2713 results about "Library" patented technology

The present disclosure provides compositions and methods for generating a plurality of nucleic acid concatemers immobilized to a support by conducting on-support circularization and ligation reactions using a plurality of linear library molecules and a plurality of immobilized splint capture primers. The present disclosure provides methods for seeding and optionally re-seeding the support to increase the density of immobilized nucleic acid concatemers that can be sequenced. In some embodiments, the immobilized concatemers can be used for conducting downstream sequencing workflows including batch sequencing and reiterative sequencing workflows. The present disclosure also provides methods for interrupting an ongoing sequencing run to re-seed the support to generate additional concatemers that can be sequenced.

The invention relates to a high-yield lipase strain and application thereof, and belongs to the technical field of bioengineering. According to the invention, grease-rich samples from different sources are subjected to enrichment treatment, a strain with lipase activity reaching 80.8 + / -1.8 U / mL is obtained through neutral red grease plate screening, the strain is identified as Burkholderia cepacia OCRI-Lip100 through sequencing and sequence comparison, the Burkholderia cepacia OCRI-Lip100 is named as Burkholderia cepacia OCRI-Lip100, and the Burkholderia cepacia OCRI-Lip100 is preserved in China Center for Type Culture Collection on July 3, 2024 with a preservation number of CCTCC M20241369. Lipase obtained by fermentation of the strain is sequenced, enzymatic properties, catalytic activity and substrate preference of the lipase are studied, the optimum catalytic temperature is 60 DEG C, the specific enzyme activity is higher than that of commercial lipase, the catalytic activity is further improved to 116 + / -0.5 U / mL when a C14 substrate is catalyzed, and triglyceride can be hydrolyzed into diglyceride. The strain provided by the invention and the lipase produced by the strain enrich the resource library of the existing lipase, and provide a basis for improving the industrial application of the lipase and realizing the high utilization rate of resources.

The invention belongs to the field of molecular biology and immunology, and particularly relates to an anti-CD3 nano antibody capable of activating the activity of T cells as well as a preparation method and application of the anti-CD3 nano antibody. The invention provides a preparation method of the anti-CD3 nano antibody. The preparation method comprises the following steps: constructing a CD3 plasmid and an overexpression cell line, and immunizing alpaca to obtain peripheral blood mononuclear cells (PBMC) of the alpaca; extracting RNA (Ribonucleic Acid) and carrying out reverse transcription to obtain cDNA; carrying out PCR amplification on the antibody gene segment and cloning the antibody gene segment to a phage display vector; and electrically transforming the vector into SS320 competent cells to obtain the nano antibody library. After two rounds of panning, detecting and screening an antibody clone capable of being combined with the CD3 protein through ELISA (Enzyme-Linked Immunosorbent Assay); an antibody sequence is selected through sequencing, and an antibody protein is expressed by using a mammalian cell high-throughput expression system; and then detecting and screening the antibody which is only specifically combined with the CD3. The method disclosed by the invention is simple, convenient and rapid to operate, and can be used for preparing active antibodies for treating potential tumors and proliferative diseases.

The invention belongs to the technical field of gene breeding, and discloses a rapid matching breeding improved parent composition, an obtaining method and application. According to the method, a basic SNP marker is obtained; carrying out GWAS analysis on the basis of the collected phenotypes, carrying out dominant genotype identification on markers associated with the phenotypes, and constructing a dominant genotype library of the functional sites; calculating the contribution degree PVE of the functional sites to phenotypes, analyzing the contribution degree PVE, calculating the linkage region Block of each material or group, and constructing a material PVE score library and a Block library; and matching and combining every two materials based on dominant genotypes, PVE of functional sites and linkage regions Blocks of the materials / groups to obtain an optimal combination parent of each material. According to the invention, more favorable genotype polymerization states can be realized.

The invention relates to the technical field of molecular biology of siberian wildrye, and particularly discloses an SNP (Single Nucleotide Polymorphism) molecular marker combination for constructing a siberian wildrye DNA (Deoxyribose Nucleic Acid) fingerprint spectrum and application. The SNP molecular marker combination for constructing the siberian wildrye DNA fingerprint spectrum is composed of 52 SNP molecular markers, and the SNP molecular marker combination has high specificity and resolution, and can reveal the real level of genetic diversity of siberian wildrye; the SNP molecular marker combination is used for establishing a siberian wildrye DNA fingerprint database, DNA fingerprint information of different siberian wildrye germplasm can be correctly reflected, resource or variety identification can be carried out on siberian wildrye, the detection result is accurate and efficient, 90 siberian wildrye germplasm resources are effectively distinguished for the first time, the identification capacity is high, and technical support is provided for siberian wildrye germplasm resource protection. The SNP marker and the application method thereof provided by the invention have the advantages of high throughput, accuracy, low cost, simplicity in operation and the like, and have a very wide application prospect.

