40 results about "Bacterial genes" patented technology

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 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 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 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 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.

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.

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.

The application discloses a restriction modification system derived from pseudomonas aeruginosa and application thereof. The restriction modification system is composed of a methyltransferase LYZSa7hsdMS and a restriction endonuclease LYZSa7hsdR. The methyltransferase M.PaeZa7HsdMS is used for carrying out 6mA methylation modification on a 5'-ACAYNNNNNCCT-3' site of a bacterial genome, a restriction endonuclease complex PaeZa7HsdMSR is combined to protect the bacterial genome, and the presence of a PrrC protein can prevent the restriction-modification system from being inhibited by a bacteriophage Stp protein. The application has a very broad application prospect in bacteriophage engineering and enhancement of the stability of an engineering bacterial genome.

The application provides an L-threonine production strain and a construction method and application thereof. The production strain is obtained by introducing a mutation into a genome of a bacterium with threonine production capacity by using genetic engineering means, so that the CreC protein coded by the genome comprises an R77P mutation site. Flask fermentation experiments show that the L-threonine yield of the Escherichia coli MHZ-0221-4 is higher than that of the control strain MHZ-0215-2, the average conversion rate of the R77P mutant strain MHZ-0221-4 after modification is 20.6%, which is increased by 4.39 percentage points compared with the starting strain. It can be concluded from the flask results that the threonine production capacity of the modified strain is obviously superior to that of the starting strain MHZ-0215-2, so it can be seen that the R77P point mutation of the gene creC can obviously improve the threonine production capacity.

The present invention provides for methods and compositions for recovering high concentrations of transcripts is technically challenging for bacteria colonizing within the host environments. The invention uses Pi-seq technology in a DNA-barcoded promoter library to improve the ability to quantify transcriptional activity of bacterial genes. The invention offers a rapid way to screen and identify biosensors for chemicals and physical conditions associated with host physiology.

Provided are antibacterial phages that selectively kill bacteria having a drug 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.

The purpose of the present invention is to establish a simple, efficient, and rapid genetic testing method for bacteria in clinical settings, and to provide: a gene amplification method for specifically detecting and evaluating the amount of bacteria associated with periodontal disease and caries; a primer set for a gene amplification reaction; a kit for detecting genes of bacteria that cause periodontal disease or caries, the kit including the primer set; and a kit for evaluating the severity of periodontal disease or caries. The present invention is a method for detecting oral bacteria that are present in plaque or saliva above or below the gingival margin, or bacteria that cause periodontal disease or caries, by detecting genes of the oral bacteria or causative bacteria using a gene amplification method, the detection method being characterized in that (1) annealing and extension reactions in the gene amplification method are implemented at substantially the same temperature, and / or (2) the gene length of a target gene as an amplification product is short.

The disclosure relates to gene editing systems comprising serine recombinases and methods of using such serine recombinases for integration of nucleic acid sequences. More specifically, the disclosure relates to sequence-defined serine recombinases having attachment sites such as a bacterial genomic recombination sequence (attB). Methods are also provided for recombinant pro-duction of said recombinases.

The invention discloses a universal CRISPR / Cas12a (clustered regularly interspaced short palindromic repeats / CRISPR associated 12a) system, which can realize visual rapid detection of acinetobacter baumannii drug resistance genes. The system is combined with an asymmetric PCR technology to amplify one housekeeping gene and four drug-resistant genes of bacteria to generate a single-stranded DNA product, so that the amplification efficiency and the signal intensity are remarkably improved, and a high-specificity substrate is provided for subsequent reaction. The single-chain amplicon and the modular ring engineering hairpin are subjected to a strand displacement reaction, and Cas12a protein activation is accurately regulated and controlled; the activated Cas12a cuts the reporter molecule, and the product presents a visual visual signal through a lateral flow chromatography test strip. The strategy has prominent universality, crRNA does not need to be redesigned or an activating agent does not need to be added when five targets are detected, plug-and-play can be achieved only by replacing the hairpin response sequence, and the method can be conveniently expanded to detection of other bacteria, viruses and drug-resistant genes. The system is easy and convenient to operate, high in specificity and good in stability, provides a simplified and universal CRISPR diagnosis new scheme for clinical bacterial genotyping, and has important clinical application and popularization value.

