350 results about "Insertion" patented technology

Systems and methods for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. Novel nucleic acid targeting systems comprise components of CRISPR systems and non-LTR retrotransposon elements.

The invention discloses a molecular marker related to thousand seed weight of wheat, a detection primer and application of the molecular marker and the detection primer, and belongs to the technical field of molecular marker-assisted breeding. The nucleotide sequence of the molecular marker TaDTX50-STS is as shown in SEQ ID NO. 1; basic groups from the 502 site to the 661 site of the sequence as shown in SEQ ID NO. 1 have insertion / deletion mutation. The InDel molecular marker related to the thousand seed weight character in a wheat genome is identified and named as TaDTX50-STS, and by detecting the polymorphism or genotype of the InDel molecular marker, the InDel molecular marker can be used for identifying or assisting in identifying the thousand seed weight character of wheat, assisting in breeding dominant varieties with high thousand seed weight of wheat and improving the wheat breeding efficiency.

The invention discloses application of Indel marker dosage typing in detection of sweet potato soft rot resistance, and belongs to the technical field of plant genetic engineering. The Indel molecular marker related to the sweet potato soft rot resistance is obtained through screening, the nucleotide sequence of the Indel molecular marker is shown as SEQ ID NO.2, and an 8bp sequence is inserted into or deleted from the 161st site of the sequence shown as SEQ ID NO.2. Experiments find that target bands of amplification products are obtained through amplification of the Indel molecular marker and electrophoresis, dosage values of two genotypes are obtained according to gray values of the dyed electrophoretic bands, and results show that the insertion type Indel molecular marker is positively correlated with the sweet potato soft rot resistance. The method is of great significance to the dose effect research and molecular assisted breeding of sweet potato gene functions.

The invention discloses enterobacter mori capable of resisting fish aeromonas and application of the enterobacter mori, the bacterial strain is classified and named as enterobacter mori SCH0241, the enterobacter mori SCH0241 is preserved in the China Center for Type Culture Collection on October 17, 2024, and the preservation number is CCTCC NO: M 20242236. The enterobacter mori SCH0241 disclosed by the invention is derived from the intestinal tract of high-stress-resistance healthy hybrid crucian carassius auratus No. 2, has good contact dependence antibacterial activity on aeromonas veronii, and can improve the capability of resisting aeromonas veronii infection of zebra fish. Through construction of an insertion mutation library and phenotype screening, it is found that a gene cluster of SCH0241, which exerts contact inhibition toxicity, is T6SS-2. The enterobacter mori SCH0241 disclosed by the invention provides a new powerful tool for biological prevention and treatment of fish diseases caused by aeromonas veronii.

Among other things, provided herein are systems that replace the natural random integration activity of a retrovirus with site-specific integration machinery. This approach allows for a more precise targeting of a gene of interest into a human genome, e.g., for therapeutic purposes. The system may include integration-deficient retrovirus (e.g., lentivirus) (IDLV), in which the natural integration activity has been reduced (e.g., by mutation to the viral integrase polypeptide). Instead, the system may comprise a site-specific recombinase (e.g., a serine recombinase, e.g., a serine integrase) capable of directing insertion of a template DNA, or portion thereof, into a desired site in the human genome.

Compositions and methods comprising a deaminase for targeted editing of nucleic acids are provided. Also provided are compositions and methods for localizing a heterologous polypeptide to a target DNA molecule, and compositions and methods for targeted editing of nucleic acids. Fusion proteins comprising an RNA-guided nuclease (RGN) and at least one heterologous polypeptide inserted therein are provided, as well as fusion proteins comprising a DNA binding polypeptide and a deaminase. The heterologous polypeptide may be a pilot editing polypeptide or a base editing polypeptide. Compositions also include nucleic acid molecules encoding a deaminase or fusion protein. Vectors and host cells comprising the nucleic acid molecules encoding the deaminase or fusion protein are also provided.

The invention discloses a DNA sequence reconstruction method and system based on multi-scale attention and contrast learning, and relates to the technical field of DNA storage data reconstruction. Comprising the following steps: collecting a plurality of DNA sequence copies, screening out abnormal length sequences, and constructing a standardized clustering data set; performing one-hot coding and filling processing on the DNA sequence; extracting context dependent features and cross-sequence variation features; an Inter-Sequence multi-head attention mechanism is constructed to calculate the similarity between the sequences, and a weighted sequence tensor is generated; a global dependency relationship in the sequence is extracted through an Intra-Sequence multi-head attention mechanism; local offset features caused by insertion and deletion errors are extracted through a multi-size convolutional network; inputting a double-layer long-short-term memory network for sequence-level modeling, and outputting base reconstruction probability distribution; and constructing positive and negative sample pairs, calculating comparison loss, combining cross entropy loss to form a joint loss function, and outputting a high-precision DNA sequence reconstruction result. The method has high accuracy and robustness under the conditions of complex noise and multiple types of errors.