The invention discloses a tiny residual focus detection method and system based on ultra-high depth sequencing, and relates to the technical field of tiny residual focus intelligent detection.The tiny residual focus detection method comprises the following steps that on the basis of a sequencing library, splitting is conducted according to a sample index to obtain a to-be-detected sample, and a consensus sequence is obtained according to a molecular identifier of the to-be-detected sample; based on a consensus sequence, filtering out the consensus sequence of which the mass value is less than 25 or the failysize is less than 3, and combining a subtype type and a distance from a fragment edge as noise introduced into an original nucleic acid molecular chain; a context sequence (context) and a chain direction are used as noise for introducing the capture level of PCR amplification; based on the noise level, in combination with tumor priori knowledge, the ctDNA level is estimated, and the MRD state is determined by detecting the significance of a molecular signal source. According to the invention, the sensitivity and specificity of MRD detection are improved.

A high-throughput screening method for an aptamer, and a use. An implementation route is divided into three parts, a first part is construction of a library of a pre-enriched aptamer and sequencing same, a second part is generation of an aptamer cluster on a slide, and a third part is combination of a target protein and the aptamer cluster. Provided is a method for high-throughput rapid detection of an aptamer. The method has the beneficial effects: sequencing time, sequence synthesis and affinity re-verification time are saved, the affinity verification costs are greatly saved, rapid screening of aptamers can be promoted, and the actual use of aptamers is promoted along with the increase in the types and numbers of aptamers. The existing platform BGISEQ 500 of Beijing Genomics Institute can be used to grow an aptamer cluster on a chip by using DNB as a template, and the use of sequencers is expanded by integrating sequencing, sequence synthesis and affinity identification.

The invention is applicable to the technical field of drug research and development, and provides a lead compound discovery method based on a large language model, which comprises the following steps: determining a target spot and constructing an initial compound library; generating fragments and forming an initial fragment library; calculating the frequency of occurrence of the fragments and the affinity contribution degree of the fragments to the target protein, and updating the fragment library; fragment sampling weight calculation and candidate fragment selection; the large language model generates molecules according to the candidate fragments; evaluating the quality of the generated molecules and updating the molecule library; and repeating the cycle until a preset iteration round number is reached. A fragment-based drug design method is combined with the large language model, rich domain knowledge of the large language model is used for replacing human experts to guide drug design, fragments are used as prompts to stimulate the internal potential of the large language model, the advantages of the two methods complement each other, exploration of the whole chemical space is completed, and the drug design efficiency is improved. The lead compound reaching the human expert level is designed in actual use, and a new technical means is provided for drug research and development.

The present invention relates to strategies for combining elements of non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) into functional enzymes to promote the production of peptides and polyketide of any sequence. The present invention is based on the use of conserved sequence motifs within the T domain (or T domain-like) gene of the NRPS / PKS, which is used according to the invention as fusion sites for the production of new (and artificial) NRPS / PKS enzymes that can produce any peptide or polyketones of interest. The present invention provides artificial NRPS / PKS of the invention, methods and means for generating them, and nucleic acid libraries encoding various modules useful for designing NRPS / PKS for any peptide sequence of interest.

The invention relates to the technical field of virus whole genome sequencing, and discloses a method for virus whole genome sequencing, which comprises the following steps: S1, extracting a sample genome, operating according to a specification of a commodity kit, extracting RNA (Ribonucleic Acid) of the sample genome, and performing library construction after reverse transcription and targeted amplification. According to the method for sequencing the whole genome of the virus, the whole genome sequence of the virus can be obtained through the sequencing method, and compared with the current detection which only stays at negative and positive detection, the whole genome sequence can be obtained on the basis through the method for sequencing, epidemiological traceability is carried out, and meanwhile the sequencing cost can be effectively reduced.

