51 results about "Essential gene" patented technology

The invention belongs to the technical field of essential gene prediction, and particularly relates to an essential gene prediction method based on DNA large model and time-frequency domain deep learning fusion, and the method comprises the steps: taking a domain DNA large model as a core representation layer, and obtaining special gene representation through cross-species corpus pre-training and task fine tuning; a T-Block and F-Block dual-channel time-frequency fusion structure is adopted, and the local dependence and long-range regulation relation of a gene sequence is synchronously captured by expanding DFT (Discrete Fourier Transform), complex value attention and iDFT (Initial Discrete Fourier Transform) conversion; designing an efficient modeling reasoning scheme of sliding window slices and gene-level aggregation aiming at an ultra-long sequence; in combination with class imbalance and a noise robust training strategy, cross-cell line / cross-platform transferable threshold output is realized through temperature scaling calibration, an uncertainty quantization and structured interface is matched, and drug target screening and experimental design decision are supported. The system supports the realization of multiple programming languages, and can complete low-delay end-to-end reasoning in a conventional hardware environment.

The present invention relates to means for recombinant manufacture. In particular, it relates to a recombinant bacterial cell comprising in its genome at least one essential gene the endogenous promoter of which has been replaced by a heterologous expression control sequence being inducible by an inducer molecule, such that the expression of said essential gene in the recombinant bacterial cell is dependent on the presence of said inducer molecule. Further contemplated are methods for generating the recombinant bacterial cell of the invention as well as a method for recombinant manufacture of a compound of interest. The present invention also provides for use the recombinant bacterial cell of the invention for recombinant manufacture of a compound of interest and a kit for manufacture of a compound of interest.

The invention discloses gene-simplified bacillus subtilis for producing surfactin and application of the gene-simplified bacillus subtilis, and belongs to the technical field of gene engineering. According to the method disclosed by the invention, the variety of non-essential genes is determined by analyzing and identifying the bad performance influencing the fermentation production of the surfactin by the bacillus subtilis. Therefore, on the basis of the bacillus subtilis 168, a phosphopantetheinyl transferase (sfp) gene is firstly integrated, so that the surfactin production capacity of host bacteria is recovered; then, genes (clusters) in five aspects of a biological membrane synthesis pathway, a metabolic by-product pathway, spore generation, a protease system and flagellum generation are simplified. After the strain EX10 is simplified, the fermentation performance is optimized, and the fermentation yield reaches up to 11.2 g / L, which is 2.1 times higher than that of the original strain. Therefore, the genome-simplified strain has a good application prospect as a chassis cell for industrially and efficiently producing surfactin.

The invention discloses recombinant bacillus subtilis with high yield of surfactin as well as a construction method and application of the recombinant bacillus subtilis, and belongs to the technical field of genetic engineering. According to the invention, non-essential genes are determined through analysis and identification, a simplified engineering strain is obtained, and the highest fermentation yield reaches 11.2 g / L; then, a PTS part sugar phosphorylase gene obtained through screening is transferred into the simplified engineering strain, the metabolism efficiency of carbohydrates is improved, transportation and utilization of the carbohydrates are optimized, a fatty acid transmembrane transporter gene is further transferred, fatty acid uptake is assisted, synthesis of surfactin is facilitated, and the yield of the surfactin is improved. The combination of the two realizes optimization of synthesis of surfactin through a composite carbon source. Compared with a simplified engineering strain, the genetically engineered bacterium obtained by the invention has the advantages that the yield of surfactin is increased by 57.1%, the yield is increased by 2.3 times compared with that of an unsimplified engineering strain EX, and the final shake-flask fermentation yield can reach 17.6 g / L. As an industrial chassis cell of high-yield lipopeptide, the cell has a good industrial application prospect.

The invention discloses a screening and expression platform construction method for non-essential gene loci of corynebacterium glutamicum, and belongs to the technical field of biology. The center sites CGLRS02940, CGLRS03085, CGLRS08555, CGLRS09020 and CGLRS13560 of the corynebacterium glutamicum identified by the invention have the remarkable advantages that when gene knockout or knockin operation is carried out, the sites do not interfere with the normal physiological metabolism process of strains, and stable expression of exogenous genes can be guaranteed; meanwhile, the gene editing efficiency is relatively high, and an editing target with high universality and high reliability is provided for genetic engineering modification of corynebacterium glutamicum.