The invention discloses an Indel marker related to a corn kernel protein content character and application of the Indel marker, and belongs to the technical field of plant molecular genetics and crop molecular design breeding. The Indel marker is located on a gdh2 gene of a chromosome 10 of a corn genome, and insertion or deletion of a nucleotide sequence as shown in SEQ ID NO.5 occurs in an intron region between a second exon and a third exon. By applying the molecular marker-assisted selection technology, high-protein new germplasms S3317 (the crude protein content is 17.0%) and JS231148 (the crude protein content is 15.6%) have been successfully cultivated, the increase amplitudes of the high-protein new germplasms and JS231148 are both more than 15% compared with those of the conventional control, and the lysine content reaches 0.41% and reaches the national high-quality protein corn standard.

Provided is a reverse prime editing system, which is used for achieving site-specific and precise small-fragment DNA editing upstream of a target site. In the reverse prime editing system, a targeted strand nickase (such as D10A-Cas9) is used to cleave a nick on a targeted strand, thereby enabling precise small-fragment DNA base insertion, deletion and substitution upstream of the target site under the action of a reverse transcriptase.

The invention belongs to the technical field of microbial engineering, and discloses a method for producing eicosapentaenoic acid (EPA) with high yield by schizochytrium limacinum based on random mutation and low-temperature screening and application, and the method comprises the following steps: driving overexpression of a G418 resistance gene through a P2520 promoter, constructing a random insertion mutant library, and screening to obtain a schizochytrium limacinum mutant strain with a randomly mutated genome; coating in a culture medium containing G418 resistance for culturing, and screening out strains which are resistant to low temperature and good in growth state at 15 DEG C; and inoculating into a fermentation culture medium, adding MgSO4 with the final mass concentration of 0.1% at the initial stage of fermentation, supplementing MnCl2 with the final mass concentration of 0.05% when fermentation is performed for 72 hours, and culturing to obtain a mutant strain. According to the invention, the G418 resistance gene carried by the plasmid is randomly inserted into the schizochytrium limacinum genome, and low-temperature induced screening is combined, so that the target limitation of traditional homologous recombination is broken through, and a stable strain with multiple mutation superposition can be obtained through enrichment.

Provided is an efficient and precise plant gene knockout method. First, a sequence containing a stop codon cluster is inserted into a genome by means of dual pegRNA to obtain, by means of screening, a stop codon cluster sequence capable of efficiently and precisely knocking out a target gene. A prime editing system and multiple pegRNA programming can be used in combination with the method to enable various genomic modifications such as efficient and precise knockout of one or more target genes, base substitutions, and small fragment insertions, deletions, and substitutions with just one prime editing protein.

The invention belongs to the technical field of crop molecular markers, and particularly discloses a molecular marker for identifying the salt tolerance of brassica napus in the germination period and application of the molecular marker. The molecular marker is located at the position of an A02 chromosome scafoldA028707654 of a brassica napus reference genome ZS11.v10, and the allelotype of the molecular marker is wild type C or mutant type CATATT insertion. The invention also provides a specific primer group for detecting the molecular marker, and the salt tolerance (sensitive type or tolerance type) of the brassica napus line can be quickly identified according to the existence of 411bp and 416bp bands through double PCR amplification and electrophoresis detection. The molecular marker is significantly associated with salt tolerance phenotypes, the detection method is rapid, accurate and low in cost, the molecular marker can be used for brassica napus salt tolerance germplasm resource screening and molecular marker-assisted breeding, and the breeding efficiency is significantly improved.

This invention provides a germline mutation detection method and system with a low false positive rate. The system is computer-executed and includes: first, performing a PCR repeat cluster consistency test on sequence alignment files generated from high-throughput sequencing reads, down-regulating the base count weights of inconsistent sites within the cluster; then, based on the sample-specific background error baseline, calculating the variation confidence index of each genomic site using an empirical Bayesian framework to obtain candidate single nucleotide variants (SNPs); obtaining candidate insertion / deletion variants through read clustering and physical verification of insertion fragment lengths; subsequently, performing a dual-engine cross-feedback iteration on the two candidate types until convergence, integrating and filtering, and outputting a structured mutation detection report. This invention significantly reduces the false positive rate of both SNPs and insertion / deletion variants while maintaining sensitivity, and improves the detection capability of complex insertion / deletion variants.

