81 results about "Bacterial genes" patented technology

The invention provides an intratumoral bacterium detection and analysis method based on circular DNA enrichment sequencing and related model construction, and belongs to the field of molecular biology. The intratumoral bacterium detection method provided by the invention comprises the following steps: extracting total DNA of cancer tissue or para-carcinoma tissue, carrying out linear digestion, purifying a linear digestion product, and enriching to obtain circular DNA; the method comprises the following steps: amplifying circular DNA, and breaking a DNA amplification product to 300-500bp; purifying DNA fragments, constructing a library, and sequencing; and performing genome comparison according to a sequencing result to obtain information of the intracellular bacteria. According to the method, complete bacterial genome and plasmid genome information can be captured, and the detection sensitivity of the intracellular bacteria and the richness of the bacterial genome information are improved. The invention further provides an intratumoral bacterium analysis method which can be used for screening generic cancer bacterial markers, and provides a cancer risk assessment machine learning model based on the intratumoral bacterium, so that the clinical application possibility of the intratumoral bacterium is improved.

The invention discloses a bacterial selenoprotein online resource platform, an application method, a terminal and a medium, and relates to the technical field of biological medicine, the online resource platform is deployed on a server, the cloud server is a Ubuntu cloud server, and Nginx, Waitpress and Flask are configured; the server side is in butt joint with a background resource, and the background resource is in butt joint with the constructed bacterial selenoprotein database; the server is in butt joint with a user interface of the front end, the user interface designs a corresponding interface framework and an interaction function based on static resources hosted by Nginx, and the interaction function is used for realizing query, analysis and use of relevant information of the bacterial selenoprotein. According to the method, a convenient online access channel of an integrated database and a real-time data analysis tool are provided for users in related fields, and important support is provided for accurate annotation of selenoprotein genes in a bacterial genome plan.

The invention discloses a gene cluster identification method and device of a bacterial genome, equipment and a storage medium. The method comprises the following steps: constructing a gene cluster recognition model by using a preprocessing unit, an ESM protein language unit, a cosine approximation calculation unit, a normalized pointwise mutual information unit, a term frequency-inverse document frequency unit, a graph convolution unit, a BERT unit and a softmax function unit; inputting a BGC sequence training sample of the bacterial genome into the gene cluster recognition model, training the gene cluster recognition model by using a cross entropy loss function, and performing iterative optimization on the training process by using an Adam optimizer; inputting the BGC sequence data set of the bacterial genome to be recognized into the target gene cluster recognition model for recognition; segments in the preliminary recognition result are corrected, and a final recognition result is obtained; by constructing an adjacent matrix and inputting the adjacent matrix into a graph convolution unit, global features contained in Pfam structural domain nodes in a BGC sequence are extracted, and the recognition and prediction performance of the model is improved.

The invention discloses a high-yield lycopene recombinant rhodobacter sphaeroides strain as well as a construction method and application thereof, and belongs to the technical field of biosynthesis and biological energy sources, the construction method comprises the following steps: knocking out a crtC gene of rhodobacter sphaeroides by using a homologous recombination method to obtain a recombinant strain RS01; the method comprises the following steps: on the basis of a strain RS01, replacing a crtI3 gene on a rhodobacter sphaeroides genome with a crtI4 gene (from rhodospirillum rubrum) by using a homologous recombination method to obtain a recombinant strain RS02; the method comprises the following steps: connecting crtB and crtE genes to a pYYDT vector to construct a plasmid pYYDT-crtB-crtE, transferring the plasmid pYYDT-crtB-crtE into escherichia coli S17, and then introducing the plasmid pYYDT-crtB-crtE into a recombinant rhodobacter sphaeroides RS02 in a conjugational transfer manner to obtain a recombinant strain RS03. The recombinant rhodobacter sphaeroides constructed by the invention can be used for efficiently producing lycopene.

