Online ISSN: 2515-8260

Author : Cohrs, R.J.

Viralign: A tool for uncovering functional viral elements

Frietze S; R.J. Cohrs; Kaufer B

European Journal of Molecular & Clinical Medicine, 2015, Volume 2, Issue 4, Pages -

The availability of broad epigenomic profiles of human tissues provides an opportunity to uncover viral sequences and their corresponding functional regulatory elements in otherwise overlooked datasets. We developed Viralign, a throughput screening method to discover and interpret viral functional information in existing short read archive data. Using a comprehensive reference database, Viralign scans sequence data for known viral sequences and generates an alignment report with read information and genome coverage. Viralign analyzes functional datasets for regulatory elements and provides coordinate and visualization files that can be viewed in a genome browser. Additionally, this method searches for potential integration sites and variants by genome assembly. In a pilot study, we performed H3K27me3 ChIP-seq in monocytes of an HHV6 infected individual and compared this to U2OS cells infected with HHV6A and HHV6B and use Viralign to detect HHV6 insertion loci and H3K27me3 enriched regions.

Three-dimensional normal human neural progenitor tissue-like assemblies: A model for persistent Varicella-zoster virus infection and platform to study oxidate stress and damage in multiple hit scenarios

Thomas J. Goodwin; M. McCarthy; N. Osterrieder; R.J. Cohrs; B.B. Kaufer

European Journal of Molecular & Clinical Medicine, 2015, Volume 2, Issue 2, Pages 61-62

The environment of space results in a multitude of challenges to the human physiology that present barriers to extended habitation and exploration. Over 40 years of investigation to define countermeasures to address space flight adaptation has left gaps in our knowledge regarding mitigation strategies partly due to the lack of investigative tools, monitoring strategies, and real time diagnostics to understand the central causative agent (s) responsible for physiologic adaptation and maintaining homeostasis. Spaceflight-adaptation syndrome is the combination of space environmental conditions and the synergistic reaction of the human physiology. Our work addresses the role of oxidative stress and damage (OSaD) as a negative and contributing Risk Factor (RF) in the following areas of combined spaceflight related dysregulation: i) radiation induced cellular damage [1,2] ii) immune impacts and the inflammatory response [3,4] and iii) varicella zoster virus (VZV) reactivation [5]. Varicella-zoster (VZV)/Chicken Pox virus is a neurotropic human alphaherpesvirus resulting in varicella upon primary infection, suppressed by the immune system becomes latent in ganglionic neurons, and reactivates under stress events to re-express in zoster and possibly shingles.