126 results about "Metabolic network" patented technology

The invention relates to a method for identifying a disease microorganism-metabolite combined marker based on a host-flora co-metabolism model. The method comprises the following steps: processing microbiome data; setting diet constraint conditions; determining classification composition of intestinal microorganisms of each individual, mapping abundance of each microorganism to a human microorganism genome scale metabolism model, and constructing an individualized flora metabolism network model; carrying out metabolic flow simulation on the constructed flora metabolism network model; integrating the constructed flora metabolism network model with the host metabolism network model, and predicting the metabolic flow and metabolite change of the whole system; and establishing a disease classifier based on a random forest machine learning algorithm to identify the microorganism-metabolite combined marker. According to the method, the complex metabolic process between the human body and the intestinal flora is restored in a metabolic network modeling and metabolic flow simulation mode, the method has the non-invasive characteristic, the time and economic cost is remarkably reduced, and meanwhile, the method has a great advantage in accuracy.

The invention relates to a construction method of escherichia coli engineering bacteria with high yield of N-acetylglucosamine. According to the method, the metabolic network of escherichia coli is directionally modified through metabolic engineering, the problems of'product re-decomposition ', by-product accumulation, poor genetic stability and the like of natural strains are solved, and efficient industrial production of GlcNAc is realized.

The invention relates to a method for regulating and controlling gene expression of lactic acid bacteria in shrimp acid fermentation based on systematic biology. The method comprises the following steps: constructing a gene regulation network of lactic acid bacteria by using whole genome data and a high-throughput sequencing technology comprising RNAseq; through clustering analysis and network reconstruction, transcription factors and enzymes of key metabolic pathways of lactic acid generation, acid resistance and glycometabolism are identified, and a dynamic regulation and control model of gene expression is established; a GeneNet or Cytoscape software tool is used, genomics, transcriptomics and metabonomics data of lactic acid bacteria are fused in a multi-layer network, a metabolism regulation and control system is constructed, and the metabolism regulation and control system comprises gene expression regulation and control and real-time change of metabolic flow; the method comprises the following steps: constructing a metabolic flux dynamic model of lactic acid bacteria based on a metabolic flux analysis MFA and a dynamic system modeling technology, and analyzing a mutual relation between a lactic acid generation path and a byproduct generation path; fBA is analyzed through flow equilibrium, and the metabolic network of lactic acid bacteria is optimized.

The invention relates to the technical field of immune cell culture, in particular to an immune cell culture data monitoring method and system based on activation analysis. When the immune cell culture equipment monitors that the signal protein is conducted on the abnormal standard signal channel, the real-time metabolic network is reduced based on the interference degree of the abnormal standard signal channel on the metabolic pathway, the metabolic enzyme concentration is calculated and analyzed, and a metabolic activity monitoring reference is generated; if it is monitored and detected in real time that unreasonable metabolism conditions exist in metabolic data of immune cell culture, peak integral deviation parameters for cell factor compensation are constructed based on the metabolic enzyme concentration deviation value of the metabolic activity monitoring benchmark to conduct injection compensation regulation and control on cell factors of the cultured immune cell sample. According to the method, the abnormal proliferation data, the abnormal proliferation-causing signal path data and the metabolic data in the immune cell culture process can be subjected to rapid and accurate activation analysis, so that the immune cell activation performance can be better optimized, and the culture quality is improved.

The invention relates to the technical field of bacterium enrichment nutrient solutions, in particular to a bacterium enrichment nutrient solution for fermentation and a preparation method of the bacterium enrichment nutrient solution. The culture medium is prepared from the following raw materials in parts by weight: maltodextrin, crystalline glucose, low-pigment yeast extract powder, refined soy peptone, dipotassium phosphate, monopotassium phosphate, magnesium sulfate heptahydrate, sodium chloride, phytic acid, L-ascorbic acid, manganese sulfate monohydrate, biotin, thiamine hydrochloride and choline chloride. Through a double-carbon-source structure, maltodextrin and crystalline glucose cooperate, metabolic oscillation is avoided, and the energy utilization rate is increased; the low-pigment yeast extract powder and the refined soy peptone are complementary, so that the rapid growth requirement of thalli is met; phytic acid is chelated with metal ions to prevent precipitation, L-ascorbic acid is used for resisting oxidation, and biotin and thiamine activate a coenzyme pathway to realize accurate regulation and control of a metabolic network.