The invention discloses a limited modification system derived from pseudomonas aeruginosa and application of the limited modification system. The transferase LYSZa7hsdMS gene is composed of a methyltransferase LYSZa7hsdMS and a restriction enzyme LYSZa7hsdR. According to the invention, a 5 '-ACAYNNNNNCCT-3' site of a bacterial genome is subjected to 6mA methylation modification by using methyltransferase M.PaeZa7HsdMS, the bacterial genome is protected by combining a restriction enzyme compound PaeZa7HsdMSR, and the existence of PrrC protein can prevent a restriction-modification system from being inhibited by phage Stp protein. The novel limited modification system provided by the invention has a very wide application prospect in bacteriophage engineering and enhancement of engineering bacterium genome stability.

The invention relates to the technical field of medicines, and particularly discloses a screening target of an antibacterial drug, application and a screening method, and the screening method comprises the following steps: testing the interaction between a candidate drug and the target; functional verification of the target protein; testing the antibacterial activity of the candidate drugs; and carrying out an in-vitro antibacterial curve test, evaluating the sterilization or antibacterial effect of the candidate drug on different bacteria, and comparing the change of bacterial gene expression before and after the treatment of the candidate drug through omics analysis (transcriptome and proteome analysis). A new direction is provided for research and development of antibacterial drugs by discovering a new antibacterial target, such as Spx and SodA, of the ISP I except for acting on bacterial ribosomes, a new drug without cross resistance with traditional antibiotics can be developed according to the drug design of the new target, the antibacterial effect is improved, the new antibacterial target of the ISP I in the colimycin and the action mechanism of the new antibacterial target are disclosed, and the application of the ISP I in the colimycin in preparation of the antibacterial drugs is promoted. And a new thought and a new method are provided for research and development of antibacterial drugs.

The invention discloses an SYBR Green I fluorescent dye quantitative PCR (polymerase chain reaction) method for identifying clostridium butyricum, and belongs to the technical field of molecular detection. The invention provides a primer pair for qPCR (quantitative polymerase chain reaction) identification of clostridium butyricum. The primer pair comprises an upstream primer and a downstream primer, the nucleotide sequence of the upstream primer is as shown in SEQ ID NO. 1; 1, and the nucleotide sequence of the downstream primer is as shown in SEQ ID NO. 2. The identification sensitivity is high, the detection limit is 7.2 * 10 < 2 > CFU / mL, the specificity is strong, and the repeatability is good. Meanwhile, the bacterial genome is obtained by cracking the bacterial liquid with the crude extraction cracking liquid, so that the genome obtaining process is simplified. According to the method, the concentration of the clostridium butyricum liquid in the sample is directly obtained through standard curve conversion, the problems that a clostridium butyricum identification method is complex, long in consumed time, low in efficiency and the like are effectively solved, and a more convenient identification method is provided for related research of clostridium butyricum.

The invention relates to the technical field of petroleum development, and discloses an inter-well connectivity calculation method based on a time step response relationship, which comprises the following steps: collecting and sequencing bacterial genome DNA of a water injection well and a producing well of an injection-production well, and determining corresponding strain types and bacterial abundance; the method comprises the following steps: constructing an impulse response model, respectively taking measured values of strain types and bacterial abundance of a water injection well and an oil production well as an input signal and an output signal in the impulse response model, introducing a Kalman filtering method to construct a response relationship based on time steps between the water injection well and the oil production well, and solving the response relationship by utilizing Laplace transformation, obtaining the strength of the response relation between the water injection well and the oil production well; representing the connectivity between the water injection well and the oil production well by utilizing the strength of the response relationship, and determining the connectivity between the water injection well and the oil production well; according to the method, the microorganism DNA sequencing result and the Kalman filtering calculation method are combined, and the dynamic change rule of the connectivity between the injection wells and the production wells is efficiently reflected in real time.

The invention discloses a bacterial gene editing tool based on an Ago2 and UvrD protein co-expression system and application. The bacterial gene editing tool comprises a first plasmid and a second plasmid, wherein the first plasmid comprises an Ago2 expression cassette and left and right homologous arms of a target gene, and the second plasmid comprises a UvrD expression cassette. According to the invention, the two plasmids are co-transformed into bacteria to obtain a strain without a target gene related sequence. The method is easy to operate, wide in application, free of potential off-target effect, high in knockout efficiency, free of resistance gene selection markers and suitable for bacteria which are difficult to edit or low in editing efficiency through a conventional gene editing method, and an excellent tool is provided for research and development of genetic engineering vaccines.

