Rolling Circle Amplification (RCA)-Mediated Genome-Wide ihpRNAi Mutant Library Construction in Brassica napus

Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA

In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.

Analysis of the Candidate Genes and Underlying Molecular Mechanism of P198, an RNAi-Related Dwarf and Sterile Line

The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotypes. In this study, a dwarf and sterile line named P198 was screened from the Brassica napus (B. napus) RNAi library. Three different methods confirmed that eight copies of T-DNA are present in the P198 genome. However, only four insertion positions were identified in three chromosomes using fusion primer and nested integrated polymerase chain reaction. Therefore, the T-DNA insertion sites and copy number were further investigated using Oxford Nanopore Technologies (ONT) sequencing, and it was found that at least seven copies of T-DNA were inserted into three insertion sites. Based on the obtained T-DNA insertion sites and hairpin RNA (hpRNA) cassette sequences, three candidate genes related to the P198 phenotype were identified. Furthermore, the potential differentially expressed genes and pathways involved in the dwarfism and sterility phenotype of P198 were investigated by RNA-seq. These results demonstrate the advantage of applying ONT sequencing to investigate the molecular characteristics of transgenic lines and expand our understanding of the complex molecular mechanism of dwarfism and male sterility in B. napus.

Novel miniaturized fluorescence loop-mediated isothermal amplification detection system for rapid on-site virus detection

New pathogen outbreaks have progressed rapidly and are highly infectious in recent years, increasing the urgency of rapid and accurate detection of pathogenic microorganisms. Based on the point-of-care testing (POCT) requirements, in this study, a real-time fluorescent loop-mediated isothermal amplification (LAMP) detection system was developed and applied to pathogen detection. The system is compact and portable, with good uniformity and reproducibility, and it can detect pathogens rapidly and effectively. For norovirus detection, the linear range was 10⁰–10⁶ copies/μL. The system can achieve the theoretical sensitivity of LAMP detection, conclusions could be obtained within 35 min, and quantitative detection was possible. The test results of 45 clinical samples were consistent with quantitative PCR (qPCR) and clinical results, and the accuracy could reach 100%. This system has the characteristics of portability, speed, and POCT accuracy, and the cost is much lower than that of commercial qPCR. Therefore, it is suitable for remote areas or places with relatively poor conditions and environments requiring on-site conditions. It can also be widely used to detect various epidemics and unexpected diseases.