Microbial Diversity

My student, Fredrick ("Freddy") Lee, published his first research paper in Environmental Microbiology this month.  Our lab's been focusing a lot recently on the honey bee microbiome and metabolic function of the community in situ .  In this manuscript (titled: Saccharide breakdown and fermentation by the honey bee gut microbiome ), we explore the capabilities of the honey bee gut community using RNA sequencing.  We also tested the effect of some commonly used enrichment protocols (the MICROBEnrich  kit from life technologies) in the pipeline Freddy used to process the bee samples.  Using three individual bees, he extracted total RNA and also used the aforementioned kit.  We made 100 cycle PE libraries for an Illumina GA IIx.  Here are the highlights: Major bacterial phyla and classes identified using 16s rRNA gene mining We used blast to map high quality short reads to our well known honey bee taxonomy  and found that, like our previous s...

A truly awesome paper on Wolbachia, variation in the pathogen-blocking phenotype, and genetics was published a while back by Luis Teixeira's group.  I've been eager to write a blog post on this particular paper, one of my favorite papers from 2013, so here goes!   <Follow along with the paper  here .> You are reading this blog, so maybe you don't need convincing that Wolbachia are totally awesome, relevant, and interesting bacteria.  They infect about half of the insect species on the planet and do so by targeting the germ line: that's right folks, these babies come pre-loaded with their bacterial symbiont.  Recently, Wolbachia have become more medically relevant because folks ( including Texieira himself with Michael Ashburner ) found out that they protect their insect hosts from virus infection -- either by reducing the load that the host carries (resistance) or by preventing disease even if the virus replicates (tolerance).  However, different W...

Whether you are reading a review of a grant application or that infamous "reviewer #3's" response to your manuscript, rejection can be tough to handle.  Listening to music may be able to help you cope with this stressful event <see research on this phenomenon here >, perhaps enough to get you past this submission cycle with enough cojones for the next.  Here are some suggestions, take 'em or leave 'em:   Phase 1: Denial and depression - no way, it can't be  "Better Man" by Pearl Jam. Can't find a better man. You're stuck in this.  "Black" by Pearl Jam. Just so obviously appropriate.  Although maybe love song for NIH/NSF. "Yeah.  I know someday you'll have a beautiful life . I know you'll be a star. In somebody else's sky. But why. Why. Why can't it be. Why can't it be mine."  Why can't that $$ be mine... "Mr. Self Destruct" by Nine Inch Nails I bring you the 90's Tre...

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 ...

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 wit...

What should a scientist look like? A pair of articles was published this morning in our local paper ( the Herald Times ).  In it are details of the many inequities faced by female scientists at Indiana University.  In those articles, some startling statistics were published, including the percentage of female faculty in the sciences at IU (~10%) and directly relevant to me, the inequity in salary (in Biology, the seven female full professors make ~$131,000 while the 22 male full professors make ~161,000).  In addition, there were some poignant anecdotes from female professors: "I never had children" said one, "I or my partner. We never had time we could take out of our careers without feeling like we might lose what we had gained."   It's nigh time to address the root of this insidious problem.  It cannot be fixed by hiring more women -- there are few of us to begin with and additionally, we all agree we want to hire both the  best and most  diverse...

An intriguing title for an article published in PLoS Pathogens on Halloween.  Needless to say, many of us in the Wolbachia community anxiously await the discovery of the mechanism behind Cytoplasmic Incompatibility.  For those of you who aren't Wolbachia -philes, the short of it is that this bacterium has figured out a nifty way to spread through insect populations. First, it's transmitted via the germ line -- so that means eggs come pre-loaded with Wolbachia from infected mothers.  Second, Wolbachia affect reproduction in a variety of ways but the most common is that infected females can mate with uninfected or infected males.  However, if you are an uninfected female -- if you don't carry the bacterium -- you cannot mate with infected males.  This drops the fecundity of uninfected females and allows Wolbachia , and the host carrying it, to spread.  There are also some interesting incompatibilities that result when hosts are infected with two diff...