The present invention relates to the technical field of oil development, and discloses a method for calculating inter-well connectivity based on the time-step response relationship, which includes collecting and sequencing the bacterial genomic DNA of the injection well and the production well of the injection-production well pair to determine the corresponding bacterial species and bacterial abundance; constructing a pulse response model, in which the measured values of the bacterial species and bacterial abundance of the injection well and the production well are used as input signals and output signals respectively in the pulse response model, introducing the Kalman filtering method to construct the response relationship based on time steps between the injection well and the production well, and using the Laplace transform to solve the response relationship to obtain the strength of the response relationship between the injection well and the production well; and using the strength of the response relationship to characterize the size of the connectivity between the injection well and the production well, and determining the connectivity between the injection well and the production well; the present invention combines the microbial DNA sequencing results and the Kalman filtering calculation method to reflect the dynamic change law of the inter-well connectivity between the injection and production wells in real time and efficiently.

The integrated bacterial gene extraction and detection device comprises a stirring module, a bearing table, an illumination module, a temperature control module and a magnetic separation module, a bearing hole communicated with the interior of the bearing table is formed in the bearing table, and the stirring module is mounted at the top end of the bearing table on one side of the bearing hole; the stirring module is arranged to be capable of stirring a sample in the test tube, the temperature control module is arranged in the bearing table and can control the temperature of the sample in the test tube, and the illumination module is arranged in the bearing table, located below the temperature control module and used for providing a visible light source for the test tube; the magnetic separation module is installed on one side wall of the bearing table and can provide or not provide magnetic attraction force for the test tube, bacteria lysis, nucleic acid extraction, isothermal amplification and fluorescence image detection are integrated, and full-process detection from a sample to a result can be completed outdoors or on site under the condition that an external large instrument is not needed.

The application discloses a gene prdR for regulating myxobacteria predation and a protein coded by the gene, and belongs to the technical field of biotechnology. The mutant DK10 with significantly improved predation capacity is obtained by using the strategy of adaptive evolution; genetic variation sites of the mutant DK10 are analyzed by using the bacterial genome resequencing technology, and functions of the genetic variation sites are researched by using the gene knockout technology, and it is found that the gene deletion of MXAN_2902 (prdR, the nucleotide sequence is shown as SEQ ID NO. 1) significantly enhances the predation capacity of Myxococcus xanthus. The nucleic acid sequence and the amino acid sequence of the transcriptional activator PrdR for regulating the predation of Myxococcus xanthus are disclosed, and the functional strain of Myxococcus xanthus capable of efficiently predating Salmonella enteritidis can be developed by using the prdR gene, and a new strategy is provided for the prevention and control of drug-resistant HVPG pathogenic bacteria.

To provide a method for rapidly and accurately quantifying bacteria in a biological sample from a subject.SOLUTION: A method of determining an amount or concentration of bacteria in a sample, the method comprising: (a) amplifying a target nucleic acid of the bacteria from genetic material obtained from the sample to form an amplification product, wherein: (b) measuring the amount or concentration of the amplification product; (c) calculating the amount or concentration of the target nucleic acids in the sample by comparing the amount or concentration of the amplification product to a reference level thereof; and (d) determining the copy number of the bacterial 16SrRNA genes in the sample from the amount or concentration of the target nucleic acids in the sample, wherein: 16SrRNA, wherein said copy number is a function of or correlates with the amount of said bacteria in said sample.SELECTED DRAWING: None

Provided herein are kits, compositions, systems, and methods for treating a subject with a tumor with kynurenine responsive and degrading bacteria (e.g., such that the bacteria reduces or eliminates the tumor). In certain embodiments, the kynurenine responsive bacteria comprise one or more nucleic acid sequences encoding: i) a kynurenine transcriptional regulator protein, ii) a kynurenine transporter protein, iii) a kynureninase (KynU) protein, and iv) at least one protein important or essential for growth of the bacteria expression of which is linked to a kynurenine responsive promoter (e.g., where the corresponding gene(s) has been deactivated or knocked out in the genome of the bacteria).

