Project description:While employing deep sequencing and de novo assembly to characterize the mRNA transcript profile of a cell line derived from the microbat Myotis velifer incautus, we serendipitously identified mRNAs encoding proteins with a high level of identity to herpesviruses. Next generation sequencing and de novo assembly of the viral genome from supernatants from Vero cells yielded a single contig of approximately 130 kilobases with at least 80 ORFs, predicted microRNAs and a gammaherpesvirus genomic organization. Phylogenetic analysis of the envelope glycoprotein (gB) and DNA polymerase (POLD1) revealed similarity to multiple gammaherpesvirus, including those from as yet uncultured viruses of the Rhadinovirus genus that were obtained by deep sequencing of bat tissues. Cumulatively, this study provides the first isolation and characterization of a replication competent bat gammaherpesvirus.
Project description:Saccahromycopsis schoenii belongs to a genus of yeasts that have the ability to attack and kill other yeast and fungi. De novo genomic sequencing and genome assembly suggests that S. schoenii might belong to the CTG clade. To examine whether it translated CTG codons to leucine (standard codon usage) or serine (alternative codon usage), we analysed its proteome during growth on full media. To see if translation is changed during nutritional stress or during predation on a prey cell (Saccharomyces cerevisiae), we analysed and quantified its proteome during these conditions compared to its proteomic expression in full media.
Project description:The proteome of the SS13 isolate assigned to the Chromatiaceae family was assessed by shotgun proteomics using a pan-proteomics database for the genus Rheinheimera and a whole genome sequencing -derived database.
Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:We isolated Mesoflavibacter zeaxanthinifaciens S86 as xylanase-producing bacteria from seawater sampled in Micronesia. Analysis of the M. zeaxanthinifaciens genome revealed that it contains a single circular chromosome of 3,704,661 bp with 3,249 putative open reading frames.
