21 results about "Reading frame" patented technology

The invention relates to the technical field of bioinformatics, and discloses a method, a system, equipment and a medium for searching for base mutation aiming at third-generation full-length transcript sequencing data, the base mutation is accurately positioned to a specific transcript by directly processing the third-generation full-length transcript sequencing data, and the method and the system for searching for the base mutation aiming at the third-generation full-length transcript sequencing data are provided. The co-occurrence relation of a plurality of mutations on the same transcript is accurately analyzed, and the defects of calculation redundancy, function misjudgment and the like caused by the fact that a mutation transcript source cannot be determined due to fragmentation splicing and the co-occurrence is simulated by depending on permutation and combination in a second-generation short-read-long sequencing technology are effectively overcome; the recall rate of transcripts which are not mapped due to a high-variation region is improved through mapping correction assisted by structural variation, and false positive is effectively inhibited through a multi-dimensional filtering condition, so that the sensitivity and reliability of mutation detection are remarkably improved; particularly, mutation events with function remodeling due to reading frame change can be accurately recognized in scenes such as neoantigen prediction where mutation function consequences need to be accurately evaluated, and the method has important value in application in the fields of precision medical treatment and the like.

The invention belongs to the technical field of genetic engineering, and particularly relates to a universal bacterial artificial chromosome recombinant virus transfer vector and a construction method thereof, the transfer vector comprises a BAC amplification vector with pUC19-loxp-gpt-IRES-EGFP as a basic skeleton and pUC19-BAC as a functional sequence; according to the universal bacterial artificial chromosome recombinant virus transfer vector and the construction method thereof, a drug screening target gene reading frame and an EGFP fluorescent protein gene reading frame are connected through an IRES double-expression connection sequence, and double screening can be carried out; in the BAC construction process, screening genes and functional sequences are respectively constructed to a high-copy T vector, so that sufficient plasmid DNA can be conveniently copied and prepared. And through a proper restriction enzyme cutting site, introduction of various homologous arms is facilitated, the alignment is wide, simultaneous operation of various genomic sequences is facilitated, and the research efficiency is improved.

The present disclosure relates to the production of multimeric polypeptides (e.g., comprising two or more subunits, each subunit comprising two or more polypeptide chains, such as a multispecific or bispecific antibody) in eukaryotic host cells. In some embodiments, provided herein are methods for producing a multimeric polypeptide in a eukaryotic host cell using a host cell that comprises a polynucleotide comprising a translation initiation sequence operably linked to an open-reading frame encoding each polypeptide of the multimeric polypeptide. Advantageously, the present disclosure demonstrates that tuning the strength of the translation initiation sequences linked to each open-reading frame allows for higher production of the multimeric polypeptide with fewer incorrectly assembled side products. The present disclosure further provides cells, methods of screening, and kits related thereto.

The invention relates to the technical field of synthetic biology, and discloses a recombinant plasmid and a recombinant bacterium for producing nortetracycline as well as a construction method and application of the recombinant plasmid and the recombinant bacterium. In order to heterologously produce the nortetracycline, the invention provides a recombinant plasmid for producing the nortetracycline, a starting plasmid of the recombinant plasmid is pOxy2, and the recombinant plasmid is obtained by knocking out oxyS and oxyR genes in the starting plasmid pOxy2, then knocking out oxyF genes and introducing ctcN and ctcM genes in an aureomycin biosynthesis pathway to the position of an oxyF original reading frame. The recombinant plasmid prepared by the invention is used for selecting a host which is rapid in growth and simple and convenient in genetic manipulation as a nortetracycline industrial production strain, so that biological synthesis of nortetracycline is realized, and no other tetracycline by-products exist.

The present invention relates to the field of bioinformatics and provides a dsRNA / siRNA target sequence design method based on thermodynamic parameters. The method comprises the following steps: standardizing the coding sequence of a candidate gene; presetting a reading frame, segmenting the coding sequence of the candidate gene by translation of the reading frame, and obtaining a plurality of candidate dsRNA / siRNA target sequences; reading and analyzing the candidate dsRNA / siRNA target sequences, and obtaining base pairs of all candidate dsRNA / siRNA target sequences; presetting the thermodynamic parameters of all base pairs, calculating the sum of the thermodynamic parameters of all base pairs, and obtaining final thermodynamic parameters of the candidate target sequences by combining correction parameters; and calculating a score for each candidate dsRNA / siRNA target sequence according to the thermodynamic parameters, and determining the dsRNA / siRNA target sequence with the highest score as the optimal dsRNA / siRNA target sequence.

The present invention provides a modified therapeutic mRNA comprising at least one nucleic acid sequence selected from at least one frameshifted nucleic acid sequence, at least one ribosome slippery sequence, and / or at least one other reading frame sequence, wherein the nucleic acid sequence comprises at least one synonymous mutation. Also provided are methods for producing the modified therapeutic mRNA, methods for reducing off-target immunogenicity to the therapeutic mRNA, and methods for reducing out-of-frame translation and / or increasing the translational fidelity of the therapeutic mRNA. The modified therapeutic mRNA for use as a drug is further provided.