The application discloses a KASP molecular marker of a Nicotiana benthamiana NbSAG101a gene and application thereof. The KASP molecular marker is an InDel insertion and deletion marker of the Nicotiana benthamiana NbSAG101a gene, is located at 256-262 bp of a second exon of the Nicotiana benthamiana NbSAG101a gene, and the nucleic acid sequence of the KASP molecular marker is shown as SEQ ID NO: 4. A wild-type allele of the Nicotiana benthamiana NbSAG101a gene is C, contains a 7 bp sequence shown as SEQ ID NO: 4, and a mutant-type allele is A, and the 7 bp sequence shown as SEQ ID NO: 4 is deleted. The KASP marker provided by the application can accurately and quickly distinguish wild-type homozygotes, heterozygotes and mutant-type homozygotes of the NbSAG101a gene, has high specificity, high accuracy, fast detection speed, low cost and high flux.

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and / or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.

Provided herein are fusion proteins and related methods and systems for increasing the efficiency of genome editing using site-specific nuclease enzymes. These fusion proteins, systems, and methods may selectively increase a desired editing outcome (e.g., insertion of a donor polynucleotide sequence). Also provided are various useful compositions for producing and using these fusion proteins and practicing these methods.

Provided in the present invention are the use of insertion / deletion polymorphism genetic markers in detecting the copy number of human chromosomal subtelomeric regions, a reagent panel for detecting the insertion / deletion polymorphisms genetic markers, and a method for detecting the copy number of human chromosomal subtelomeric regions.

Provided are polynucleotides comprising a mobile bacterial island nucleotide sequence (B-INS) comprising one or more modifications (a modified B-INS) that include deletion or modification of restriction enzyme recognition sites to inhibit restriction enzyme cleavage of the B-INS, and an insertion of at least one cargo sequence into the B-INS. The B-INS is packaged within a bacterium into a phage-like particle that contains a bacteriophage capsid, tail and tail fiber proteins. The phage-like particle function as an antibacterial drone "ABD" and infects bacteria. The cargo sequence is introduced into bacteria infected by the ABD and kills the infected bacteria or inhibits growth of infected bacteria.

The invention provides a papaya CpMp gene, a protein, a primer pair, a recombinant expression vector and application, and belongs to the technical field of plant genetic engineering. The nucleotide sequence of the papaya CpMp gene is as shown in SEQ ID No. 1. The papaya CpMp gene has the effect of regulating and controlling the length of inflorescence stalks. According to the present invention, by using the difference of the CpMp gene on the Y chromosome and the Yh chromosome, i.e., the 4691bp transposon insertion exists on the CpMp promoter on the Yh chromosome, and the transposon insertion does not exist on the CpMp on the Y chromosome, the CpMp gene is adopted as the molecular marker to distinguish the male plant from the male-female plant, and the difference can be used in the early sex verification work of the papaya;

This invention proposes a molecular marker for *Lactobacillus japonicus*, which was deposited on February 7, 2023, at the China General Microbiological Culture Collection Center (CGMCC) with accession number CGMCC No. 26505. The molecular marker comprises a nucleotide sequence selected from one of the following: (1) the nucleotide sequence shown in SEQ ID NO: 24; (2) a nucleotide sequence having at least 97%, 98%, 99%, or higher homology to the nucleotide sequence shown in SEQ ID NO: 24; or (3) a nucleotide sequence having one or more nucleotide substitutions, deletions, or insertions in the nucleotide sequence shown in SEQ ID NO: 24. Using the molecular marker of this invention, not only can the target *Lactobacillus japonicus* be screened quickly and easily, but it can also highly specifically identify the target *Lactobacillus japonicus*, eliminating interference from other strains.

The application belongs to the field of molecular biology, and particularly relates to a specific marker of an exon region of a Oplegnathus punctatus hmcn2 gene, a primer pair, a detection method, a kit and application. The specific marker of the exon region of the Oplegnathus punctatus hmcn2 gene is a nucleotide sequence of non-insertion and insertion specific markers of the exon region of the Oplegnathus punctatus hmcn2 gene DNA fragments, and the sequence is shown in bases of SEQ ID NO:1 and SEQ ID NO:2. The specific marker is applied to identification of female and male genetic sex of the Oplegnathus punctatus. The application establishes a method for realizing rapid genetic sex identification by rapidly detecting an exon DNA insertion variation of the Oplegnathus punctatus hmcn2 gene, and the method has a wide application prospect in the fields of sex identification of the Oplegnathus punctatus, preparation of high male seedlings and family selection breeding.

