104 results about "Archaea" patented technology

The present invention relates to systems and methods for real time, rapid detection, identification, and enumeration of a wide variety of analytes, which include but are not limited to, cells (Eukarya, Eubacteria, Archaea), microorganisms, organelles, viruses, proteins (recombinant or natural proteins), nucleic acids, prionss, and any chemical, metabolites, or biological markers. The systems and methods, which include the laser/optic/electronic units, the analytic software, the assay methods and reagents, and the high throughput automation, are particularly adapted to detection, identification, and enumeration of pathogens and non-pathogens in contaminated foods, clinical samples, and environmental samples. Other microorganisms that can be detected with the present invention include clinical pathogens, protozoa and, viruses.

The invention relates to a method for editing prokaryotic genomes using an endogenic CRISPR-Cas (CRISPR-associated) system. An editor plasmid carrying both an artificial CRISPR cluster and a donor DNA is required to be established for the genome editing of a prokaryote containing the endogenic CRISPR-Cas system, after NDA interference is caused by the endogenic CRISPR-Cas to the genome, and the genome is edited through homologous recombination. The method has the advantages that a range of applicable hosts is wide, all bacteria and archaea containing the endogenic CRISPR-Cas being available for operation; the method is applicable to operations in various editing manners, such as deletion, insertion and point mutation; the editing efficiency is higher, screening positive rage is high, and the background is low; a flow is simple, a short period of time is required, and the workload of prokaryotic genome editing is greatly reduced.

The present disclosure provides CasX proteins, nucleic acids encoding the CasX proteins, and modified host cells comprising the CasX proteins and/or nucleic acids encoding same. CasX proteins are useful in a variety of applications, which are provided. The present disclosure provides CasX guide RNAs that bind to and provide sequence specificity to the CasX proteins, nucleic acids encoding the CasX guide RNAs, and modified host cells comprising the CasX guide RNAs and/or nucleic acids encoding same. CasX guide RNAs are useful in a variety of applications, which are provided. The present disclosure provides archaeal Cas9 polypeptides and nucleic acids encoding same, as well as their associated archaeal Cas9 guide RNAs and nucleic acids encoding same.

Disclosed are methods for screening biological samples for the presence unknown microbes, such as bacteria and archaea or unknown eukaryotes using rRNA gene sequences or other highly conserved genetic regions, across multiple biological samples using a unique sequence tag (barcode) corresponding to the sample. The screening process tracks the unknown microbe or eukaryote in a diluted sample where the DNA has been prepared using whole genome amplification. The whole genome of the unknown microbe or eukaryote is then sequenced and assembled.

The present invention is directed toward improving the efficiency of chain terminator incorporation by Family B archaeon DNA polymerases. Previously, the low efficiency of ddNTP, and more especially dye-labeled ddNTP, incorporation has limited the usefulness of this group of DNA polymerases in protocols requiring chain terminator incorporation.

Mycorrhizal and rhizobial associations represent the two most important symbiotic relationships between higher plants and microorganisms, providing access to otherwise limiting supplies of phosphate and nitrogen, respectively. Although many higher plants are able to establish a symbiotic relationship with arbuscular mycorrhizal fungi, legumes are unusual among plants because they also form associations with nitrogen fixing soil bacteria called rhizobia. This symbiosis requires the production of bacterial signals, “Nod factors” that trigger several key developmental responses in the host plant (Dénarié et al., 1996). The DMI1 gene of the model legume M. truncatula plays a major role both in the early steps of Nod factor signaling and in the establishment of mycorrhizal symbiosis. Dmi1 mutants do not exhibit many of the early responses to Nod factors and are incapable of forming nitrogen fixing root nodules. Here we describe the cloning and preliminary characterization of DMI1. The DMI1 gene encodes a novel protein with low global similarity to ligand-gated cation channels of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. Interestingly a putative A. thaliana DMI1 orthologous gene is expressed in roots. As A. thaliana is unable to establish a mycorrhizal symbiosis, this finding suggests that DMI1 may also exhibit a function that is independent of symbiotic interactions.

The present disclosure provides methods and devices for rapid and efficient modification of a variety of cell types, including mammalian cells, plant cells, archaea, yeasts, and bacteria, by novel methods of introducing exogenous materials, e.g. nucleic acids.

