting repeated sequences, and then obtaining hit nucleic acid sequences; comparing the hit nucleic acid sequences I with the small nucleic acid fragments containing overlapping regions, and obtaining non-hit nucleic acid sequences; repeating the above steps once, designing PCR primers, extracting the genomic total DNA of more than 10 strains of strains belonging to the genus or close genus of the target microorganism strain, constructing a nucleic acid pool, and verifying by PCR amplification. The specific nucleic acid screening method for identifying close relatives provided by the application can efficiently obtain specific nucleic acid sequences of the target microorganism strain in a large amount, the reproducibility of the experimental results is extremely high, the whole experimental process is simplified, and the method has good applicability.