The invention discloses an ultrahigh-sensitivity sample component evaluation and traceability method and device. The method comprises the following steps: acquiring a sample, and carrying out nucleic acid extraction, library construction, capture enrichment and sequencing to generate sequencing data; preprocessing the sequencing data to obtain high-quality sequencing data; identifying SNP loci and genotypes thereof in the high-quality sequencing data, and constructing an SNP combination database; carrying out quantitative statistics on the double allelic genotypes of the SNP sites, and calculating the variation abundance of secondary alleles; constructing an SNP site variation abundance background distribution model according to the genotype information and allele variation abundance of the SNP sites; and performing cross contamination assessment on the sample by using the constructed SNP combination database and the variation abundance background distribution model. According to the method, qualitative evaluation of multi-source components in the sample, quantitative calculation of the cross contamination proportion and traceability analysis of non-self sources are achieved.

The present disclosure provides methods for reducing sequencing errors comprising one or any combination of: (i) removing deaminated bases in any nucleic acid molecule throughout a library preparation workflow which includes immobilised splints which bind to the library, the use of a compaction oligonucleotide, optionally with an intervening sequence, formation of closed circular nucleic acids, creating gaps using glycosylase and lyase activities at positions with deaminated bases. The library may be sequenced using pairwise sequencing, e.g. with dark sequencing and / or sequencing using a multivalent labelled probe for the formation of an avidity molecule and soluble primer and polymerase. Method for sequencing concatemers in which the concatermers are contacted with polymerases, soluble primers and a multivalent labelled molecule which forms a complex with the polymerase. Detecting polymerase position and nucleobase bound to the polymerase in the complex. These methods generate higher quality base calls during downstream sequencing workflows.

The invention provides a three-generation sequencing read analysis method, application and device. The method comprises the steps that a read segment is obtained, the read segment is obtained by sequencing a sequencing library through a three-generation sequencing platform, and molecules of the sequencing library comprise a sequencing primer recognition sequence, a tag sequence and a UMI sequence; based on the sequencing primer recognition sequence in the read, determining an identity marker area of the read; comparing the identity marking area with at least one standard tag sequence, and determining the tag sequence of the read section in the identity marking area based on the comparison result; and determining the UMI sequence of the read based on the tag sequence in the identity marking area. According to the method, the characteristic of high insertion and deletion error rate in a three-generation full-length transcriptome sequencing result is fully considered, the utilization rate of three-generation sequencing data is improved based on a sequence alignment method, and the accuracy of transcript quantification is improved based on K-mer UMI sequence correction.

A dual screen technique using DEL and 2DCS screens with libraries of synthesized small molecules and synthesized RNA structures (4,096 targets) delivers bona fide ligand-RNA 3D fold target pairs. One of the newly discovered ligands bound a 5′GAG / 3′CCC internal loop that is present in pri-miR-27a, the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand is cell-active, potently and selectively inhibits pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells.

The invention discloses a method for aided analysis of influence of 5 'UTR on mRNA translation efficiency based on a machine learning model, and relates to the technical field of synthetic biology and computational biology, the method comprises the following steps: S1, constructing a 5' UTR plasmid library; s2, transcribing the 5 'UTR plasmid into an independent mRNA (messenger ribonucleic acid) with a luciferase-opt luciferase, and taking the luminous intensity of the luciferase-opt luciferase as the translation intensity of the mRNA; s3, analyzing characteristics related to protein expression intensity of the mRNA; and S4, constructing a random forest algorithm model on the basis of the features analyzed in the step S3 to predict the influence of the 5 'UTR on the mRNA translation efficiency. According to the method for auxiliary analysis of the influence of the 5 'UTR on the mRNA translation efficiency based on the machine learning model, a feasible technical route reference is provided for sequence optimization of mRNA in subsequent mRNA vaccine development, so that the mRNA vaccine can efficiently express target protein in a body.

The invention provides a nucleic acid aptamer for specific recognition of morphine and application of the nucleic acid aptamer, and belongs to the technical field of biosensing and detection. The nucleotide sequence of the nucleic acid aptamer is as shown in SEQ ID NO: 1. The screening method is based on a Capture-SELEX technology and comprises the key steps that streptavidin magnetic beads are used for fixing an ssDNA library, estradiol, deabietic acid and totarol are introduced to serve as reverse screening substances so as to remove non-specific sequences, and finally the high-specificity aptamer is obtained through high-throughput sequencing and affinity determination. The dissociation constant of the aptamer and morphine is 127.31 nM, and the aptamer shows high affinity and high specificity. The invention further relates to application of the aptamer in preparation of a sensor and a kit for detecting morphine, and a new technical means is provided for rapid detection of morphine.