The present invention discloses a method, detection system, and application thereof for simultaneously detecting multiple bacteria. The method comprises screening target sequences rich in AT bases in different bacterial genome sequences; designing primers that are both universal and specific for a single bacterial genome sequence; calculating the reaction denaturation temperature and annealing temperature based on the GC percentage, primer sequence length, and theoretical amplification product sequence length of the primer pair; screening suitable single bacterial primer pairs based on the sequence amplification length, reaction denaturation temperature, and annealing temperature to form a primer set for detecting multiple bacteria; setting nucleic acid amplification reaction conditions, performing a nucleic acid amplification reaction under conditions that partially melt the template, and obtaining an amplified product. The present invention achieves partial melting of double-stranded DNA through specific screening based on massive genomic data and accurate calculation of the Tm value of AT-rich regions, greatly reducing the possibility of nonspecific amplification in nucleic acid amplification technology.

The application discloses a method for identifying Klebsiella pneumoniae gene circadian rhythm expression by using a bioluminescence reporting system. The application constructs a recombinant bioluminescence Klebsiella pneumoniae driven by a metabolic gene malate:quinone oxidoreductase mqo promoter (Pmqo), and directly observes the change rule of bacterial gene expression under entrainment and free-running conditions of temperature cycle by monitoring the luminescence characteristics. The luxCDABE gene operon comprises genes for coding luciferase and substrate synthesis enzyme, wherein luxA and luxB code for heterodimer luciferase, luxC, luxD and luxE synthesize aldehyde as a substrate for the luciferase luminescence reaction. The luciferase catalyzes the oxidation of aldehyde to generate visible blue-green light with a wavelength of 450-490 nm. The Lux bioluminescence reporting system has the advantages of not needing to add an exogenous substrate and not affecting the normal physiological functions of the host, and can be applied to the identification of Klebsiella pneumoniae gene circadian rhythm expression.

The invention relates to the technical field of molecular biology, in particular to Argonaute protein derived from normal-temperature prokaryotes and gene editing application of the Argonaute protein. The amino acid sequence of the Argonaute protein is as shown in SEQ ID No.1, or the Argonaute protein has more than 90%, more than 95%, more than 98%, preferably more than 99% of identity with the sequence as shown in SEQ ID No.1, has the same function and comes from normal-temperature prokaryotes. The prokaryote Ago protein and PLD nuclease AgaP coupled with the prokaryote Ago protein are used for endowing a host with a virus defense function for the first time, and a strain with antiviral capacity can be constructed; furthermore, on the basis of the function of the Ago protein, the NpAgo can be used for remarkably improving the gene editing efficiency in escherichia coli, and the practical application of bacterial gene editing is effectively improved.

The present invention provides a method and apparatus for identifying horizontally transferred sequences from bacterial genomes in recipient insect genomes, relating to the field of biotechnology. The method provided by the present invention for identifying horizontally transferred sequences from bacterial genomes in recipient insect genomes more comprehensively and accurately identifies and analyzes fragments horizontally transferred from a certain type of bacteria to the genome of this species at the whole genome level; based on the horizontally transferred sequence fragments, horizontally transferred genes, gene fragments, and non-coding region fragments are further identified. This provides a comprehensive analysis of horizontal gene transfer between the genomes of a certain eukaryote and a certain type of bacteria, laying a solid, comprehensive, and reliable foundation for further research into the effects of horizontally transferred genes (fragments) on eukaryotes.

The present invention relates to the field of Biotechnology and genetic engineering. In particular, the present invention relates to the field of a novel genetic tool with site-specific integration and FLP-FRT recombination excision of antibiotic selection marker for utility in applied and industrial research, biotherapeutic development and diagnostics.