The invention provides application of novel burkholderia cepacia as a marker for tumor diagnosis, screening, prediction or prognosis. The invention provides a qualitative and quantitative detection method for detecting the Burkholderia cenocepacia bacteria in the glioma for the first time. On one hand, through co-culture with Burkholderia cenocepacia bacteria, the malignant phenotypic capabilities of proliferation, invasion and the like of glioma cells can be remarkably enhanced; more importantly, the abundance value of the 16S rRNA gene of the Burkholderia cenocepacia bacteria can be used as a molecular marker for prognosis evaluation of the glioma and a target spot for treatment of the glioma. A new thought is provided for diagnosis of glioma, and important clinical value is achieved.

To provide a technique capable of contributing to the diagnosis of pancreatic cancer, reducing a physical burden, and inexpensively and quickly examining the possibility of suffering from pancreatic cancer.SOLUTION: The method for examining pancreatic cancer includes detecting the amount of N-acetylneuraminic acid lyase gene derived from bacteria in a sample from a subject. Advantageous Effects of Invention According to the present invention, pancreatic cancer can be tested using a biological sample obtained noninvasively, such as feces, saliva, blood, or body fluid, without imposing a hospital visit burden or a physical burden related to the test on a subject. Since the amount of the nanA gene derived from bacteria can be measured by PCR and the comprehensive analysis of intestinal bacterial flora is unnecessary in the present invention, pancreatic cancer can be rapidly and inexpensively examined.SELECTED DRAWING: Figure 4

This invention provides a method for screening multivalent binding probes for bacterial detection, comprising the following steps: (1) using an algorithm to screen nucleic acid sequences within the top 1000 range of multiplicity scores for the target bacterial genome; (2) performing secondary screening on the nucleic acid sequences obtained in step (1) to obtain multivalent binding probes for bacterial detection, wherein the secondary screening includes at least one of the following: (2-1) screening nucleic acid sequences with G and C base content in the range of 40%-60%; (2-2) screening nucleic acid sequences in which the maximum continuous length of a single G / C base does not exceed 3 and the maximum continuous length of G-C alternation does not exceed 5; (2-3) screening nucleic acid sequences in which the Gibbs free energy change for forming a hairpin structure and the Gibbs free energy change for forming a homodimer structure are both > -5 kcal / mol. This method is scientific and systematic, and can assist technicians in efficiently and accurately judging and selecting multivalent binding probes suitable for bacterial detection.

The application discloses a non-fixed composite quality control product for high-throughput sequencing of DNA pathogenic macro genome and a preparation method thereof, and belongs to the technical field of DNA detection. The preparation method comprises the following steps: S1, preparing a DNA positive quality control product: (1) extracting bacterial genomic nucleic acid and fungal genomic nucleic acid; (2) obtaining viral genomic nucleic acid; (3) extracting human genomic nucleic acid; (4) mixing 1% target pathogenic genome and 99% human genome per milliliter of the DNA positive quality control product according to the following relative abundance: 1% target pathogenic genome, 99% human genome; the target pathogenic genome comprises bacterial genomic nucleic acid, fungal genomic nucleic acid and viral genomic nucleic acid; (5) mixing the target pathogenic genome according to a preset relative abundance p pD The application successfully constructs a complex background system similar to a clinical sample by adding human genomic DNA to the DNA positive quality control product and preparing a negative quality control product by using human cells, and provides a quality control effect closer to the actual situation.

The present application relates to the technical field of bacterial genetic engineering, in particular to a Bacillus thuringiensis fur gene knockout strain, a construction method and application thereof, wherein the Bacillus thuringiensis fur gene knockout strain is obtained by knocking out the iron uptake regulatory protein fur gene of the 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 first single exchange, eliminating a plasmid, detecting a positive transformant, performing second single exchange, screening a positive clone, and eliminating the plasmid to obtain the fur knockout strain; and the application of the Bacillus thuringiensis fur gene knockout strain in producing siderophores and melanin is also disclosed. The technical scheme provided by the present application provides the Bacillus thuringiensis fur gene knockout strain, a construction method and application thereof, and a new method for producing melanin and siderophores.