The invention relates to the technical field of high-throughput sequencing, and discloses a kit and a library construction method and a target variation detection and analysis method thereof, the kit comprises a pre-library construction reagent and a target region liquid phase hybridization capture reagent; wherein the pre-library construction reagent comprises a repair reagent, a joint, a connection reagent, an amplification reagent and purified magnetic beads; the target area liquid phase hybridization capture reagent comprises a hybridization reagent, a cleaning reagent, an amplification reagent, a purification magnetic bead, a target gene probe and a CNV / LOH probe. The invention provides a rapid, accurate and low-cost construction method of a library containing a targeting gene probe and a CNV / LOH probe and application of the library, through one-time library construction and sequencing, the advantages of a high-throughput targeting sequencing technology and a CNV-Seq technology are integrated; multi-gene point mutation, insertion and deletion, gene copy number variation, large-fragment copy number variation and heterozygosity deletion can be detected at the same time.

The invention relates to a method for screening FMT (intestinal flora transplantation) donors easy to colonize. Comprising the following steps: collecting excrement of a receptor before intestinal flora transplantation, performing full-length 16s DNA sequencing on the excrement and a donor library, calculating the abundance and satisfaction degree of the donor and the receptor, and the like. The method provided by the invention can be used for screening a donor sample library easy to colonize for the FMT and screening and matching proper donors for patients, so that the colonization of donor strains after the FMT and the effectiveness of the FMT are ensured.

Provided herein are fusion polypeptides comprising an amino acid sequence of a bacteriocin, the amino acid sequence of the bacteriocin being a cleavage intein both on both the N-terminus and on both the C-terminus that cyclizes the bacteriocin. Also provided are nucleic acids and genetic vectors encoding the fusion polypeptides, as well as microbial cells genetically engineered with the nucleic acids or genetic vectors. Also provided are methods of making the cyclic bacteriocin, methods of screening using a library of nucleic acids or genetic vectors encoding the fusion polypeptides, and methods of controlling growth of organisms using the cyclic bacteriocin made by the methods provided herein.

The invention provides a method for deducing the abundance of each family in a group based on mixed pool simplified genome sequencing, which comprises the following steps of: (1) establishing a parent 2b-rad library, and extracting SNP (Single Nucleotide Polymorphism) genotypes and sites by using a 2b-rad standard process; combining the SNP genotypes of the 2n parents into genotypes of n parent pairs according to a male parent and female parent relationship; comparing the genotypes of the parent pairs, and determining family specific tags; (2) extracting offspring individual tissues, mixing, and carrying out DNA extraction and 2b-rad library building sequencing on the mixed sample tissues; counting the sequencing depth of all the specific tag sites and calculating the secondary allele frequency of the specific tag of the mixed sample filial generation; and (3) calculating the proportion of each family in the offspring according to the sequencing depth of the specific tag site and the secondary allele frequency of the specific tag of the mixed offspring. According to the method, the overall feature distribution of the family can be accurately evaluated without sequencing each individual, so that the cost is greatly reduced.

Methods and systems for targeted detection of circulating tumor DNA (ctDNA) molecules are disclosed herein. In some cases, a molecular sequencing library depleted of methylated DNA can be generated and used to detect ctDNA in a cell-free DNA sample reliably at a lower sequencing depth and lower cost than existing methods.

The invention relates to a method for carrying out pathogenic microorganism identification and gene variation state joint detection on a pulmonary alveolar lavage fluid sample based on high-throughput sequencing. The method comprises the following steps: extracting nucleic acid from the pulmonary alveolar lavage fluid sample; constructing a metagenome capture library, and constructing a lung cancer polygene library; carrying out final library pooling; performing high-throughput sequencing; and analyzing data. Compared with the prior art, the scheme provided by the invention is based on a technical path of'macro 'captured by metagenome and'target' of targeted high-throughput sequencing; after the constructed final library is subjected to high-throughput sequencing and data analysis, index output (pathogenic microorganism identification, host chromosome copy number variation, gene mutation, gene fusion, gene copy number variation and methylation state) of multiple biomarkers can be met in one-time detection.

The invention discloses a bidirectional reversible conversion method and system between a peptide molecule SMILES and a sequence expression. The core innovation lies in that a new sequence description syntax is defined to retain information of a polypeptide special bond and specific modification of amino acid; a main chain atom index and adjacency traversal topology identification algorithm is adopted, and end group and topology integrated detection and coding are carried out; a residue recognition algorithm for main chain cutting and template library matching is compatible with any standard or non-standard amino acid residues, an extensible end group library / monomer template library and an automatic increment mechanism, and automatic recognition and sequence annotation of S-S disulfide bonds; the invention relates to a high-fidelity assembly algorithm of HELM anchor points and topology aware cyclic peptide processing. The method solves the problems of incapability of supporting a complex polypeptide topological structure, poor reversibility, insufficient expansibility of a monomer library and the like in the prior art, can be widely applied to scenes of quantitative structure-activity relationship model construction, large-scale polypeptide data cleaning and the like, and has remarkable practicability and innovativeness.