The invention discloses a glutamic acid decarboxylase mutant and a preparation method thereof and application. An amino acid sequence of the mutant is as shown in SEQ ID No. 2, and a nucleotide sequence is as shown in SEQ ID No. 1. The invention further discloses an expression unit containing genes for encoding the glutamic acid decarboxylase mutant, a recombinant plasmid and a transformant. According to information of comparison with a thermococcus kodakarensis glutamic acid decarboxylase (GAD) amino acid sequence, a method of site-directed mutagenesis is adopted to introduce proline residue at an amino acid locus corresponding to lactobacillus brevis GAD, and the thermal stability of the GAD is improved through rational design. The mutant has better thermal stability in the process of catalyzing L-glutamic acid or sodium salts thereof to generate gamma-aminobutyric acid and is favorable for industrial production of gamma amino acid butyric acid (GABA).

The invention provides a method for treating high-salt wastewater by using halophilic microorganisms. The halophilic microorganisms can adapt to a high-salt environment to perform normal growth metabolism, and comprise haloduric and halophilic bacteria, yeasts, archaea and microfauna. The method for treating the high-salt wastewater by using the halophilic microorganisms comprises the following steps: adding a halophilic microbial flora into a biochemical system; performing mixed culture on the halophilic microbial flora in an influent salt concentration range of 1-25% to improve the pollution degradation capability of the halophilic microbial flora and obtain a halophilic microbial aggregate with good mud-water separation performance and precipitation performance, such as active sludge and a biomembrane; and stabilizing the process parameters and influent water quality of the biochemical system to ensure that the biochemical effluent reaches a standard or meets design requirements. By adopting the method provided by the invention, the high-salt wastewater with the influent salt concentration of 1-25% of the biochemical system can be subjected to biochemical treatment, and the halophilic microbial agent only needs to be added once, so that the investment and operation costs can be reduced.

A method of using micro-organisms to continuously and sustainably regenerate zeolite cation exchange capacity (CEC) for removing nitrogen (ammonium, nitrite, and nitrate) from wastewater. The zeolite immobilizes the ammonium ions, and the micro-organisms ingest the ammonium from the surface of the zeolite thereby freeing the cation exchange sites to trap more ammonium. The zeolite is continuously regenerated by the microbes, sustainably maintaining available ion exchange capacity for removing ammonium, and does not need to be shut down for regeneration or replacement. The microbial complex contains nitrifiers, anammox, denitrifiers, archaea, and others. All the micro-organisms co-exist in the same reactor promoting symbiotic interactions, thereby increasing treatment efficiency. The end product is di-nitrogen gas which dissipates into the atmosphere. The system does not require aeration, operates by gravity flow, and has very low energy requirements. Maintenance is minimal, and the system can significantly reduce greenhouse gas emissions (nitrous oxide).

Notes: This document uses the terms ammonia and ammonium interchangeably, just as the compounds themselves are interchangeable (NH3+H⁺NH4⁺). In aquatic systems ammonia (NH3) is predominantly found in the ionic form as ammonium (NH4).

A method for quantifying ammonia oxidizing archaea in lacustrine deposit. The method comprises the following steps of (1) extracting DNA, and (2) constructing an ammonia oxidizing archaea plasmid standard substance and analyzing a sample, wherein the copy number of Ammonia oxidizing archaea in an unknown sample is obtained through processes of a detection of a Ct value of the unknown sample and a contrast of an amplification standard curve and the Ct value after the amplification standard curve is obtained. In the invention, ammonia oxidizing archaea in lacustrine deposit is detected quantificationally through a real-time fluorescent quantitative polymerase chain reaction (PCR) technology. The method is a rapid, simple and accurate method for researching a nitrogen cycle mechanism of lacustrine deposit.

