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Figure 5 in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)

Figure 5. Effect of dsRNA feeding on leaf consumption was assessed in L. decemlineata larvae at different instars: (a) third instar and (b) fourth instar, following the feeding assay. Bars indicate standard error (SE) on columns. Different letters on the columns denote significant differences determined by ANOVA followed by the Tukey HSD test at a 5% significance level.

Figure 4 in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)

Figure 4. Influence of dsRNA ingestion on weight gain was calculated in the L. decemlineata larvae at different instars: (a) third instar and (b) fourth instar, following the feeding assay. Bars indicate standard error (SE) in columns. Different letters on the columns denote significant differences determined by ANOVA followed by the Tukey HSD test at a 5% significance level.

Figure 3 in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)

Figure 3. Effect of the dsRNA feeding on the V-ATPase expression levels in the L. decemlineata larvae at different instar stages: (a) First instar, (b) second instar, (c) third instar, and (d) fourth instar. Bars indicate the standard error (SE) in the columns. Different letters on the columns denote significant differences determined by ANOVA followed by the Tukey HSD test at a 5% significance level.

Figure 2. Mortality percentages after feeding the L in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)

Figure 2. Mortality percentages after feeding the L. decemlineata larvae dsRNA-treated leaves at different instars. (a) First instar, (b) second instar, (c) third instar, and (d) fourth instar. The percent mortality was compared in the larvae fed potato leaves pretreated with E. coli HT115 (DE3) cells expressing dsV-ATPase compared to the two controls, E. coli HT115 (DE3) cells with empty L4440 plasmid (dsEmp) and E. coli HT115 expressing dsGFP. Different letters on the data points denote significant differences determined by ANOVA followed by the Tukey honest significant difference (HSD) test at a 5% significance level.

publicSep 2022View details →

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Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?

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Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

Rotaviruses transcribe eleven distinct protein-coding RNAs that must be stoichiometrically co-packaged prior to their replication to make an infectious virion. During infection, rotavirus transcripts accumulate in cytoplasmic ribonucleoprotein (RNP) condensates, termed viroplasms. Understanding the mechanisms of viroplasm assembly and RNA enrichment within is crucial to gaining greater insight into their function and stoichiometric assortment of individual transcripts. We analysed the subcellular distribution of individual RV transcripts and viroplasm transcriptome by combining multiplexed DNA-barcoded single-molecule RNA FISH of infected cells. Using DNA-PAINT microscopy, we provide evidence of the early onset of viral transcript oligomerisation that occurs prior to the formation of viroplasms. We demonstrate that viral sequences lacking the conserved terminal regions fail to undergo enrichment in rotavirus RNP condensates. We show that individual viral transcripts exhibit variable propensities to partition into viroplasms, irrespective of their absolute numbers in cells, suggesting a selective RNA enrichment mechanism distinct from other known cellular RNP granules. We suggest that rotavirus replication factories represent unique RNP condensates enriched in eleven types of cognate transcripts that may facilitate the assembly of a multi-segmented RNA genome.

opencc-by-4.0Oct 2021View details →

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Infection by dsRNA viruses is associated with enhanced sporulation efficiency in Saccharoymces cerevisiae

Upon starvation, diploid cells of the facultative sexual yeast Saccharoymces cerevisiae undergo sporulation, forming four metabolically quiescent and robust haploid spores encased in a degradable ascus. All endosymbionts, whether they provide net benefits or costs, utilise host resources; in yeast, this should induce an earlier onset of sporulation. Here, we tested whether the presence of endosymbiotic dsRNA viruses (M satellite and L-A helper) correspond with higher sporulation rate of their host, S. cerevisiae. We find that S. cerevisiae hosting both the M and L-A viruses (so-called "killer yeasts") have significantly higher sporulation efficiency than those without. We also found that the removal of the M virus did not reduce sporulation frequency, possibly because the L-A virus still utilises host resources with and without the M virus. Our findings indicate that either virulent resource use by endosymbionts induces sporulation, or that viruses are spread more frequently to sporulating strains. Further exploration is required to distinguish cause from effect.

opencc-zeroApr 2022View details →

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Infection by dsRNA viruses is associated with enhanced sporulation efficiency in Saccharoymces cerevisiae

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publicApr 2022View details →

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Data from: Quantitative PCR primer design affects quantification of dsRNA-mediated gene knockdown

RNA interference (RNAi) is a powerful tool for studying functions of candidate genes in both model and non-model organisms and a promising technique for therapeutic applications. Successful application of this technique relies on the accuracy and reliability of methods used to quantify gene knockdown. With the limitation in the availability of antibodies for detecting proteins, quantitative PCR (qPCR) remains the preferred method for quantifying target gene knockdown after dsRNA treatment . We evaluated how qPCR primer binding site and target gene expression levels affect quantification of intact mRNA transcripts following dsRNA-mediated RNAi. The use of primer pairs targeting the mRNA sequence within the dsRNA target region failed to reveal a significant decrease in target mRNA transcripts for genes with low expression levels, but not for a highly expressed gene. By contrast, significant knockdown was detected in all cases with primer pairs targeting the mRNA sequence extending beyond the dsRNA target region, regardless of the expression levels of the target gene. Our results suggest that at least for genes with low expression levels, quantifying the efficiency of dsRNA-mediated RNAi with primers amplifying sequences completely contained in the dsRNA target region should be avoided due to the risk of false negative results. Instead, primer pairs extending beyond the dsRNA target region of the mRNA transcript sequences should be used for accurate and reliable quantification of silencing efficiency.