The invention belongs to the technical field of directed evolution modification of protein, and particularly relates to an engineered bacillus subtillis chassis cell for inserting unnatural amino acid, which is formed by uniformly replacing termination codons UAG or UGA of 57 essential genes of bacillus subtillis with UAA. On the basis, two sets of mutually orthogonal translation systems are introduced to decode the UAG and the UGA respectively, and finally site-specific insertion of the two non-natural amino acids at the preset site of the target protein is realized; a stable and reliable cell platform is provided for obtaining protein molecules carrying two different chemical functional groups and carrying out multi-site refined modification research.

The invention discloses a data processing device and method for predicting essential genes of non-model organisms in the field of bioinformatics and application. The technical problem to be solved by the invention is how to screen essential genes of non-model organisms. The method comprises the following steps: respectively obtaining a label corresponding to each protein from a protein sequence of a target species and protein sequences of n model biological species on the basis of annotations; embedding the protein sequence and the tag into the protein language model, and outputting an embedded vector; constructing a residue contact graph for each protein based on the embedded vector; modeling, integrating and outputting the features of each amino acid residue in the residue contact graph by using a graph neural network to obtain an integral protein embedding vector; inputting all the protein embedded vectors into a classifier model for training, and outputting a necessary probability value of a protein gene by using an activation function; and obtaining a necessary probability value P1 of the gene of the protein based on the classifier model. The invention can be applied to the prevention and control of agricultural diseases and the development of biopesticides.

The present invention is premised on the genes FGSG_10360, FGSG_13150, and FGSG_06123 being essential genes for the growth of Fusarium graminearum. In the present invention, dsRNA for the essential genes are provided together with the genes to contribute to the inhibition of the expression of the genes FGSG_10360, FGSG_13150, and FGSG_06123. According to the present invention, it is possible to develop a Fusarium graminearum-targeting antifungal agent that targets FGSG_10360, FGSG_13150, and FGSG_06123. The dsRNA according to the present invention can be effectively used in the development of an RNAi-based therapeutic agent for Fusarium ear blight.

The present application relates to a kind of plasmid construction method for identifying and deleting large fragment non-essential gene region and its application in gene editing.The plasmid is the gene editing plasmid pMHAGE containing mini-CRISPR cluster and multiple donor DNA fragments.The plasmid carries artificial CRISPR cluster and multiple donor DNA simultaneously, and multiple donor DNA can carry out multiple forms of gene editing to prokaryote using CRISPR-Cas system through homologous recombination, the identification and deletion of large fragment non-essential gene region, realize the simplification of prokaryote genome.The plasmid application host range is wide, and all bacteria and archaea using CRISPR-Cas system can be operated;It can be used to identify large fragment non-essential gene region and editable non-essential gene region combination on genome;With the ability of screening growth phenotype and the optimal non-essential gene region large fragment deletion of genome simplification chassis cell resistance;Simple process, short time cycle, greatly reduce the workload when prokaryote genome simplification.

The invention provides a genetic engineering strain, a construction method of the genetic engineering strain and application of the genetic engineering strain in biosynthesis of 5-hydroxytryptophan. According to the engineering bacterium, four key modules required by 5-HTP synthesis are sequentially introduced into a host genome in a genome integration mode through a CRISPR technology, and the four key modules comprise an aroGfbr-ppsA-tktA module for enhancing chorismate precursor supply, a trpEfbr-trpG module for catalyzing o-aminobenzoic acid generation, a salABCD gene cluster responsible for hydroxylating o-aminobenzoic acid into 5-hydroxy o-aminobenzoic acid, and a salABCD gene cluster responsible for hydroxylating 5-hydroxy o-aminobenzoic acid into 5-hydroxy o-aminobenzoic acid. And a trpDCBA module for converting the intermediate into the final product 5-HTP. The modules are respectively integrated into a plurality of non-essential gene regions, so that stable genetic expression is realized, and a complete metabolic pathway can be operated without plasmids or inducers. The strain can continuously accumulate 5-hydroxytryptophan (5-HTP) under a glucose fermentation condition, and has the advantages of simplicity and convenience in construction, high hereditary stability, low production cost, suitability for industrial-scale fermentation and the like.

The application discloses a tumor cell line drug response prediction method integrating multiple omics and essential gene information, relates to the field of tumor drug response prediction, and is a DROEG prediction method (Drug Response based on Omics and Essential Genes). Four kinds of omics data, including gene expression data, copy number variation data, methylation data and somatic mutation data, and CRISPR gene effect data (CERES Score) are introduced to construct a drug response model, and the effect of the model is comprehensively evaluated by a qualitative evaluation method and a quantitative evaluation method. The application introduces CRISPR essential gene information, establishes a drug response prediction model, is more accurate than existing methods, has the functions of quantitative and qualitative prediction and evaluation, is more suitable, and is more flexible to operate.