The invention discloses a prediction method for identifying a protein-protein interaction site. According to the method, a deep learning framework is constructed based on protein chain hierarchical graph construction and double-branch graph neural network learning. The method comprises the following steps: firstly, constructing a corresponding hierarchical graph for each protein chain, including a residue-level graph and an atomic-level graph; next, the method constructs an isotropic graph neural network (EGNN) module to extract residue-level embedding with isotropic features. After a GraphSAGE module is further used for extracting atomic-scale embedding, the method integrates layered graph features by using a comparative learning strategy so as to learn residue-scale and atomic-scale consistency embedding. Finally, an improved gated multi-head attention mechanism is used for fusion embedding weighting, and residue-level interaction classification prediction is performed through a multi-layer perceptron. A comprehensive evaluation result on a plurality of data sets shows that the method is remarkably superior to an existing method. In conclusion, according to the method, various advanced technologies such as graph structure denaturation, multi-scale modeling and comparative learning are fused, and an accurate and steady solution with expansion potential is provided for protein interaction prediction. The method can assist researchers in deeply recognizing key protein acting sites and promoting analysis work of cell signal channels and metabolic networks.

The invention discloses a Yarrowia lipolytica strain for synthesizing ergothioneine and application of the Yarrowia lipolytica strain, and belongs to the technical field of genetic engineering and bioengineering. According to the invention, a key enzyme TrEGT1 is subjected to semi-rational transformation, so that the ergothioneine yield of a strain expressing a mutant is increased by 240.9%, precursor metabolic network screening is further modularized, precursor flux is enhanced, a competitive approach of a precursor is knocked out and weakened, and strategies such as fermentation process optimization and the like are further optimized; and when the constructed strain is fermented in a 5L bioreactor, the yield of ergothioneine can reach 10.3 g / L. The highest-level ergothioneine synthesis reported at present is realized, the feasibility of synthesizing the ergothioneine by using the Yarrowia lipolytica as the chassis cell is verified, and a reference value is provided for efficiently synthesizing the ergothioneine by using other chassis cells.

The invention relates to the technical field of bioinformatics, particularly discloses a metabolite target interaction prediction method and system for myocardial injury, and aims to solve the problems that complex heterogeneous data processing is insufficient, and dynamic changes of a metabolic network are difficult to capture and fine time sequence prediction is difficult in the prior art. According to the method, multi-source heterogeneous data is integrated, a myocardial injury risk factor and metabolite target knowledge base is constructed, and machine learning and deep learning technologies are utilized to realize risk factor weighting and static and sequential dynamic risk assessment. By fusing the static risk level and the dynamic adjustment factor, the system can predict the metabolite target interaction related to the individual high-risk state and generate personalized prevention and intervention strategy suggestions according to the metabolite target interaction. The system comprises a plurality of functional modules including data acquisition and preprocessing, knowledge base construction, feature engineering, risk modeling, time sequence optimization, target prediction and the like, so that early, dynamic and accurate prediction of myocardial injury risks and recognition of personalized intervention targets are realized.

The invention provides a comprehensive energy efficiency evaluation method and system for a smart park, and the method comprises the steps: constructing a nonlinear metabolism matrix reflecting the energy incidence relation between equipment, and solving the optimal metabolic flux distribution through mixed integer nonlinear programming; defining an interaction rule base with a metabolic network, dynamically triggering rules according to real-time sensor data, and adjusting real-time metabolic flux; calculating the quantized value of each current energy efficiency index according to the real-time metabolic flux, quantifying the uncertainty through a fuzzy entropy theory, dynamically distributing multi-target weights, and calculating a comprehensive energy efficiency score; and calculating the quantized value of each energy efficiency index in the optimal state according to the optimal metabolic flux distribution, comparing the fuzzy entropy, determining a to-be-optimized energy efficiency index, and identifying high risks and potential risks to formulate an optimization strategy. According to the method, various equipment and energy flow conditions in the park are considered, the energy efficiency level of the system is accurately reflected, dynamic adjustment and evaluation are carried out according to real-time data, uncertainty factors of the energy system are identified and solved, and efficient and stable operation of the system is guaranteed.

