Showing posts from January, 2014

What's the DEal? Differential Expression using RSEM

We've been looking for ways to analyze transcriptomes correctly, with sufficient power, not too many type I and II errors, and not much fuss.  For those relatively unfamiliar with performing differential expression analyses on RNA-seq data, a great review of the statistical methods employed to analyze these data can be found here.

What it all comes down to is the fundamental problem associated with RNA seq experiments -- the absence of a single transcript could be due to down regulation OR, could be due to the up regulation of ANOTHER gene.  That's right, what you are measuring are RELATIVE expression levels, and given libraries of the same size, you cannot accurately distinguish the first scenario from the second unless you've spiked the libraries with some standards of known quantity (which, interestingly enough, has been done before with success by Mary Ann Moran's group here).

From Mary Ann Moran's paper on the subject, we have this very nice depiction of the …

How does an obligately intracellular symbiont maintain genetic diversity? The Wolbachia story

I recently had the pleasure of finally sitting down to read some publications (both open access!) on my favorite bacterium, Wolbachia pipientis.  These recent pubs interested me because they focused on the population genetics of Wolbachia within individual hosts, upon host transfer, and after many generations.  The BIG question that comes out of this body of work, in my mind, is how are low-titer strains in the maternally transmitted population maintained!  (We can discuss ongoing hypotheses at the end of this post)

The first paper I'll tackle (Schneider et al) asks if Wolbachia strains exist as diverse quasi-species within a host and reveals that diversity using host transfer techniques.  In "Uncovering Wolbachia Diversity upon Artificial Host Transfer" by Schneider et al., the authors use the cherry fruit fly Wolbachia (wCer strains) as the inoculum for injection of two new hosts: Drosophila simulans or Ceratitis capitata.  For those unfamiliar with the technique, what…