In one aspect, a method of treating an NK cell to induce a gene edit. The method may include contacting an NK cell with a transfection composition including poly-L-glutamic acid (y- PGA), a single-stranded oligo deoxynucleotide (ssODN) enhancer, or a combination thereof; contacting the NK cell with an editing composition including: a DNA-PK inhibitor, and an HD AC inhibitor; electroporating the NK cell; and contacting the NK cell with a recovery composition including DNase I. In another aspect, a method of preparing an engineered NK cell comprising a fluorescent reporter at an endogenous locus. In another aspect, a method of treating an NK cell to introduce an exogenous nucleic acid.

The present disclosure provides compositions and methods for delivering a gene of interest to a subject. Aspects of the application relate to nucleic acids encoding modified retroelement-derived polypeptides and gene delivery constructs that can direct integration of a nucleic acid sequence into a target nucleic acid (e.g., a genome of a subject).

This invention discloses transcription factors As NF-YB3 Its application in regulating drought resistance in oats falls under the field of biotechnology. (Transcription factors) As NF-YB3 The amino acid sequence is shown in SEQ ID NO.1. As NF-YB3 The CDS sequence of the gene is shown in SEQ ID NO.2, and the gDNA sequence is shown in SEQ ID NO.3. Overexpression As NF-YB3 The gene significantly enhances the drought resistance of oats, while also increasing the activity of CAT and SOD enzymes in oats, slowing down the water loss rate of detached leaves, and improving seedling survival rate under drought stress. AsNF-YB3 forms a heterotrimeric complex with AsNF-YA1 and AsNF-YC5, and its 4bp insertion / deletion mutation in the promoter region regulates oat drought resistance by affecting AsARF1 binding and gene expression. This provides a new gene resource and technical pathway for agricultural stress-resistance breeding.

This invention relates to a primer set and method for high-throughput assessment of drug resistance levels in rodent populations. The invention provides a set of universal degenerate primers for amplifying the Vkorc1 gene in multiple rodent species. The primer set includes primers for amplifying exon 1, exon 2, and exon 3 of the Vkorc1 gene, respectively. By designing universal degenerate primers and coupling them with next-generation sequencing technology, this invention can simultaneously amplify the Vkorc1 gene coding region of at least 15 rodent species across genera and families. This significantly improves the species universality and detection throughput of rodent drug resistance monitoring, reduces the cost of large-scale screening, overcomes the limitation of Sanger sequencing in accurately analyzing heterozygotes with insertions and deletions, and enhances the ability to discover new resistance mutations. It provides a standardized and low-cost technical solution for efficient assessment of rodent drug resistance.

The present invention relates to methods and devices for identification and quantification, including low abundance nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicing, exon insertions, exon deletions, intron insertions, or other rearrangements and / or methylated nucleotide bases at the genomic level.

Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and / or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.

The invention relates to the field of bioinformatics and artificial intelligence analysis, in particular to a chromosome anomaly detection system and method based on a random forest model. According to the method, variation detection is carried out on the purified file, base replacement, insertion and deletion events are recognized, the allele frequency of each variation site is calculated, a standardized VCF format file is generated, the allele frequency spectrum of the variation sites is divided into a plurality of continuous intervals according to the preset step length, and the variation sites are extracted. Counting the number of sites of the sample data falling into each interval in a whole genome range and on each chromosome, and carrying out normalization calculation to generate a standardized feature vector; a random forest classification model trained by historical sample sequencing data with diagnosis tags is adopted to automatically judge all chromosome anomalies of the samples based on the standardized feature vectors of the samples; the method is superior to the existing SNP Array technology in the aspects of detection precision, detection range, chimeric recognition capability, intelligent degree, platform compatibility and the like.

Methods are provided for detecting gene deletions and driver mutations using tumor-specific methylation patterns from cell-free DNA and tissue biopsies. The methods exploit the mutual exclusivity between tumor-specific methylation and homozygous gene deletion, enabling detection through absence of expected methylation signals. Applications include detection of MTAP, PTEN, and RB1 deletions, as well as prediction of EGFR single nucleotide (SNV) and small (up to 50 base pair) insertions and deletions (indel) driver mutations, enabling identification of patients eligible for targeted therapies.