Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards...

A rapid and sensitive reverse transcription polymerase chain reaction (RT-PCR) and nested-PCR were used to detect bovine viral diarrhea virus 1 (BVDV-1) in bull semen. Selected primers could amplify a part of the 5´UTR of the BVDV genome. A 294 bp DNA fragment was amplified and specificity of the results was confirmed by direct sequencing of the PCR product. Prior to RNA extraction, the seminal...

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, hi...

Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer a comprehensive survey of the population of genes (transcripts) in any sample of interest. This paper introduces a statistical model for estimating isoform ...

Whole-transcriptome sequencing ('RNA-Seq') has been drastically changing the scale and scope of genomic research. In order to fully understand the power and limitations of this technology, the US Food and Drug Administration (FDA) launched the third phase of the MicroArray Quality Control (MAQC-III) project, also known as the SEquencing Quality Control (SEQC) project. Using two well-established...

Abstract The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development the past decade. earliest studies main applications were body fluid tissue identification, using targeted RNA transcripts a reverse transcription endpoint PCR method. A number markers have been identified for forensically most relevant fluids tissues method successf...

Most RNA viruses undergo mutations inside the host at an incessant rate that allows them to elude the immune response. This constant evolution in RNA viruses is due to the low fidelity in replication carried out by the virus encoded RNA dependent RNA polymerases. This mis-incorporation of bases leads to establishment of a quasispecies of virus in the host. This makes it a challenge to combat vi...

Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to...

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6 -methyladenosine (m6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6 A-containing RNA prior to sequencing, since m6 A modifications...