Strategies, systems, compositions, and methods for genetically modifying cells to include one or more loss-of-function modifications and / or to include one or more gain-of-function modifications, as well as modified cells (and compositions of such cells) that include one or more loss-of-function modifications and / or that include one or more gain-of-function modifications, are described. In certain aspects, such modified cells include at least one gain-of-function modification within a coding region of an essential gene.

The present invention relates to a fusion polypeptide comprising an IL10 polypeptide, which can be prokaryotically expressed and secreted in bacterial cells. The present invention also relates to a modified bacterium having anti-tumor activity in tumors and the ability to prokaryotically express and secrete an IL10 polypeptide, wherein the bacterium comprises an essential gene expression cassette controlled by an obligate hypoxia-inducible promoter, and the bacterium is deficient in at least one gene, or its functional expression product, involved in or regulating an endogenous antioxidant stress response pathway. The present invention also relates to a pharmaceutical composition comprising the modified bacterium and its anti-tumor use.

The present invention provides a method for producing a target protein by culturing cells, the method being capable of stably maintaining a target plasmid without using an antibiotic. The present invention relates to a method for producing a target substance, the method including a step for culturing cells that are transformed with a target plasmid (A), wherein: each of the transformed cells includes the target plasmid (A) and a temperature-sensitive plasmid (B) and are obtained by a method that includes a step for culturing cells in each of which the function of an essential gene on the chromosome has been reduced at a temperature at which the temperature-sensitive plasmid (B) is eliminated; the target plasmid (A) includes the essential gene and a target substance gene and does not include an antibiotic-resistant gene; and the temperature-sensitive plasmid (B) includes the essential gene and the antibiotic-resistant gene.

Disclosed are compositions and methods related to RNA interference (RNAi) and the use of RNAi active sequence for treating diseases and disorders. Particular disclosed are toxic RNAi active sequences such as siRNA and shRNA for killing cancer cells. The disclosed toxic RNAi active sequences typically include trinucleotide repeats and preferentially target the expression of multiple essential genes for cell survival and / or growth.

The invention relates to the technical field of plant genetic engineering, in particular to a gene down-regulation method based on regulation of precursor mRNA (messenger Ribonucleic Acid) splicing efficiency, which comprises the following steps: firstly, identifying at least one intron 5'terminal splicing site containing a GT sequence in a target gene; aiming at the site, designing a guide RNA (Ribonucleic Acid) sequence capable of targeting the downstream fourth or fifth nucleotide, and verifying the cleavage activity of the guide RNA sequence; constructing a gene editing vector by using the guide RNA sequence which is verified to be effective and a Cas9 nuclease coding gene; introducing the vector into a plant cell, carrying out genetic transformation and regeneration to obtain a transformed plant, and screening out a mutant which is subjected to site-directed editing at a target site through DNA (Deoxyribose Nucleic Acid) sequencing; and finally, extracting RNA (Ribonucleic Acid) of the mutant, reversely transcribing into cDNA (Complementary Deoxyribonucleic Acid), and analyzing transcript change through PCR (Polymerase Chain Reaction) amplification and gel electrophoresis. According to the invention, stable, heritable and accurate knock-down of gene expression is realized, and a new tool is provided for essential gene function research and crop character improvement.

Provided herein are methods and transgenic systems termed Ifegenia (Inherited Female Elimination by Genetically Encoded Nucleases to Interrupt Alleles) comprising transgenic animal strains encoding Cas9 and / or gRNA that targets a female essential gene which are capable of passing down these genes as well as mutant female essential genes in wild populations in order to suppress the population of the animals, as well as methods and systems for making such animals. In some instances, the methods and systems provided herein result in both somatic and heritable germline mutations of the female essential gene resulting in daughter killing, and female essential gene mutant males reproductively viable to pass along the female essential gene mutation and related transgenes into subsequent generations. The methods and systems are adaptable to population control of insects, in particular mosquitoes such as Anopheles gambiae.

An engineered biological containment system comprising a first nucleic acid comprising at least a portion of a fragment of a first essential gene; a second nucleic acid comprising at least a portion of a fragment of a second essential gene; a third nucleic acid that activates transcription of the first nucleic acid; and a fourth nucleic acid encoding a non-natural amino acid encoding tool wherein the second nucleic acid comprises one or more nucleotide sequences encoding a first termination codon and optionally a nucleotide sequence encoding a second termination codon at the end position of the second essential gene coding region.