The invention provides a primer combination, a kit and a method for human intestinal flora based on nanopore sequencing, and belongs to the technical field of intestinal microbiome. The primer combination comprises an amplification primer pair used for amplifying the bacterium 16S rRNA gene, the amplification primer pair is composed of a forward amplification primer and a reverse amplification primer, the forward amplification primer comprises a nucleotide sequence as shown in SEQ ID No.1, and the reverse amplification primer comprises a nucleotide sequence as shown in SEQ ID No.2. When the primer combination, the kit and the method are used for detecting the intestinal flora of the human body, more comprehensive flora information can be obtained, for example, bifidobacterium adolescentis which cannot be detected in the prior art can be obtained. The primer combination, the kit and the method can be used for detecting personal intestinal flora, provide a more reliable scientific basis for individualized health management, and can also be used for clinical scientific research.

This application provides a method and system for constructing a metagenomic database of clinical pathogenic microorganisms. The method includes: collecting and correcting species information of pathogenic microorganisms; performing searches based on the corrected pathogenic microorganism genome results; filtering and counting bacterial genomes; screening and filtering reference genomes of viral pathogenic microorganisms; downloading the screened pathogenic microorganism genomes; breaking the genomes obtained from the above screening results into fixed-length fragments; classifying reads with overlapping regions to obtain contaminated regions in the genome; labeling contaminated sequences in all genomes; removing contaminated sequences from the genome; constructing an alignment database for the obtained genomes based on the k-mer algorithm and the lowest common ancestor algorithm; managing the database, regularly updating and maintaining the database; optimizing data storage by partitioning the database into different databases according to species boundaries and different setting criteria.

The invention discloses a hot spot self-assembly colorimetric-Raman sensing platform and an escherichia coli detection method, the hot spot self-assembly colorimetric-Raman sensing platform comprises an isothermal amplification system, a CRISPR-dCas9 system, GNPs-probe and SA-GNPs, a target bacterial gene is taken as a DNA template, RPA amplification is carried out through the isothermal amplification system, and a double-chain amplification product modified by terminal biotin is obtained; the CRISPR-dCas9 system is used for targeted recognition of a double-chain amplification product modified by terminal biotin to form a composite product; gNPs-probe is composed of gold nanoparticles, a Raman signal molecule and a DNA probe, and the GNPs-probe is combined with the stem-loop structure of the sgRNA of the composite product through the DNA probe; sA-GNPs is combined with the biotin of the composite product through streptavidin; gNPs-probe and SA-GNPs are assembled on the composite product, so that a colorimetric-Raman sensing platform for detecting target bacteria is formed. According to the present invention, the cross validation of the generated colorimetric, ultraviolet and Raman multi-mode signals is adopted to improve the result reliability, the isothermal amplification and the self-assembly hot spot are adopted to enhance the multiple sensibilization detection signal, and the specificity is enhanced based on the specific primer group and the CRISPR-dCas9 system mediated secondary recognition, such that the rapid and accurate detection of the bacteria in the actual sample is finally achieved.

The invention provides a bacterial drug resistance prediction method and system based on a time sequence electronic health record, and relates to the technical field of drug resistance prediction, and the method comprises the steps: extracting patient features from the electronic health record; performing two-dimensional and three-dimensional feature extraction on the drug molecules to obtain drug features; extracting bacterial characteristics according to the bacterial genome sequence; extracting drug sensitivity characteristics according to a drug sensitivity test of microorganisms; respectively aligning other features with the drug sensitive features; initializing a modal shared space, fusing the drug sensitive test time difference into a query vector, and calculating the attention of the shared space to each modal feature; aggregating all the features into a shared space according to the attention to obtain comprehensive features of the drug sensitive test; and inputting the comprehensive features into a pre-constructed prediction model to obtain a prediction result. According to the method, the problems that time features are not utilized in drug resistance early warning, interaction between patient features is ignored, and modeling of drug molecules and bacteria is lacked are solved, and the accuracy of drug resistance prediction is improved.

Provided are antisense oligonucleotides targeted against bacterial genes involved in biochemical pathways and / or cellular processes, and related compositions and methods of using the oligonucleotides and compositions, alone or in combination with other antimicrobial agents, for instance, in the treatment of an infected mammalian subject.