The invention discloses a hybrid central metabolic network chassis cell with both carbon atom economy and energy generation pathway as well as a construction method and application of the hybrid central metabolic network chassis cell, and belongs to the technical field of genetic engineering and microorganisms. The Escherichia coli central metabolic network is reconstructed, so that the Escherichia coli central metabolic network has a carbon sequestration module and an energy generation module at the same time. The carbon sequestration module continues to fix CO2 while avoiding CO2 release caused by pyruvic acid decarboxylation, the highest carbon yield can reach 133%, the carbon yield exceeds that of an NOG pathway reported only from the perspective of no CO2 release, and the carbon yield is two times that of a natural glycolysis pathway. And the direct product of the constructed mixed type central metabolic network is acetyl coenzyme A, and the acetyl coenzyme A contains an energy generation module, so that the chassis cell provided by the invention can meet the synthesis requirements of acetyl coenzyme A derivatives with high or low required reducing power, and has universality.

The invention discloses a saccharomyces cerevisiae recombinant strain based on a uracil metabolism gene URA3 as well as a construction method and application of the saccharomyces cerevisiae recombinant strain. The construction method comprises the following steps: taking saccharomyces cerevisiae rich in farnesyl pyrophosphate as an original strain, introducing a uracil metabolism gene URA3, synchronously overexpressing a ribosome biosynthetic gene UTP10 and an iron metabolism gene FIT3, and utilizing the uracil metabolism gene URA3 to express up-regulation correlation with the ribosome biosynthetic gene UTP10 and the iron metabolism gene FIT3, so as to obtain the farnesyl pyrophosphate-rich saccharomyces cerevisiae. The metabolic flux of the terpenoids is enhanced, and the saccharomyces cerevisiae recombinant strain for efficiently producing the terpenoids is constructed. According to the method, a metabolic network of yeast is systematically optimized, and combined regulation and control on precursor flux distribution, protein translation capability and metal ion steady state are realized, so that the microbial synthesis efficiency of sesquiterpenoids such as patchouli alcohol and beta-elemene is remarkably improved.

The invention provides a preparation method of 11-seed fermentation oil and fermentation liquor with multiple effects, and belongs to the technical field of fermentation. The method comprises the following steps: S1, preparing recombinant saccharomycetes; s2, jointly fermenting lactobacillus, recombinant saccharomycetes and 11 seed oil; s3, separating an oil phase and a water phase, and taking the oil phase; and S4, dehydrating the oil phase to obtain the 11-seed fermentation oil. And S5, further refining the water phase to obtain the 11-seed fermentation liquor. The 11-seed fermented oil prepared by transforming a microbial metabolic network is rich in dihydroquercetin, and has multiple effects of resisting oxidation, resisting wrinkles, tightening, repairing cells and the like. In the fermentation process of the 11-seed fermentation oil, 11-seed fermentation liquor can be obtained, and the fermentation liquor has multiple effects of resisting oxidation, relieving, moisturizing, resisting wrinkles, tightening and the like.

The invention discloses a method for improving the self-luminous intensity of a plant, which is characterized in that an AroGL175Q gene or an RgTAL gene and a PtC3H gene or the AroGL175Q gene, the RgTAL gene and the PtC3H gene are expressed in a plant containing a fungus bioluminescence system FBP, so that a transgenic plant of which the caffeic acid content, the milk tree alkali content and the luminous intensity are obviously increased is obtained. According to the invention, through metabolic network optimization and transformation, phenylpropane metabolites required by middle and upper streams of a fungus bioluminescence pathway are increased, and synthesis of caffeic acid and milk tree alkali in plants is increased, so that bioluminescence enhancement is realized. The precursor supply bottleneck of a fungus bioluminescence system is broken through, and an innovative solution is provided for creating efficient self-luminous plants.

The disclosed multiscale framework includes innovatively coupling genome-scale metabolic models with an agent-based model and an adapted continuum model of the biofilm; employing a systematic bottom-up approach to identify interrelationships between local substrate and mediator transport and the dynamic biofilm characteristics; and elucidating the interdependence of genomic data and microscale biofilm properties, thereby enabling a deeper understanding of the behavior of species within the biofilm.

