15 results about "Genomic library" patented technology

The invention discloses a preparation method of recombinant catechol-2, 3-dioxygenase and an application of the recombinant catechol-2, 3-dioxygenase. According to the invention, a novel catechol-2, 3-dioxygenase group C23O927 is identified from a constructed metagenome library, and the catechol-2, 3-dioxygenase group C23O927 is a key enzyme for catalyzing degradation of polycyclic aromatic hydrocarbon pollutants. A C23O927-pET32a (+) recombinant expression vector is constructed and converted into host bacteria, heterologous expression of target protein is achieved, and the prepared recombinase belongs to acid enzymes and has good resistance to high temperature, acid, alkali, high-concentration metal ions, organic solvents and surfactants. The recombinase provided by the invention can be used in an acidic environment, has very good enzymatic activity, can catalytically degrade various catechol compounds, can be better used for treating polycyclic aromatic hydrocarbon polluted environments, and has important significance for developing more products which can tolerate various extreme environments and efficiently catalyze degradation of polycyclic aromatic hydrocarbons.

A sequencing module configured to provide metatranscriptomic reads from an oral sample from a subject; metatranscriptomic reads from the sequencing of oral sample and identify and cluster microbes identified in the oral sample into taxon clusters (TCs) using the metatranscriptomic reads mapped to a metagenomic library; generate TC-specific orthogroups for each of the TCs via protein clustering; determine KEGG orthology for each of the TC-specific orthogroups, or genes directly; generate phylogenomic functional categories (PGFCs) from grouping of gene expression counts by the KEGG modules for each of the TCs; retain the PGFCs having an MCR above an MCR threshold to obtain input data; and identify or predict, using a classifier model including variables selected by a feature selection machine learning algorithm, dental caries in said subject based on the input data.

[Problem] To provide: an adapter for binding to polynucleotide fragments that is used for preparing a genome-wide gRNA library for genome editing systems; a gRNA library that is obtained by using the adapter; and uses of the gRNA library. [Solution] An adapter having a structure described in A). A) A structure having i) to iii). i) A polynucleotide chain having sequences i)-1 to i)-3. i)-1: Sequence corresponding to the forward primer. i)-2: Sequence of the recognition site of a restriction enzyme capable of excising a gRNA spacer sequence from the 5' end of a polynucleotide fragment bound to the adapter. i)-3: Sequence of the recognition site of a restriction enzyme capable of cleaving an adapter having the structure of A) from the polynucleotide fragment. ii) A polynucleotide chain having the sequence complementary to i). iii) A single-stranded polynucleotide chain for formation of a loop connecting the 5' end of i) and the 3' end of ii) of the double strand resulting from the binding of i) and ii).

The application belongs to the field of molecular biology and biotechnology, and particularly relates to a probe combination for capturing a mammalian mitochondrial genome and application thereof. The nucleotide sequences of the probe combination are the sequences shown in SEQ ID NO: 1~24537 in turn. The probe combination has good capture efficiency on the mitochondrial genome of mammals, and can obtain a complete mitochondrial genome sequence. Moreover, the probe combination has very high sensitivity, and for low-concentration DNA and highly degraded difficult samples, more than 90% of the samples can still capture the target sequence. The application can mix 4~16 mammalian sample fragmented whole genome libraries, capture, sequence and splice by using the probe combination, obtain the corresponding mitochondrial genome sequence, reduce the cost of obtaining the mtDNA complete sequence of a single sample by 70~75%, and greatly improve the feasibility of large sample quantity research.

Nucleic acid error inhibition is provided. In various embodiments, DNA is extracted from a collection of plasma samples. A sequence library having a duplex adaptor is prepared. The library is prepared by linking a duplex adaptor having a unique molecular identifier (UMI) to the end of each of a plurality of strands of the extracted DNA and amplifying the extracted DNA with a first polymerase chain reaction (PCR). A subset of the whole genome library is selected and amplified with a second PCR to increase the amount of PCR replicas. A plurality of duplex reads are sequenced from the amplified subset.

A system for producing a therapeutic oligomer includes a computing device configured to design a proposed therapeutic oligomer sequence, wherein designing further comprises generating a genomic library for an organism from a gene target, initiating a sequence identification function, identifying a genomic locus that the proposed therapeutic oligomer sequence is predicted to bond to as a function of an off-target sequence function, selecting the proposed therapeutic oligomer sequence as a function of the sequence identification function, the genomic locus, and a criterion element, and synthesize a therapeutic oligomer as a function of the proposed therapeutic oligomer sequence.

The present invention provides a pBeloBCA11-MCS(+) recombinant plasmid, a construction method, and an application thereof. The recombinant plasmid can expand the endonuclease recognition sites of the low-copy plasmid vector pBeloBCA11 at the molecular level, improve the recombination between the pBeloBCA11 plasmid and the target fragment, promote the construction of large-fragment genomic libraries, and facilitate applications in gene cluster-related research.