An improved promoter and a use thereof. An improvement is to mutate a nucleic acid sequence between −35 region and −10 region in a promoter region into recognition sites for an endonuclease. The improvement can overcome the problem that a strong promoter in a vector based on blue-white screening initiates the transcription or translation of foreign genes and a transcription or translation product might be toxic to a host and cannot be cloned, avoid the deficiency that frameshift mutation of a gene due to a lack of 1-2 bp of the vector at digestion sites results in false positive clones, and eliminate a false negative phenomenon that a plate is rich in blue spots due to a small fragment of foreign DNA and a reading frame of the gene which is unchanged by inserting the foreign DNA.

The present invention is directed to a live-attenuated Mycobacterium tuberculosis composition comprising an isolated microorganism belonging to a M. tuberculosis MTBVAC strain having a i) PhoP-phenotype by the inactivation by a genetic deletion of the Rv0757 gene, wherein the open-reading frame (ORF) sequence of phoP consists of SEQ ID NO 4, and ii) the deletion of a second gene, Rv2930 (fadD26), that prevents PDIM production (PDIM-phenotype), wherein the open-reading frame (ORF) sequence of fadD26 consists of SEQ ID NO 2, for use in therapy in a human subject in need thereof, wherein the composition is administered to said subject via pulmonary delivery.

Provided herein are composition and methods for gene therapy of LEM domain-containing protein 2 (LEMD2) cardiomyopathy. Viral vectors are used to deliver LEMD2 reading frame for gene augmentation in cardiac cells that harbor loss-of-function LEMD2 mutations. A murine model for LEMD2 cardiomyopathy is also described.

The invention relates to a SmERF1B gene cloned from eggplant and application of the SmERF1B gene in regulating and controlling the anthocyanin content of eggplant peel. The maximum reading frame sequence of the SmERF1B gene is represented by SEQ ID NO.1, and the amino acid sequence coded by the SmERF1B gene is represented by SEQ ID NO.2. The eggplant is transformed by adopting an agrobacterium tumefaciens-mediated method, and the result proves that compared with a non-transformed plant, the anthocyanin content in the peel of the transgenic eggplant is obviously increased, so that the color of the peel is darkened. The method is helpful for further understanding the eggplant peel coloring mechanism, so that the eggplant peel coloring can be regulated and controlled by utilizing a molecular means, and a new eggplant variety with high anthocyanin content is bred.

1. The name of the design product: English combination reading frame. 2. The use of the design product: for English teaching. 3. The design points of the design product: in shape. 4. The picture or photo that best indicates the design points: perspective view.

The invention provides a method for screening Duchenne muscular dystrophy exon jump splicing regulation sites, and particularly provides a method for screening potential gene editing sites for inducing exon jump based on mini genes. Potential gene editing sites capable of inducing all or part of exons to jump are screened based on mini-genes. The gRNA can be designed according to the sites, after the gRNA and editing tool enzyme are used together, mRNA which is slightly shortened but correct in reading frame can be generated, the mRNA can generate functional Dystrophin protein during expression, and normal functions of muscle cells are recovered, so that the DMD disease is treated.

The invention provides a Ribo-seq-based method and a Ribo-seq-based system for analyzing an HBV protein translation level, and belongs to the technical field of bioinformatics and virology. The method comprises the following steps: constructing a linear HBV reference genome sequence and optimizing a starting point of the linear HBV reference genome sequence; the Ribo-seq sequencing data is compared to a linear HBV reference genome sequence, and a P-site signal of each nucleotide position is obtained; separating the P-site signals according to the reading frames to obtain respective signal intensity distribution of the reading frames; calculating the median signal density and the signal leakage rate of the protein in the pure region of the HBV protein; correcting the observation signal of the target reading frame in the mixing region of the overlapping protein; and outputting the corrected translation signal intensity of the HBV protein. By adopting the Ribo-seq-based method and system for analyzing the HBV protein translation level, the HBV protein translation level can be accurately quantified.

This disclosure provides a DNA construct comprising: (a) a start exon encoding a start codon; (b) a first frameshift exon downstream of the start exon, the first frameshift exon including a first receptor splice site, wherein inclusion or exclusion of the first frameshift exon in alternative splicing determines the downstream reading frame of a mature mRNA transcript; and (c) a first specific exon downstream of the first frameshift exon, the first specific exon including a second receptor splice site, a first reporter gene, and a second reporter gene, wherein the first reporter gene is located upstream or downstream of the second reporter gene, and wherein the first reporter gene and the second reporter gene are in different reading frames, wherein exclusion of the first frameshift exon causes the first reporter gene to be in the same reading frame as the start codon, and wherein inclusion of the first frameshift exon causes the second reporter gene to be in the same reading frame as the start codon.