Disclosed herein are methods and compositions for increasing culture stability of a bacterial culture comprising a plurality of a modified bacterium comprising a modified prophage. Also disclosed herein are methods and compositions for decreasing the likelihood of replication of a modified prophage in a bacterial genome as compared to the likelihood of replication of a corresponding prophage lacking the prophage modification in a corresponding bacterial genome. Also disclosed herein are methods and compositions for preventing excision of a prophage in a bacterium. Also disclosed herein are methods and compositions for generating a modified prophage having an impaired ability to lyse a host bacterial cell.

Peptide nucleic acids, compositions containing the peptide nucleic acids, and methods utilizing the peptide nucleic acids are described. The peptide nucleic acids, compositions, and methods are designed to inhibit global regulatory bacterial genes and useful for preventing biofilm formation on biotic and abiotic surfaces. The PNAs are designed to account for nuanced interspecies variations in these regulatory genes, thus allowing for simultaneous inhibition of multiple bacterial species as well as polymicrobial biofilms. The disclosure outlines the composition of wide range PNAs (wrPNAs) and applications for delivery.

The first subject of the invention is a set of primers for amplifying the nucleotide sequence of the Chlamydia trachomatis bacterium dnaK gene. The second subject of the invention is a method for detecting Chlamydia trachomatis bacteria. Another subject of the invention is a method of detecting an infection caused by the Chlamydia trachomatis bacterium. The fourth subject of the invention is a kit for detecting an infection caused by the Chlamydia trachomatis bacterium.

A computer-implemented method for the rapid and non-invasive detection of sepsis and identification of bacterial antibiotic resistance, the method comprising: - collecting a biological sample from a patient suspected of having sepsis; - extracting cell-free DNA from the biological sample; - preparing a sequencing-ready library from the extracted DNA; - performing long-read, single-molecule sequencing on the prepared library; - processing the sequencing data to obtain raw sequencing reads; - performing quality control on the sequencing reads, wherein low-quality reads are removed; - filtering the remaining sequencing reads to isolate bacterial genomic sequences; - mapping the filtered bacterial sequences against a reference set of bacterial genomes associated with sepsis; - identifying bacterial species present in the sample based on the mapped sequences; - analyzing the bacterial genome sequences for antibiotic resistance markers using statistical methods.

The invention discloses a method for efficient traceless editing of a myxobacteria genome and application. According to the invention, a TnpB cutting system ISDra2 of deinococcus radiodurans is combined with a homologous recombination system MxRedET of myxobacteria, so that a one-step traceless editing platform (MxDIRECT) is formed. The ISDra2 is responsible for accurately positioning and cutting target DNA, and the MxRedET immediately realizes efficient fragment integration or replacement at a cut, so that operations such as gene knockout, insertion and replacement are realized. According to the method, the editing efficiency of myxobacteria is improved to 100% from original 1%, the period is shortened to 5-7 days from 3-6 months, and one-step double-site traceless editing can be achieved through double-site design. The longest DNA of about 80 kb can be knocked out through a single incision, and the longest DNA can reach 200 kb through double incisions; and mononucleotide replacement can be carried out at any position, so that accurate base editing is realized. The technology provides an efficient and accurate tool for modifying functional genes and metabolic pathways of the myxobacteria chassis cells, and obviously promotes the research of synthetic biology.

To provide a formulation including components contributing to epidermal and dermal health.SOLUTION: The present invention provides a bacterium belonging to Staphylococcus epidermidis species, strain BG-PG180, deposited as accession number NITE P-04076, which enhances expression of the ceramide synthase 3 gene and also enhances expression of the hyaluronan synthase 3 gene. A formulation prepared using this strain can enhance expression of the ceramide synthase 3 gene and also enhance expression of the hyaluronan synthase 3 gene.SELECTED DRAWING: None

The invention relates to the technical field of bacterial genetic engineering, in particular to a bacillus thuringiensis fur gene knockout strain and a construction method and application thereof, and the bacillus thuringiensis fur gene knockout strain is obtained by knocking out an iron uptake regulatory protein fur gene from a bacillus thuringiensis genome. The construction method of the bacillus thuringiensis fur gene knockout strain comprises the following steps: constructing a gene knockout donor strain, performing single exchange for the first time, eliminating plasmids, detecting positive transformants, performing single exchange for the second time, performing positive clone screening, and eliminating plasmids to obtain the knockout fur strain. Meanwhile, the invention also relates to application of the bacillus thuringiensis fur gene knockout strain in production of siderophores and melanin. The technical scheme provided by the invention provides a bacillus thuringiensis fur gene knockout strain as well as a construction method and application thereof, and provides a novel method for producing melanin and siderophore.