The invention provides a phage group enrichment method as well as a kit and application thereof, and belongs to the technical field of gene sequencing. According to the method, the phage group in the sample is enriched based on lysozyme and DNA binding dye, and then antibiotic is combined to inactivate bacteria and degrade DNA and RNA, so that the interference of the extracted bacteria DNA in the phage group is reduced, the total enrichment fraction of the established phage library is obviously improved, the ViromeQC concentration fraction of the phage library is greater than 10, and the application prospect is wide. The research requirement of a bacteriophage group is met, and the application value is wide.

The invention discloses preparation of a human CD56 immune phage display antibody library, which comprises the following steps: S1, animal immunization: expressing recombinant hCD56 protein in escherichia coli, then immunizing a Balb / c mouse, and detecting immune titer; s2, splenocyte preparation: extracting RNA (Ribonucleic Acid) of immune mouse spleen cells, and performing reverse transcription to obtain cDNA (Complementary Deoxyribonucleic Acid); s3, preparation of an initial bacteriophage display library: amplifying a heavy chain variable region and a light chain variable region by using a PCR technology, and then assembling to form scFv; constructing scFv phagocytids, electrically transforming the scFv phagocytids into TG1 competent cells, and constructing a bacterial library; s4, constructing a phage single-chain library of the hCD56: infecting the bacterial library by using a helper phage M13K07, and constructing a phage single-chain antibody library; and S5, elutriation and screening of a phage library: specifically enriching a phage single-chain antibody library, screening positive clones from the phage single-chain antibody library, and determining a sequence. According to the invention, the human hCD56 antibody scFv sequence fragment can be screened out, and the research and development period is shortened.

The invention belongs to the field of preparation of medical intermediates, and particularly relates to a preparation method of an On-DNA sulfinic acid structure compound. The method for preparing the On-DNA sulfinic acid structure compound comprises a step of oxidizing On-DNA thiol (phenol) into the On-DNA sulfinic acid structure compound under alkaline and heating or illumination conditions, a solvent used in the reaction step is a mixed solution of water, dimethyl sulfoxide, N, N-dimethylformamide, acetonitrile, ethanol or tetrahydrofuran, the reaction temperature is not more than 80 DEG C, and the reaction time is not more than 2 hours. And the illumination wavelength ranges from 365 nanometers to 535 nanometers. The On-DNA sulfinic acid structure compound obtained in the invention can be directly used for constructing a structure compound with a sulfonyl group, the reaction condition is mild and convenient, a new method and a new idea are provided for construction of a DNA coding compound library, and the On-DNA sulfinic acid structure compound has a very good application prospect in lead drug development.

The present disclosure relates in some aspects to methods for analyzing target nucleic acids and their spatial locations in a biological sample using Argonaute proteins. In some aspects, a barcode probe library comprising a plurality of probes each comprising a plurality of barcode subunits that identifies a target analyte is detected in situ in the sample. Also provided are compositions and kits for use in accordance with the methods.

The invention discloses an advanced data encryption protection technology for DNA information storage, and the specific technical scheme of the technology comprises the steps: coding to-be-encrypted data into small information blocks and transcoding the small information blocks into a DNA sequence through a coding and encryption scheme, after the DNA sequence is synthesized, introducing interference information through random errors or fractures, the interference intensity of random combination interference noise is effectively improved; the method for decrypting the DNA library carrying the encrypted information comprises the steps of sequencing, fragment assembly, information small block reconstruction, reordering and decoding, and finally decoding the original information based on an erasure coding scheme. The technology has a wide application prospect in the field of data storage and protection.

Disclosed herein is a system for detection of a molecular community in a molecular network, the system comprising an information handling system that comprises at least one processor; and a non-transitory storage medium storing instructions readable and executable by the processor to perform a method comprising receiving molecular data from an analytical device and / or a data repository; generating an unpruned molecular network from the molecular data; treating the unpruned network with a community detection algorithm to form one or more molecular communities; parsing the molecular communities to prevent the formation of singletons; and identifying at least one molecule present in the molecular community by comparing the molecular community with reference spectra from a library of spectra or by using a molecular structure prediction tool.