scholarly journals Development and validation of SYBR Green- and probe-based reverse-transcription real-time PCR assays for detection of the S and M segments of Schmallenberg virus

2020 ◽  
Vol 32 (5) ◽  
pp. 710-717
Author(s):  
Ahmet Kursat Azkur ◽  
Wim H. M. van der Poel ◽  
Emel Aksoy ◽  
Renate Hakze-van der Honing ◽  
Murat Yildirim ◽  
...  

Schmallenberg virus (SBV), discovered in Germany in 2011, causes congenital malformations in ruminants. Reverse-transcription real-time PCR (RT-rtPCR) assays based on various segments of SBV have been developed for molecular detection. We developed alternative RT-rtPCR assays for SBV detection to avoid earlier reported mutations and hypervariable regions of the S and M segments of the viral genome. For SYBR Green-based detection of the S segment, the R2 value and efficiency of the developed assay were 0.99 and 99%, respectively. For probe-based S segment detection, 2 assays were developed; the first had an R2 value of 0.99 and 102% efficiency, and the second had a R2 value of 0.98 and 86% efficiency. The probe-based M segment assay had an R2 value of 1.00 and 103% efficiency. Detection limits of the RT-rtPCR assays with new primer sets were 102 and 101 copies/µL for the S and M segments, respectively. Field samples from cattle and sheep were also used for primary validation of the developed assays. Our assays should be suitable for SBV detection in ruminants and for in vitro studies of various SBV strains.

2020 ◽  
Vol 119 (11) ◽  
pp. 3909-3913
Author(s):  
Zaida Rentería-Solís ◽  
Tran Nguyen-Ho-Bao ◽  
Shahinaz Taha ◽  
Arwid Daugschies

Abstract Trichomonas gallinae are parasitic flagellates of importance in wild and domestic birds. The parasite is worldwide distributed, and Columbine birds are its main host. Current research focuses mostly on epidemiological and phylogenetic studies. However, there is still a lack of knowledge regarding parasite-host interaction or therapy development. Real-time PCR is a useful tool for diagnostic and quantification of gene copies in a determined sample. By amplification of a 113-bp region of the 18S small subunit ribosomal RNA gene, a SYBR green-based real-time PCR assay was developed. A standard curve was prepared for quantification analysis. Assay efficiency, linearity, and dissociation analysis were successfully performed. Specificity, sensibility, and reproducibility analysis were tested. This assay could be a useful tool not only for diagnostic purposes but also for future in vivo and in vitro T. gallinae studies.


2018 ◽  
Vol 30 (4) ◽  
pp. 589-592 ◽  
Author(s):  
Halcyon J. Killion ◽  
William Edwards ◽  
Jessica Jennings-Gaines ◽  
Mary Wood ◽  
Karen Fox ◽  
...  

A real-time PCR assay for the leukotoxin gene of Bibersteinia trehalosi was developed and validated to better identify this pathogen, which is a cause of respiratory disease in bighorn sheep. The specificity of the PCR primers was evaluated with DNA from 59 known isolates of the Pasteurellaceae family. For validation, 162 field samples were compared using both the new assay and an indirect method using 2 sets of published protocols. The real-time PCR assay was found to be specific for the leukotoxin gene of B. trehalosi and provides a rapid and direct approach for detecting leukotoxin-producing forms of this organism from samples containing mixed species of leukotoxin-positive Pasteurellaceae.


2004 ◽  
Vol 16 (2) ◽  
pp. 241
Author(s):  
A.S. Lequarre ◽  
J.M. Traverso ◽  
J. Marchandise ◽  
I. Donnay

Changes in length of the polyA tail of an mRNA is determinant for its stability and translation. During oocyte maturation, although some genes are specifically polyadenylated, an important decrease of polyadenylated mRNA is generally observed. Both degradation and de-adenylation can be responsible for this decline but little information about these processes is available yet for in vitro-matured bovine oocytes. Total RNA was extracted from 2 pools of 50 immature and 2 pools of 50in vitro matured bovine oocytes, after addition of 1pg of polyadenylated rabbit globin mRNA to each pool. The RNA of each pool was then divided in 8 samples, half of them were reverse-transcribed using hexamers and the other half using oligo(dT). Six genes were amplified in every sample using real-time PCR and specific molecular beacon probes: (1) rabbit globin, an exogenous gene added as a reporter for the efficiency of extraction and RT;; (2) histone H2A, an endogenous gene reporter for RNA quantity and quality in each pool [This housekeeping gene, that is not adenylated, should be maintained at a constant level through the maturation process (Robert et al., 2002 Biol of Reprod. 67, 1425–1472)]; (3) two antioxidant enzymes, peroxyredoxin 6 (PRDX-6) and G6PDH preventing oxidative stress during maturation [PRDX-6 also has a phospholipase A2 activity that could be implicated in prostaglandins synthesis during maturation]; (4) GDF-9, an oocyte-specific gene involved in cumulus expansion during maturation;; and (5) cyclin B1, one subunit of the MPF factor whose activity is required for meiosis resumption. The PCR result of each gene was normalized with the globin value of the same sample. After this standardization, the variability of the results among the 4 samples of a same pool similarly reverse transcribed did not exceed 15%. Within a pool, the mean PCR signal obtained for a specific mRNA using oligo(dT) was compared with the mean signal obtained with hexamers. Results obtained for immature and mature oocytes are reported in the Table 1. Before maturation, the PCR signals were higher when reverse transcription was performed using oligo(dT) instead of hexamers but that was not the case after maturation. Most messengers coding for these genes probably lost their polyA tails during maturation. This loss was much less pronounced for cyclin B1 messengers. Furthermore, for all genes studied, the PCR results obtained after reverse transcription using hexamers and normalized with the histone H2A value did not show a decrease during the maturation process. In conclusion, deadenylation, more than degradation, would be responsible for the disappearance of maternal polyadenylated mRNA during maturation. Table 1 Ratio of the PCR signals obtained after RT with oligo(dT) v. hexamers


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