The invention belongs to the technical field of bioengineering, and particularly relates to a Kluyveromyces marxianus strain for convenient integration expression of multiple genes and application of the Kluyveromyces marxianus strain. The kluyveromyces marxianus strain provided by the invention is constructed by transplanting a saccharomyces cerevisiae chromosome I which is cyclized and loaded with kluyveromyces marxianus centromere and an autonomous replication sequence into kluyveromyces marxianus FIM-1 and deleting three essential genes of the kluyveromyces marxianus. In the Kluyveromyces marxianus strain, all genes on the annular chromosome of the saccharomyces cerevisiae are actively transcribed, the genes of all expression cassettes can be normally expressed, and the annular chromosome is stably inherited in the Kluyveromyces marxianus FIM-1; the method can be used as a repository of exogenous genes, and is applied to stable loading and expression of multiple genes, a whole pathway and pathway genes.

The invention provides a big language model and multi-modal data-based complex character gene mining method and system, and belongs to the technical field of gene data analysis, the method comprises the following steps: obtaining a statistical data set containing multi-modal data of different bean populations; annotating all genes in the statistical data set based on a reference genome to obtain a whole genome semantic map; if the large language model receives a site of a target significance character, calculating a comprehensive score of each gene at the site by using the large language model based on the whole genome semantic map and the site, and determining a complex character gene based on the comprehensive score of each gene; and if the large language model does not receive the locus of the target saliency character, determining candidate genes by using the large language model based on the target saliency character, and determining complex character genes from the candidate genes by using the large language model based on the whole genome semantic map. According to the invention, the most essential gene influencing the target significance character can be positioned.

The invention relates to the technical field of biology, in particular to application of a bombyx mori sorbitol dehydrogenase gene BmSdh2 in relieving diapause of bombyx mori. The nucleotide sequence of the silkworm sorbitol dehydrogenase gene is as shown in SEQ ID NO: 1 or SEQ ID NO: 2. The gene editing technology is utilized to realize successful knockout of the bombyx mori diapause essential gene, and mutation of a corresponding target spot on a genome is detected. PCR amplification and genome sequencing are used for detection of gene mutation, the obtained homozygous mutant material offspring does not enter diapause, the diapause-controllable practical silkworm strain is constructed, and large-scale factory breeding can be realized.

The invention belongs to the technical field of biological genetic engineering, and particularly relates to a corn kernel development regulation gene ZmPPR299, an encoding protein thereof, an SNP (Single Nucleotide Polymorphism) site, a molecular marker and application of the molecular marker, the gene ZmPPR299 is located in a corn chromosome 5, and functional verification shows that the gene encodes a PPR protein located in chloroplast, and the molecular marker can be used for regulating the development of corn kernels. The chloroplast gene is an essential gene for regulating corn kernel development and chloroplast functions; the mutation of the gene can cause the lagging of embryo and endosperm development, the reduction of basal transfer layer cell proliferation, and the insufficient filling of starch grains and protein bodies, and finally, the results show that the grains shrink, the hundred-grain weight is obviously reduced, and the leaves of seedlings lose green. The invention also develops a specific CAPS molecular marker and a detection primer thereof based on a single base mutation site of the gene, and the genotype of the mutant can be rapidly and accurately identified. The gene resource and the molecular marker provided by the invention have important application values in analysis of a corn kernel development regulation network, development of molecular assisted breeding and creation of high-yield and high-quality new corn germplasm.

The invention relates to the technical field of biological medicines, in particular to application of a DBC1 gene in preventing or treating alopecia diseases, and any one of the following applications of the DBC1 gene is as follows: preparing a medicine or a health care product for maintaining the number or function homeostasis of Treg cells; preparing medicines or health-care products for maintaining or increasing the number of the hair follicle stem cells; preparing medicines or health-care products which support normal growth of hair follicles and are complete in structure; preparing medicines or health-care products for driving hair regeneration; and preparing medicines or health-care products for maintaining the stability of the peripheral immune microenvironment of the hair follicle stem cells. The invention discloses a key effect of the DBC1 gene in hair regeneration, and the DBC1 is confirmed to be a necessary gene for promoting hair regeneration through a gene knockout animal model, systemic knockout and specific knockout for the first time.

