58 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 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 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.

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 invention provides a method for monitoring a yeast fermentation process and pre-judging product quality. The method comprises the following steps: collecting yeast samples and recording fermentation days; the method comprises the following steps: extracting total DNA (Deoxyribonucleic Acid) of a sample, and respectively and quantitatively detecting the copy number of 16S rRNA genes of bacteria and the copy number of 18S rRNA genes of fungi; inputting the bacterial 16S rRNA gene copy number, the fungus 18S rRNA gene copy number and the fermentation day number into a random forest classification model, and outputting a normal or abnormal fermentation state; and pre-judging the product quality based on the fermentation state. The method breaks through the limitation of traditional dependence on sensory experience and a culture method, the microbial biomass is reflected in real time through absolute quantification of the microbial gene copy number, the detection time is remarkably shortened, and the accuracy of the random forest classification model is extremely high.

The invention relates to an antibacterial peptide TroLEAP2-21 and application of the antibacterial peptide TroLEAP2-21 in preparation of products for resisting bacteria and maintaining fish tissue integrity, and belongs to the technical field of biological polypeptides, and the amino acid sequence of the antibacterial peptide is shown as SEQ ID NO.1. The invention also provides an application of the trachinotus ovatus antibacterial peptide TroLEAP2-21 in preparation of antibacterial products, and the bacteria are lactococcus gasseri and staphylococcus epidermidis. The antibacterial peptide TroLEAP2-21 can change the permeability of a bacterial cell membrane, induce depolarization of the bacterial cell membrane, degrade bacterial genome DNA (Deoxyribonucleic Acid) and cause bacterial morphological change, so that an antibacterial effect is achieved.

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.

This invention belongs to the field of biodetection technology and discloses a method and application for analyzing antiviral and proviral bacteria based on metatranscriptome sequencing. Based on metatranscriptome sequencing, this invention utilizes different viral and bacterial marker genes to analyze and calculate the RPM values ​​of viral and bacterial species. Using the RPM values ​​of viruses and bacteria, Spearman correlation analysis is performed to obtain a correlation table showing the interactions between all bacteria and viruses. This invention overcomes the problem of incomplete bacterial genomes in metatranscriptome sequencing, enabling the detection of all viruses and bacteria in a single mosquito sample. The antiviral and proviral effects of bacteria are detected by the correlation between bacterial rpoB genes and viral RdRp load. Furthermore, the large mosquito sample size involved in this invention enhances the statistical reliability and ecological universality of the study, resulting in highly representative research results.

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 present invention discloses a method for isolating microorganisms from tissues. A lysis solution containing the surfactant Triton X100 is used to lyse cells, and the cell membrane of the cells is ruptured by the surfactant Triton X100 without destroying the bacteria containing the cell wall, thereby maintaining the intact structure of the bacteria and being used for subsequent high-throughput sequencing of the metagenome / macrotranscriptome and even single bacterial genome / transcriptome. The method of the present invention can efficiently and accurately isolate microorganisms from tumor tissues, improve the separation efficiency and purity of microorganisms, and avoid the problem of loss of microbial species in existing methods. The method of the present invention is suitable for high-throughput sequencing of microorganisms and can provide high-quality samples and data support for the study of tumor microbiome. The method of the present invention is simple to operate, low-cost, and has broad application prospects and clinical 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.