Ultradeep Pyrosequencing of Hepatitis C Virus to Define Evolutionary Phenotypes
[Abstract] Analysis of hypervariable regions (HVR) using pyrosequencing techniques is hampered by the ability of error correction algorithms to account for the heterogeneity of the variants present. Analysis of between-sample fluctuations to virome sub-populations, and detection of low frequency variants, are unreliable through the application of arbitrary ...
Sequencing of Ebola Virus Genomes Using Nanopore Technology
Author: Thomas Hoenen,
date: 11/05/2016,
view: 6276,
Q&A: 0
[Abstract] Sequencing of virus genomes during disease outbreaks can provide valuable information for diagnostics, epidemiology, and evaluation of potential countermeasures. However, particularly in remote areas logistical and technical challenges can be significant. Nanopore sequencing provides an alternative to classical Sanger and next-generation ...
Purification of Bacterial RNA from Infected Macrophages
[Abstract] Studying the transcriptome of bacterial pathogens during infection is a very informative and effective tool for discovering genes that contribute to successful infection. However, isolating bacterial RNA from infected cells or tissues is a challenging process due to the much higher amounts of host RNA in the lysates of infected cells. We have ...
Quantification of HIV RNA and Human Herpesvirus DNA in Seminal Plasma
[Abstract] Multiple viruses can co-infect the genital tract, modifying the immunologic and virologic milieu and possibly playing a role in viral transmission and pathogenesis. The aim of our studies has been to understand the complex relationships between HIV-1 RNA, and multiple human herpesviruses known to frequently replicate in the genital tract of ...
RNA Isolation from Synechocystis
Authors: Kirill S. Mironov and
Dmitry A. Los,
date: 03/20/2015,
view: 14461,
Q&A: 2
[Abstract] The protocol describes the procedure of total RNA isolation from cells of the cyanobacterium Synechocystis sp. PCC 6803. This protocol is also applicable to Synechococcus elongatus PCC 7942 and PCC 6301, Thermosynechococcus vulcanus, and other unicellular and filamentous species of cyanobacteria that do not have thick ...
In vitro Transcription (IVT) and tRNA Binding Assay
Author: Sonja MK Schoenfelder,
date: 09/20/2014,
view: 8705,
Q&A: 0
[Abstract] This protocol describes the coupling of (i) “live” in vitro RNA transcription with (ii) binding by a radiolabeled, pre-formed tRNA followed by native gel electrophoresis and phosphorimager scan to visualize the complex. The necessity arose from the stable structure that one RNA forms in the absence of its interaction partner. The T-box ...