The present invention provides a method for screening regulatory sites of exon skipping splicing in Duchenne muscular dystrophy. Specifically, the present invention provides a method for screening potential gene editing sites that induce exon skipping on the basis of mini-genes. The present invention screens potential gene editing sites that can induce all or part of exon skipping on the basis of mini-genes. gRNAs can be designed for these sites, and after these sites are used together with an editing tool enzyme, an mRNA that is slightly shortened but has a correct reading frame can be generated. Such an mRNA can produce a functional Dystrophin protein when expressed, and restore the normal function of muscle cells, thereby treating DMD disease.

The invention belongs to the field of biomedicine, and particularly relates to a raoultella ornithinolyticus antibacterial peptide and application thereof.The raoultella ornithinolyticus antibacterial peptide is a polypeptide (also called antisense peptide) formed by coding of the same reading frame on a complementary chain of a DNA positive-sense chain of a functional domain in truncated CpxA, an amino acid sequence of the raoultella ornithinolyticus antibacterial peptide is shown as SEQ ID NO: 2, the raoultella ornithinolyticus antibacterial peptide is combined with meropenem (MEM) to synergistically inhibit growth of a strain B1645-1B carrying NDM-1, and the raoultella ornithinolyticus antibacterial peptide has a great application prospect and provides a new medicine for treating infectious diseases caused by raoultella ornithinolyticus and solving medicine resistance.

The application belongs to the field of biomedicine and particularly relates to an ornithine-degrading Raoultella antibacterial peptide and application. The ornithine-degrading Raoultella antibacterial peptide is formed by a polypeptide (also referred to as antisense peptide) encoded by a complementary strand of a functional domain DNA sense strand in truncated CpxA in the same reading frame. The amino acid sequence of the ornithine-degrading Raoultella antibacterial peptide is shown as SEQ ID NO:2. The ornithine-degrading Raoultella antibacterial peptide and meropenem (MEM) jointly inhibit the growth of NDM-1 strain B1645-1B, has a very large application prospect, and provides a new drug for treating infectious diseases caused by ornithine-degrading Raoultella and solving drug resistance.

The application provides a method and system for analyzing HBV protein translation level based on Ribo-seq, and belongs to the technical field of bioinformatics and virology. The method comprises the following steps: constructing a linear HBV reference genome sequence and optimizing the start point thereof; aligning Ribo-seq sequencing data to the linear HBV reference genome sequence to obtain P-site signals of each nucleotide position; separating the P-site signals according to reading frames to obtain signal intensity distribution of each reading frame; calculating the median signal density and signal leakage rate of the protein in the pure area of the HBV protein; correcting the observed signal of the target reading frame in the mixed area of the overlapping protein; and outputting the corrected translation signal intensity of the HBV protein. The method and system for analyzing HBV protein translation level based on Ribo-seq can accurately and quantitatively analyze the translation level of the HBV protein.

This invention discloses a small basic membrane intrinsic protein TtSIP1;2 of mitochondrial aquaporin and its encoding gene. TtSIP1; 2 Its cDNA reading frame sequence is shown in SEQ ID NO.2, and the encoded amino acid sequence is shown in SEQ ID NO.1. This invention... TtSIP1;2 The gene-encoded protein TtSIP1;2 is associated with the tolerance of Saccharomyces cerevisiae to high salt, high osmotic pressure (simulated drought), high temperature, and H2O2 (oxidative stress). TtSIP1;2 The gene can enhance yeast's tolerance to various abiotic stresses, improve its survival rate under stress, and promote yeast vitality. Overexpression of this gene in Arabidopsis thaliana can improve the salt and drought tolerance of transgenic plants. This invention... TtSIP1;2 Genes can be applied to the genetic improvement of stress tolerance in engineered bacteria and plants, and can be used to cultivate transgenic engineered bacteria or plant varieties with improved tolerance to high salt, drought, high temperature and oxidative stress.

The application provides a nevus basal cell carcinoma syndrome gene mutation site and application thereof, the gene mutation site is a frame shift mutation c.724_725delCA of a 5th exon of a PTCH1 gene, the mutation causes a subsequent codon reading frame change, and causes a PTCH1 protein frame shift mutation p.Q242Vfs*9.The c.724_725delCA mutation site of the application expands the pathogenic gene spectrum of NBCCS.The PTCH1 gene c.724_725delCA mutation in the application can be applied in NBCCS diagnosis, and a kit containing a mutation detection primer or probe and a genetic counseling and prenatal diagnosis method based on the mutation can be prepared.

Novel compositions of TCR [gamma] variable reading framework protein (TARP) peptides in combination with cationic lipids such as DOTAP, and in particular R-DOTAP, induce high levels of TARP-specific multifunctional cell lytic T cells. Compositions and methods of use are provided. The compositions comprise pairs of N-terminal and C-terminal overlapping peptide sequences that replicate the key central antigen region of TARP and encompass intact proteins selected and designed to be efficiently processed by antigen presenting cells to inhibit the expression of the TARP when delivered in combination with immunostimulatory nanoparticles comprised of R-DOTAP cationic lipids. A cytotoxic T cell specific for the TARP-derived T cell peptide antigen is initiated.