Project description:Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. The use of high-throughput sequencing of DNA barcodes is a promising method to identify adulterants, but is not yet widely used in practice. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components, so the results of genomic analysis require an independent confirmation method. Perhaps the most promising way to increase the accuracy of food ingredient identification is to use an orthogonal method based on very different physical principles than DNA sequencing, which involves the analysis of other plant cell components, to verify the results of HTS analysis. In this work, we decided to evaluate the suitability of a multi-omic approach, including coupled DNA barcode HTS analysis and proteomic analysis, to estimate food fraud in herbal beverages. To resolve disputed discordant results obtained during genomic and proteomic investigation of samples, we used traditional botanical morphology method. Among the samples studied, the combined approach revealed two adulterations of Epilobium with Lythrum, which could be dangerous for the unsuspecting consumer.
Project description:Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. To evaluate methods for demultiplexing barcode-multiplexed data, we generated a dataset by labeling samples separately with barcode-tagged antibodies, mixing those samples, and progressively overloading a droplet-based scRNA-seq system.
Project description:Precise and tunable genetic tools are essential for high throughput functional genomics. To address this need in the important gram-negative pathogen Pseudomonas aeruginosa, we developed and characterized a tightly regulated CRISPRi system that enables precise and tunable repression of essential genes. The system utilizes a rhamnose-inducible promoter to control both the Streptococcus pasteurianus-derived dCas9 and gene-specific sgRNAs, each encoded on separate plasmids for modularity and efficiency. The combination of tight regulation and high conjugation efficiency facilitated the rapid and facile construction of strains with regulated depletion of 16 essential genes spanning diverse pathways. Comparison of phenotypes across the different genetically depleted strains, including growth rate, susceptibility to antibiotics, and changes in transcriptional programs, revealed novel aspects of gene function or small molecule mechanism of action. Finally, the rhamnose-inducible CRISPRi system supports the generation and stable maintenance of pooled mutant libraries, thereby paving the way for future genome-wide, systematic assessment of individual gene vulnerabilities, which will provide critical insights for target prioritization in antibiotic discovery efforts against this recalcitrant pathogen.
2025-12-11 | GSE313177 | GEO
Project description:Biosensor Assisted Next-Generation Droplets High-throughput Screening Agent for Screening Vitamin B12 Producers from Soil