The invention relates to the technical field of microbes, and discloses a method for producing propionic acid by mixed bacteria system fermentation. The method comprises the following steps: carrying out sequencing batch anaerobic fermentation on a fermentation system composed of Methanogenic archaea/propionic-acid-producing bacteria-containing anaerobic sludge and an anaerobic fermentation culture medium, wherein in the fermentation process, the ammonium ion concentration in the fermentation system is enhanced to 1-2 g/L and kept constant, and methane is collected; and after the fermentation finishes, collecting the fermentation liquid, extracting the propionic acid, and adding the residual flora-containing solid into the anaerobic fermentation culture medium for the next fermentation round. The ammonium ion concentration is regulated to control the flora distribution of the Methanogenic archaea/propionic-acid-producing bacteria-containing anaerobic sludge, so that the fermentation environment is beneficial to the proliferation of the propionic-acid-producing bacteria; and the method can obtain a large amount of methane in the process of producing high-concentration high-purity propionic acid, has the advantages of unrestricted material sources and lower input-output ratio, and is beneficial to industrialized implementation.

The invention relates to a straw feed and a preparation method thereof. The preparation method comprises the following steps of culturing extremely halophilic archaea-halogranum amylolyticum TNN58; after the culturing of thalli is completed, performing cell pyrolysis by a water pyrolysis method. After centrifugal treatment, solids mainly comprise biological degradable plastics PHBV and part of intracellular substances, and precipitates can be used for PHBV extraction; supernatant contains a large quantity of nutrient substances, so that when the supernatant is added to straw, the content of nutrient substances such as protein in the straw can be effectively increased, and the nutrient value of the straw can be increased.

The invention provides an anaerobic biodegradation method for the azo dye gold orange II. According to the anaerobic biodegradation method, a sequencing batch mode is employed; methane is used as an electron donor; azo dye gold orange II is used as an electron acceptor; and denitrification anaerobic methane oxidation (DAMO) archaea is adopted for anaerobic biodegradation of the azo dye gold orangeII. When the DAMO archaea oxidizes methane into carbon dioxide, generated electrons are transfered to the azo dye gold orange II so as to reduce the azo dye gold orange II into p-aminobenzenesulfonicacid and 1-amino-2-naphthol, and thus, the anaerobic microbial degradation of the azo dye by the DAMO archaea is realized. The anaerobic biodegradation method of the invention has great advantages ineconomical performance and environmental protection; and the DAMO archaea widely exists in nature, which is beneficial for large-scale application of the DAMO archaea in anaerobic microbial treatmentof azo dyes and even other organic substances.

The invention discloses an application of an extremely halophilic archaea (Natrinema altunense sp.) NaSOD gene in improving rice salt tolerance. The base sequence of the extremely halophilic archaea NaSOD is shown by SEQ ID NO.3. The over-expression NaSOD genetically modified rice has the advantages of higher ROS scavenging capability and capability of reducing membrane lipid peroxidation caused by salt treatment so that higher photosynthetic rate can be guaranteed. According to the invention, the extremely halophilic archaea NaSOD gene is transferred into the rice so that the salt tolerance of the rice can be obviously improved.

The invention discloses a marine ammonia-oxidizing archaea enrichment device capable of automatically controlling dissolved oxygen. The enrichment device comprises a reactor, a water feeder, a low-temperature water-bath kettle and a control cabinet, wherein a main body of the reactor is a funnel-shaped tank body, a reactor pressure balance opening and a reactor DO probe are arranged at the upper end of the funnel-shaped tank body, a reactor water inlet is formed in the lower end of the funnel-shaped tank body, and a temperature-controllable jacket is arranged outside the funnel-shaped tank body; the water feeder is divided into four parts, namely, a water-distribution zone, an aeration zone, a sedimentation zone and a water drainage zone, the water-distribution zone is provided with a water feeder DO probe, a feeding pipe and a water feeder water outlet, the aeration zone is provided with an aerating disc, the sedimentation zone is provided with a water feeder water inlet pipe and the water drainage zone is provided with a water feeder gas outlet and a water feeder water drainage opening. The enrichment device can provide low-temperature, low-dissolved-oxygen, low-shearing-force and high-salinity environment required for the growth of marine ammonia-oxidizing archaea; by virtue of the dissolved oxygen probe, an air pump and a nitrogen steel cylinder, the dissolved oxygen in the reactor influent water is controlled at a relatively low level so that the effective enrichment of marine ammonia-oxidizing archaea is achieved and the high-purity enriched culture product is obtained.

