9 results about "Genome scale" patented technology

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.

This invention provides a high-throughput method for constructing dual sgRNA libraries and its applications. The method utilizes high-throughput microarray synthesis technology to prepare a set of DNA fragments containing multiple dual sgRNA expression cassettes in a single step. After amplification, these fragments are assembled with a target vector containing a first promoter and a second gRNA backbone sequence in a first round of directed assembly to obtain a preliminary recombinant plasmid set. Then, linearized enzyme digestion and homologous recombination technology are used to insert a fragment containing a transcription termination sequence and a complete second promoter to complete the construction of the dual sgRNA expression unit. Finally, transformation and amplification yield the dual sgRNA plasmid library. This invention avoids the high error rate and high cost of long-chain oligonucleotide synthesis by utilizing microarray synthesis and simplifies the operation process through two rounds of directed assembly, significantly improving the throughput, fidelity, and efficiency of library construction. It is applicable to the construction of genome-wide dual sgRNA libraries, providing an efficient and reliable technical platform for high-throughput gene function screening, drug target discovery, and gene interaction research based on CRISPR.

The invention belongs to the technical field of biomedical information technology, cancer genomics and clinical diagnosis, and discloses a method and a device for automatically rating tumor somatic mutation carcinogenicity based on multi-dimensional evidence. According to the method, variation data to be rated are acquired and subjected to standardized annotation, crowd frequency, cancer hot spots, functional experiments and prediction information are automatically integrated based on a preset rating rule set, multi-dimensional evidence is calculated and predicted, and mutation is rated as carcinogenic, possibly carcinogenic, indefinite in meaning, possibly benign or benign after quantitative scoring. The device is an interactive system and supports variation retrieval, real-time rating, evidence review and result adjustment. According to the method, the problems of strong subjectivity, poor consistency, low efficiency and insufficient standardization of manual rating in the prior art are solved, efficient, accurate and repeatable rating of whole genome scale variation is realized, and reliable support is provided for genome diagnosis and targeted therapy.

The invention discloses a method for realizing wheat whole genome large-scale mutation and germplasm creation by editing repetitive sequences. CRISPR / Cas9 target sites with the copy number higher than 20,000 in wheat genomes are screened, tandem repeat sequences and dispersed repeat sequences are edited in a targeted mode, and heritable large-scale variation, chromosome structure variation and agronomic character variation of the whole genome scale are induced and generated in progeny plants. By editing repetitive sequences, large-scale mutation with chromosome and subgenome specificity can be realized, the created mutant library not only provides heritable variation mutant types different from those of traditional physical and chemical mutagenesis methods, but also generates materials such as chromosome aneuploidy (such as monosome, tetrasome and whole-arm deletion) and the like. And a unique genetic resource is provided for wheat functional genomics research and germplasm improvement.

The present invention relates generally to the amplification of RNA, such as for MERFISH or other applications. One set of embodiments generally relates to methods of synthesizing nucleic acids. Some embodiments relate to systems and methods for RNA in situ amplification that may allow for genome-scale imaging of RNA, including short RNA and RNA isoforms differentiated by short sequences. In some embodiments, RNA, such as mRNA, can be transcribed to cDNA using a reverse transcriptase. Reverse transcriptase may also be used to associate a promoter (e.g., T7 promoter) with RNA, for example, by using a template conversion oligonucleotide (TSO). The promoter sequences can then be used for amplifying RNA, for example, using techniques that can be performed in situ, such as in vitro transcription. In-situ amplification or increase of the amount of RNA may be useful for certain applications, such as MERFISH, as RNA is more easily detected. Other aspects relate generally to methods of using such techniques, kits involving such techniques, and the like.

The present invention relates generally to genomics. Some embodiments relate to imaging the 3D organization of a genome or a portion of a genome in sequence space at high throughput. Some embodiments relate to imaging the 3D organization of a genome or a portion of a genome in the context of transcriptional activity and nuclear structure. Further, certain embodiments relate to chromatin structure, 3D chromatin organization, chromosome- chromosome interactions and chromatin-nuclear structure interactions, and their relationship to transcription, among others. Further, various embodiments relate to imaging methods that allow mapping of the 3D organization of a genome or a portion of a genome in the context of nuclear structure and transcriptional activity. Some embodiments relate to large-scale multiplexed fluorescence in situ hybridization methods for imaging chromatin loci and / or nascent RNA transcripts on a chromosome or genome scale.

To provide a cell culture process search method by which optimum culture conditions can be searched, a cell culture process search program, and a cell culture process search device.SOLUTION: The cell culture process search method includes a process condition generation step of generating a plurality of process conditions, a culture result prediction step of acquiring a culture prediction result of cells for each of the generated process conditions, the step including a simulation method including a metabolic flux analysis or a flux balance analysis using a mechanism of cells or a genome-scale metabolic model, and a step of finding an optimal process condition from the culture prediction result, and an optimized process condition acquisition step of selecting an optimal medium composition and culture condition on the basis of a proliferation amount of cells or a bioproduction generation amount of an antibody, and in the optimized process condition acquisition step, the generated process condition and the culture prediction result are input, and an optimal process is calculated using a regression model which is a learned model by machine learning.SELECTED DRAWING: Figure 7

Existing techniques fail to provide a method to cumulate effects of interactions between groups of gut-associated microbes to predict efficiency of a probiotic organism in an individual. The present disclosure collects a test biological sample from the subject requiring personalization and extracts DNA from test biological sample and information specific to dietary preferences of the subject. Organisms from probiotic organisms dataset are obtained and a plurality of genome scale metabolic models are created for microbes comprised in gut microbiota of subject and obtained probiotic organisms. Metabolic simulations are performed to ascertain monoculture and co-culture growth of every pair of organisms comprised in gut microbiota of subject and obtained probiotic organisms. Sustainability is computed for evaluating capability of each organism to proliferate within gut. Net-effect is computed by quantifying an overall influence of each probiotic organism. An efficacious probiotic organism is selected based on at least one of net-effect and sustainability.

The application discloses a method for constructing a large fragment deletion mutant library of Magnaporthe oryzae, and belongs to the field of agricultural biotechnology.The method comprises the step of adding DEB to the protoplast of the Magnaporthe oryzae for culture and inducing the production of conidia.The application utilizes the chemical mutagen DEB to obtain the Magnaporthe oryzae mutant at a high frequency on a whole genome scale, and provides a new technical path for the functional genomics research of the Magnaporthe oryzae.The method provided by the application is helpful to systematically analyze the pathogenic mechanism, the infection process and the environmental adaptation regulation network of the Magnaporthe oryzae, and provides support for mining new disease-resistant targets and disease-resistant mechanisms.The method has the advantages of high efficiency, low cost and short cycle, and has wide application potential in the genetic research of plant pathogenic fungi.