The invention relates to the technical field of amino acid compositions, and discloses a compound amino acid composition for enhancing telomerase activity, which comprises the following components (by weight): 20-25 parts of L-arginine; 15 to 20 parts of L-lysine; 25 to 30 parts of L-glutamine; 10 to 15 parts of L-serine; 5 to 8 parts of L-glycine; 3 to 5 parts of L-proline; 2 to 4 parts of N-acetyl-L-cysteine; 1 to 2 parts of L-tryptophan; 1 to 2 parts of beta-alanine; 2 to 3 parts of L-carnitine; 1-2 parts of taurine; through the synergistic effect of multiple mechanisms, the compound amino acid composition not only significantly enhances the telomerase activity (up to 195%), but also can maintain the telomere length, inhibit cell aging and provide antioxidant protection. The comprehensive regulation effect is derived from a unique metabolic network formed among the components, and mutual promotion and regulation are realized. Experimental results show that the long telomere length (8.3 kb vs control group 7.1 kb) can be maintained in 30-day long-term culture.

This invention provides a method for hypertension risk assessment, relating to the field of epigenetic detection technology. It includes: performing event alignment and residual modeling on a qualified signal set to establish a base probability at the locus level and forming baseline features through neighborhood consistency screening; constructing a tunneling sensitization model and contextual attention, fusing discriminative and generative evidence to obtain enhanced features; quantifying IGF2BP3 and aligning and fusing it with the enhanced features; constructing an IGF2BP3-mediated metabolic network based on this, performing time-series modeling and stability assessment, and extracting final-state features; fusing the final-state risk vector with multi-gene scores to complete adaptive grading and compliant report generation. This method is robust, interpretable, and easy to deploy.

The invention discloses a method for improving yield of branched chain aldehyde of lactococcus lactis based on regulation and control of a luxS gene and application, and belongs to the field of system biology. Gene function verification and genome scale metabolic network model analysis are creatively combined, the phenotypic effect of the luxS gene is confirmed, and more importantly, the internal action mechanism of the luxS gene is disclosed from the system level, that is, the whole metabolic network flow is influenced by regulating and controlling multiple key enzymes such as transaminase, decarboxylase, dehydrogenase and decarboxylase. The invention reveals that the quorum sensing core gene luxS has a new function of regulating and controlling synthesis of branched chain aldehyde in lactococcus lactis for the first time, and an intercellular communication system is directly linked with production of specific flavor metabolites. The invention provides a brand-new and higher-level regulation target and thought for producing flavor substances by microbial fermentation, and gets rid of the limitation that only metabolic pathway terminal enzyme is singly modified traditionally.

The embodiment of the invention discloses a construction method of a multi-source organic solid waste whole-process substance flow and energy flow metabolic network diagram and a related device. A basic theoretical analysis and research framework is set up; constructing an urban typical organic solid waste material flow model according to the basic theoretical analysis and research framework; and according to the urban typical organic solid waste material flow model, constructing a Yifen city typical organic solid waste metabolic network. It can be seen that the embodiment of the invention is beneficial for solving the following problems: 1, composition and characteristics of the organic solid waste can be better understood by establishing a substance flow and energy flow metabolic network diagram, so that a more efficient and more economical treatment process is designed; 2, through the metabolic network diagram, the influence of the organic solid waste treatment process on the environment can be better known, so that measures are taken to reduce the influence of the organic solid waste on the environment.

The invention belongs to the technical field of biological medicines, and particularly relates to an application of LAP3 and an agonist thereof in macrophage immune inflammation mediated diseases. The invention provides application of leucine aminopeptidase 3 or leucine aminopeptidase 3 agonist substances in preparation of drugs for prevention, treatment and / or adjuvant treatment of macrophage immune inflammation mediated diseases. According to the invention, it is found for the first time that the expression level of LAP3 in macrophages is increased under an acute stress condition, and the limiting effect of LAP3 on generation and development of sepsis and acute hepatitis is disclosed; the invention discloses that the knockout of the LAP3 can remodel a macrophage metabolic network, reduce oxidative phosphorylation, promote ROS (reactive oxygen species) production and activate TAK1, thereby promoting the activation of a downstream inflammation signal channel and finally promoting macrophage inflammation. A new target spot and a theoretical basis can be provided for clinical diagnosis and treatment of macrophage-mediated inflammation by illuminating the effect of LAP3 on regulating and controlling macrophage inflammation and a molecular mechanism of LAP3.