opencc-zeroMay 2020View details →

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Source data for Incarbone et al (2021) - "Immunocapture of dsRNA-bound proteins provides insight into tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector"

Source data for Incarbone et al (2021) - "Immunocapture of dsRNA-bound proteins provides insight into tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector" Includes full scans of blots mounted in figures and additional microscopy acquisitions, including brightfield channel

opencc-by-4.0Aug 2021View details →

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Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection

Thi file contain results of 24 grapevines leaf samples analyzed using dsRNA-MiSeq (Illumina Miseq) and dsRNAcD sequencing (ONT nanopore), that were used in the following article ''Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection''  submitted in Frontiers in Microbiology

opencc-by-4.0Mar 2023View details →

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Data from: Quantitative PCR primer design affects quantification of dsRNA-mediated gene knockdown

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publicDec 2019View details →

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Enhancement of Bacillus thuringiensis toxicity by feeding Spodoptera littoralis larvae with bacteria expressing immune suppressive dsRNA

Figure 1C Calibration curves used for qRT-PCR absolute quantification of Sl 102 and GFP dsRNA present in E. coli suspensions used in the bioassays   Figure 2 Transcript levels of Sl 102 gene in S. littoralis 4th instar larvae orally treated for 3 days with dsRNA. The Sl 102 gene was down-regulated upon ingestion of Sl 102 dsRNA administered by oral gavage, both in the case of dsRNA synthesized in vitro (Sl 102 dsRNA-synt) and suspensions of sonicated bacteria expressing Sl 102 dsRNA (Sl 102 dsRNA-bac). Delivery with artificial diet showed a silencing response that was dose-dependent and more pronounced when bacteria were used as delivery vectors. GFP dsRNA synthesized in vitro and bacteria expressing GFP dsRNA were used in control experiments. The values reported are the mean ± standard errors (*P < 0.0001, Student’s t test) Figure 3 Encapsulation assay in S. littoralis 4th larvae treated for 3 days with Sl 102 dsRNA synthesized in vitro (Sl 102 dsRNA-synt) or transformed HT115 E. coli expressing Sl 102 dsRNA (Sl 102 dsRNA-bac). Chromatography beads injected into the body cavity of control larvae were encapsulated and melanized (a). On the contrary, the efficiency of encapsulation was lower in silenced larvae, independently from the dsRNA administration method (gavage or with artificial diet) (b). The encapsulation index was affected by oral delivery method and, in the case of oral administration on artificial diet, by dsRNA quantity. GFP dsRNA synthesized in vitro and bacteria expressing GFP dsRNA were used in control experiments. The values reported are the mean ± standard errors (*P < 0.0001, Student’s t test) Figure 4 Bioassay with S. littoralis 4th instar larvae exposed to dsRNA before Bt treatment. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 E. coli expressing Sl 102 dsRNA (Sl 102 dsRNA-Bac, corresponding to 200 ng of dsRNA) and then with 12 µg/cm2 of Xentari™ for 3 more days (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (a), when the weight was assessed on the surviving experimental larvae (b). Bacteria expressing GFP dsRNA were used in control experiments. The timing of the treatments is indicated with arrows. The values reported are the mean ± standard errors (in a *P < 0.0001 based on log-rank test; in b different letters denote statistical difference based on Kruskal–Wallis test, followed by Dunn’s multiple-comparison post hoc test)   Fig. 5 Bioassay with S. littoralis 4th instar larvae simultaneously exposed to dsRNA and Bt. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 E. coli expressing Sl 102 dsRNA (Sl 102 dsRNA-Bac, corresponding to 200 ng of dsRNA) and with 9 µg/cm2 of Xentari (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (a) when the weight was assessed on the surviving experimental larvae (b). Bacteria expressing GFP dsRNA were used in control experiments. The timing of the treatments is indicated by arrows The values reported are the mean ± standard errors (in a **P < 0.0001 and *P < 0.0046 based on log-rank test; in b different letters denote statistical difference based on Kruskal–Wallis, followed by Dunn’s multiple comparisons post hoc test) Fig. 6 Bioassays with S. littoralis 5th instar larvae simultaneously exposed to dsRNA and Bt. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 E. coli expressing Sl 102 dsRNA (Sl 102 dsRNA-Bac, corresponding to 200 ng of dsRNA) and with 12 µg/cm2 of Xentari (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (a), when the weight was assessed on the surviving experimental larvae (b). Bacteria expressing GFP dsRNA were used in control experiments. The timing of the treatments is indicated by arrows. The values reported are the mean ± standard errors (in a *P < 0.0001 based on log-rank test; in b different letters denote statistical difference based on Kruskal–Wallis test followed by Dunn’s multiple-comparison post hoc test)

opencc-by-4.0Apr 2020View details →

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Figure 1 in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)

Figure 1.Phylogenetic relationship of the Vacuolar ATPase proteolipid subunits of several insect species. The phylogenetic tree was constructed using the neighbor-joining approach.

openGEO-OpenDec 2022View details →

Sequence determinants of dsRNA processing by DICER [Massively Parallel Assay]

GEO Series GSE202530. Homo sapiens. 18 samples. Type: Non-coding RNA profiling by high throughput sequencing.

openGEO-OpenJul 2023View details →

Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [dsRNA-seq]

GEO Series GSE221426. Mus musculus. 8 samples. Type: Other.

openGEO-OpenDec 2023View details →

Malignant A-to-I RNA editing by ADAR1 drives T-cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing

GEO Series GSE221112. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.