Daniela Sempertegui-Bayas
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Research Subjects
Daniela Sempertegui-Bayas has a total of 5 co-authors. Here are the top co-authors by number of shared publications:
- Andres S. Espindola
Oklahoma State University, Entomology and Plant Pathology, 127 Noble Research Center, Stillwater, Oklahoma, United States, 74078-1010
1 shared publication - Danny F. Bravo-Padilla
Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA
1 shared publication - Francisco Manuel Ochoa Corona
Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, U.S.A.
1 shared publication - Kitty F. Cardwell
Institute for Biosecurity and Microbial Forensics, Oklahoma State University, United States
1 shared publication - Viviana Freire-Zapata
Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA
1 shared publication
Latest Publications
- Open Access
TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics
High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.
Open AccessTASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics
High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.