The invention discloses a screening method for targeted zinc amino acid chelate metabolism genes based on a Crispr whole genome library. The method comprises the following steps: constructing a zinc transporter gene knockout intestinal epithelial cell single gene knockout cell strain; transfecting the Crispr whole genome knockout library into an intestinal epithelial cell single gene knockout cell strain to obtain an intestinal epithelial cell double gene knockout cell strain; treating the intestinal epithelial cell double-gene knockout cell strain with different zinc sources, dyeing with a fluorescent dye, and sorting zinc transport difference intestinal epithelial cell double-gene knockout cell strains through flow cytometry; the separated cell lines are subjected to gDNA extraction, gRNA sequence amplification and high-throughput sequencing, and key target genes for regulating and controlling metabolism of different amino acid chelated zinc are analyzed and identified through bioinformatics. The invention establishes a method for high-throughput screening of the specific metabolism gene of the amino acid chelated zinc, and a Zn metabolism regulation gene library is also obtained through screening at the same time.

The application is particularly a method for automatically annotating a data set of a cytological pathology deep learning model, comprising the following parts: step one: using a single cell micro-operation device to automatically locate and suck cells on a glass sheet dyed by cytological pathology; step two: using a fully automated liquid processing workstation to construct a single cell whole genome library and sequence the extracted cells; step three: determining the benignity and malignancy of the cells through analysis of the single cell whole genome sequencing data, so as to construct a training data set of the cell dyeing picture after sequencing for training a deep learning model. In the application, combined with scDNA-Seq and automatic robot technology for single cell and liquid operation, the ETC annotation method guided by scDNA-Seq provides a standard and scalable method for automatic ETC annotation, and represents a general method for developing a deep learning model for pathological diagnosis of malignant tumor cells in different types of body fluids.

The invention discloses a method for screening a regulatory gene Cg1120 of a transcriptional regulatory factor AtrN under a high intracellular NADPH condition and application of the regulatory gene Cg1120, and the method comprises the following steps: carrying out molecular modification on an original strain, integrating a pntAB gene and a dCas9 gene on a genome to obtain a modified strain which is high in intracellular NADPH level and carries dCas9 protein, and screening the regulatory gene Cg1120 of the transcriptional regulatory factor AtrN by predicting a promoter sequence of the transcriptional regulatory factor AtrN. And constructing a fluorescent reporter plasmid, introducing the whole genome sgRNA library and the fluorescent reporter plasmid into the modified strain, and screening potential regulatory genes through the change of relative fluorescence intensity. The level of NADPH is indirectly adjusted, so that the intracellular redox level is adjusted.

The invention relates to the field of biomedicine, in particular to a biomarker liver phosphofructokinase PFKL for predicting the solid tumor resisting curative effect of an HDAC (histone deacetylase) inhibitor and application of the biomarker PFKL in preparation of a kit for predicting the solid tumor resisting curative effect of the HDAC inhibitor. Through a whole genome CRISPR-Cas9 library screening technology, in-vitro drug sensitivity and in-vivo CDX and PDX models are combined, the key effect of the liver-type phosphofructokinase PFKL in the process of regulating and controlling the drug effect of the HDAC inhibitor is disclosed, it is proved that the liver-type phosphofructokinase PFKL can be used as a biological marker, and the solid tumor resisting curative effect of the HDAC inhibitor is effectively predicted. The method has important clinical values for early evaluation of the curative effect of the HDAC inhibitor of clinical tumor patients, making of individualized treatment schemes and improvement of the survival rate of the tumor patients.

The invention discloses a method for constructing an escherichia coli whole genome CRISPRi library and an application of the escherichia coli whole genome CRISPRi library in target product synthesis, and belongs to the technical field of gene engineering. According to the invention, an sgRNA plasmid library is designed according to escherichia coli BL21 (DE3) genome information, and a sensor plasmid and an sgRNA library plasmid are simultaneously introduced into a tetR-Ptet-dCas9 expression strain to obtain a CRISPRi library which can be used for screening strains with high yield of target products. According to the present invention, by using lactyl-N-neotetraose as a model product, eight inhibition genes, such as cysW, pyrG, sprE, pcnB, YqjA, TnaB, TolB and ihfB, beneficial to the production of the lactyl-N-neotetraose are obtained; according to the invention, a screening method with feasibility is established, a key gene beneficial to synthesis of a target product is identified and obtained, and an efficient method is provided for enhancing synthesis of the target product of a strain.

The application discloses a single-cell exon sequencing method and application thereof, and the method comprises the following steps: S1, tumor single-cell sorting; S2, MDA amplification of the sorted tumor single cells to obtain a genomic library; S3, detection of MDA amplification product uniformity, selection of multiple sites located on different chromosomes and design of corresponding amplification primers, detection of amplification effects of the multiple sites of each single-cell MDA product by qPCR, and determination of whether the genome is uniformly amplified; S4, gDNA library preparation: the amplified DNA is broken into 150-200bp fragments, and a gDNA library is obtained through end repair, tailing, adapter addition and amplification; S5, exon capture and library construction: the prepared gDNA library is hybridized with specific probes, specific regions are captured, and an exon library is obtained by PCR amplification and addition of index tags; and S6, sequencing of the exon library.

Provided herein are compositions and methods for standardizing a sequencing library. Also provided herein are adapter conjugates and hybridized cyclic adapters, compositions comprising the same, and methods of producing the same. Also provided herein are methods of standardizing genomic DNA libraries for next generation sequencing using the adapter conjugates, hybrid circular adapters, and compositions comprising them.