The invention belongs to the technical field of biological detection, and discloses a method for analyzing antiviral and virus-promoting bacteria based on metatranscriptome sequencing and application. According to the method, on the basis of macro transcriptome sequencing, RPM values of virus and bacterial species are analyzed and calculated by utilizing different virus and bacterial marker genes. The RPM values of the viruses and the bacteria are utilized, and a correlation table showing the interaction relation between all the bacteria and the viruses is obtained through Spearman correlation analysis. According to the method, the problem that bacterial genomes are incomplete in metatranscriptome sequencing is solved, all viruses and bacteria in a single mosquito sample can be found, and the anti-virus and virus-promoting effects of the bacteria are detected through the rpoB gene of the bacteria and the load correlation of the virus RdRp. Moreover, the mosquito sample size involved in the method is large, the statistical reliability and ecological universality of research are enhanced, and the representativeness of research results is high.

The application discloses a bacterial genome gene cluster identification method, device, equipment and storage medium, the method comprises the steps: constructing a gene cluster identification model by using a preprocessing unit, an ESM protein language unit, a cosine approximation degree calculation unit, a normalized point-by-point mutual information unit, a term frequency-inverse document frequency unit, a graph convolution unit, a BERT unit and a softmax function unit; inputting a BGC sequence training sample of a bacterial genome into the gene cluster identification model, training the gene cluster identification model by using a cross-entropy loss function, and iteratively optimizing the training process by using an Adam optimizer; inputting a BGC sequence data set of a bacterial genome to be identified into a target gene cluster identification model for identification; correcting fragments in the preliminary identification result to obtain a final identification result; by constructing an adjacency matrix and inputting the adjacency matrix into the graph convolution unit, global features contained in Pfam domain nodes in the BGC sequence are extracted, and the identification and prediction performance of the model is improved.

This invention belongs to the fields of microbiology and molecular biology, specifically relating to a homologous recombinase combination in myxobacteria and its application in gene editing. Specifically, this invention provides four pairs of homologous recombinase systems capable of efficiently mediating in vivo recombination in myxobacteria. Each pair includes a protein YqaJ with exonuclease function and a protein RecT with single-strand annealing function. This invention provides a method for myxobacterial gene editing: under the action of homologous recombinase pairs, mutant strains are obtained through positive screening using resistance tags. The resistance tags are then successfully removed through the combined action of the Cre / loxP system and the reverse screening gene galK. This method achieves a gene editing efficiency of up to 100%, has a short cycle time, requires no purification, and can be used for iterative deletion of multiple genes to achieve genome simplification in myxobacteria, or for inserting functional promoters and other elements to activate silent gene clusters. This method is of great significance for the bioexploration and functional genomics research of myxobacteria.

Provided are antibacterial phages that selectively kill bacteria having a resistance gene or the like. Antibacterial phage for this includes CRISPR-Cas13a with a target sequence that recognizes a specific gene as a target. This target sequence is designed as a spacer sequence for crRNA of 14-28 bases. Specific genes are drug resistance genes and toxins. The drug resistance genes are included in bacterial genomes and / or plasmids having one or any combination of the group including: methicillin-resistant Staphylococcus aureus, vancomycin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, penicillin-resistant pneumococcus, multidrug-resistant Pseudomonas aeruginosa, multidrug-resistant Pseudomonas aeruginosa, carbapenem-resistant Pseudomonas aeruginosa, carbapenem-resistant cephalosporins, third-generation cephalosporin-resistant Pseudomonas aeruginosa, third-generation cephalosporin-resistant E. coli, and fluoroquinolone-resistant E. coli.