Provided are a preparation method and system for a recombinant adeno-associated virus (rAAV) and a recombinant bacmid. The method comprises: first reconstructing a recombinant bacmid containing a recombinant baculovirus genome that produces essential functional elements for an rAAV, at least one of the essential functional elements being inserted into the N-terminal or C-terminal of a locus of an essential gene of the recombinant baculovirus genome; and then transfecting the obtained recombinant bacmid containing the recombinant baculovirus genome that produces the rAAV into a host cell line for culturing to prepare an rAAV. Compared with recombinant baculoviruses obtained by conventional Tn7 recombinant preparations of recombinant bacmid, the recombinant baculovirus obtained by inserting a core element containing Cap, Rep and ITR into two sides of a baculovirus essential gene has a more stable rAAV serial passage production level in a cell and has a higher rAAV yield.

The application discloses a double-stranded RNA molecule capable of efficiently inhibiting expression of an oxidized sterol binding protein 1 gene of Phytophthora capsici, and belongs to the field of agricultural biotechnology.The double-stranded RNA molecule is composed of nucleic acid sequences shown in SEQ ID No.1 and SEQ ID No.2.The application also discloses application of the double-stranded RNA molecule in preventing and treating plant diseases caused by the Phytophthora capsici.The double-stranded RNA molecule can inhibit the invasion of the Phytophthora capsici by directly treating the Phytophthora capsici or spraying the Phytophthora capsici on plants.Meanwhile, the double-stranded RNA molecule is specific to essential genes of the Phytophthora capsici, and does not have the problem of drug resistance, so that the double-stranded RNA molecule can be used for preparing biological pesticides, and provides an effective way for preventing and treating diseases caused by the Phytophthora capsici.

The invention discloses a gametophyte male sterility related gene OsPTDb and application thereof. The amino acid sequence of the OsPTDb gene is as shown in SEQ ID NO. 1; the OsPTDb gene encodes an ascorbic acid oxidase which is an essential gene for male gametophyte development, the insemination of the male gametophyte cannot be completed and gametophyte male sterility is generated due to the abnormal function of the gene, and the OsPTDb gene plays an important role in the aspects of preventing transgene from escaping along with pollen, breeding sporophyte male nuclear sterility and the like.

The invention provides a cDNA (complementary deoxyribonucleic acid) clone plasmid of an avian infectious bronchitis virus (IBV) for expressing secretory luciferase as well as a virus strain and a vaccine obtained by rescuing, and belongs to the technical field of biological medicines. The invention provides a construction method of cDNA (complementary deoxyribonucleic acid) clone plasmids of IBV (infectious bursal virus), which is completed by a one-step method based on yeast homologous recombination in a segmented amplification mode. The IBV infectious cDNA clone constructed by the method has good stability, an IBV genome can be transformed on a gene level by directly utilizing in-vitro homologous recombination, and the efficiency of constructing a recombinant virus is improved. According to the invention, a non-essential gene of the infectious cDNA clone is replaced by a Gluc reporter gene, and the obtained infectious cDNA clone directly transfects mammalian cells to rescue recombinant viruses. The recombinant virus is constructed through a virus rescue method, the growth characteristic of the recombinant virus is basically consistent with that of a parent virus, and genetic stability is kept.

The present invention relates to a genetically engineered bacterium for increasing GDP-L-fucose production, and belongs to the field of genetic engineering technology. The present invention uses Escherichia coli as a starting strain, knocks out the undecenyl glucose phosphate phosphotransferase encoding gene wcaJ, and inserts a terminator after the GDP-mannose pyrophosphorylase encoding gene manC to obtain a genetically engineered bacterium for increasing GDP-L-fucose production; the nucleotide sequences of the undecenyl glucose phosphate phosphotransferase encoding gene wcaJ and the GDP-mannose pyrophosphorylase encoding gene manC are shown in SEQ ID NO.1-2. Compared with other strains, the present invention blocks the expression of subsequent non-essential genes, greatly reduces the substances and energy consumed by the strain in other pathways, reduces the survival pressure of the strain, and allows the strain to focus a lot of energy on synthesizing the target product GDP-L-fucose, thereby increasing the yield of GDP-L-fucose.

The application discloses a data processing device and method for predicting essential genes of non-model organisms in the field of bioinformatics and application. The technical problem to be solved by the application is how to screen essential genes of non-model organisms. In the application, the protein sequences of a target species and the protein sequences of n model organism species are respectively based on annotation to obtain the corresponding labels of each protein; then the protein sequences and the labels are embedded into a protein language model to output embedding vectors; based on the embedding vectors, a residue contact map is constructed for each protein; the features of each amino acid residue in the residue contact map are modeled and integrated using a graph neural network to output a whole protein embedding vector; all protein embedding vectors are input into a classifier model for training and using an activation function to output essential probability values of protein genes; and based on the classifier model, essential probability values P1 of the genes of the proteins are obtained. The application can be applied to agricultural disease prevention and control and biological pesticide development.