The invention provides a method for promoting the anaerobic degradation of petroleum hydrocarbon in an oil reservoir to produce methane. The method comprises the following steps of (1), detecting andanalyzing the structure of a microbiologic population in the oil reservoir, so as to judge whether the oil reservoir contains a syntrophic hydrocarbon-degrading methanogenesis strain or not; (2), whenthe syntrophic hydrocarbon-degrading methanogenesis strain is contained in the oil reservoir, adding an additive A into the oil reservoir, and then shutting a well, wherein the additive is hydrogen nutritional methanogenesis archaea or mixed flora containing the hydrogen nutritional methanogenesis archaea; when the methanogenesis syntrophic hydrocarbon-degrading strain is not contained in the oilreservoir, adding an additive B into the oil reservoir, and then shutting the well, wherein the additive B is mixed bacteria containing the hydrogen nutritional methanogenesis archaea and syntrophichydrocarbon-degrading bacteria.

The invention relates to a special specie DNA Marker for detecting coal geology microbe archaea in the denaturing gel gradient electrophoresis (DGGE) molecule detection of coal geology environment microbe florae, and belongs to the field of molecular microbial ecology. The DNA Marker for detecting coal geology microbe archaea species is composed of a DNA fragment a with the nucleotide sequence represented by SEQ. ID. NO.1, a DNA fragment b with the nucleotide sequence represented by SEQ. ID. NO.2, a DNA fragment c with the nucleotide sequence represented by SEQ. ID. NO.3, a DNA fragment d with the nucleotide sequence represented by SEQ. ID. NO.4, a DNA fragment e with the nucleotide sequence represented by SEQ. ID. NO.5, a DNA fragment f with the nucleotide sequence represented by SEQ. ID. NO.6, a DNA fragment g with the nucleotide sequence represented by SEQ. ID. NO.7, and a DNA fragment h with the nucleotide sequence represented by SEQ. ID. NO.8.

The invention discloses a preparation method for archaea thermophilic esterase and (S)-ketoprofen. The method comprises preparation of a strain, a plasmid, enzymes and a culture medium, PCR amplification and construction of recombinant plasmid, and inducible expression of a gene and purification of protein. Specifically, the method comprises the following steps: (1) designing a pair of primers, carrying out amplification with a whole genome sequence of Thermotogamaritima as a template, carrying out enzyme digestion with endonuclease, connecting the primers to pET15b which has undergone enzyme digestion by same endonuclease, transforming ligation productsinto escherichia coli DH5 alpha, carrying out screening to obtain a recombinant plasmid and carrying out double digestion and sequencing confirmation; and (2) carrying out inducible expression of the gene and purification of the protein so as to obtain the archaea thermophilic esterase. According to the invention, through usage of a genetic engineering method, the gene of the esterase is cloned and expressed in escherichia coli, the protein of the esterase is prepared, and the protein has a high purity (more than 95%). The optimal reaction temperature and the reaction pH value of the esterase are 70 DEG C and 5.0 to 5.5, respectively; the esterase has good acid resistance and can maintain about 50% of its activity when treated for 60 min in a reaction system where the temperature is 70 DEG C and the pH value is 4.5.

Methods of using archaeal serine protease sequences are disclosed.

The invention discloses a method for increasing PHA yield by inhibiting halophilic archaea EPS yield, and belongs to the field of producing polymer by microbial fermentation. According to the technical method, adjusting on concentration of NaCl in fermentation liquor can be used for inhibiting synthesis of EPS, so that propensity synthesis of PHA is promoted. When NaCl concentration in fermentation liquor is controlled to be 200g/l-250g/l, the yield of EPS can be inhibited, so that synthesis amount of PHA is remarkably improved. The technical method for synthesizing PHA by adjusting Haloferaxmediterranei propensity is simple to implement, and is easy for engineering operation.

The invention relates to a culture method for prolonging ammonia-oxidizing archaea (AOA) passage time and belongs to the technical field of bioengineering. The culture method comprises synchronously inoculating a medium with nitrobacteria (NOB) and AOA, carrying out culture at a temperature of 25-37 DEG C for 6 weeks, carrying out subculture, adding an antibiotic into the medium with NOB and AOA and carrying out passage 3-4 times to obtain pure AOA culture. Through coculture of NOB and AOA, AOA passage time is prolonged, passage number is reduced and AOA activity is guaranteed. Through use of the antibiotic, NOB growth is inhibited and pure AOA is obtained. The culture method is very simple and convenient.