78-63

‘Nuf said.

This doesn’t look right

A short time ago, a study describing the discovery of a bacterium that could apparently utilize arsenate in place of phosphate was published in Science.  This report has since generated a lot of discussion and debate in the blog-o-sphere, most of it rather uncomplementary.  I count myself among those who are skeptical of the more daring of the authors’ claims.

Something I found curious was the gel in Fig. 2A, an analysis of nucleic acids isolated from bacteria grown in arsenate-rich (middle lane) or phosphate-rich (right lane) media:

Now that’s a streamlined NIH grant proposal

Rocket Boys.  Enjoy.

Jack of all trades

One of the more intriguing enzymes that handles RNA is polynucleotide phosphorylase (PNPase).  This enzyme is a phosphorolytic 3’->5’ exonuclease; that means that it acts on the 3’ end of an RNA chain and moves towards the 5’ end, and that it adds phosphate (as opposed to water) to the broken phosphodiester bond.  This means that the products of the nucleolytic reaction are a shortened RNA chain and a nucleotide 5′-diphosphate.  The nucleolytic activity is appropriate, as the enzyme is a principal exonuclease component of the RNA-degrading machine known as the degradosome.

But RNA breakdown is not the only enzymatic activity possessed by PNPase.  As I noted in an earlier essay, PNPase was a first (perhaps THE first) nucleotidyltransferase, or RNA polymerase.  Indeed, it was an early candidate for the RNA polymerase (you know, the DNA-dependent RNA polymerases that are responsible for transcription).  This activity reflects the fact that the nucleolytic activity, when reversed, is actually a nucleotidyl transferase activity, in which RNA chains can be extended (in a template-independent fashion) using nucleotide diphosphates as substrates.  The clearest in vivo manifestation of this activity is evident in the many reports that show that PNPase can act as a poly(A) polymerase in vivo [see the review by Slomovic et al. for more on this]; this is true in bacteria and in organelles such as the chloroplast or mitochondria.

Daddy’s stories – Australian Rules Football

So, if you’ve got kids who were raised in the 90′s and after, they probably have a hard time believing you when you tell them about the good old days, when there were music videos on MTV and sports (other than poker) on ESPN after midnight.

I’ve told my kids (more times than they can care to hear, I’m sure) that they were raised on the oddball sports that ESPN showed at the wee hours (the times when I got to rock the babies back to sleep after the 2AM feeding) back when – things like Australian Rules Football.  I tried explaining these novelties, seemingly to no avail.

Recap

The RNA 2010 Meeting has come and gone.  Previously, in a sort of preview of coming attractions, I gave a list (from the conference web site) of the many invited speakers.  What I thought I would do here is toss out some random comments, to give readers a small taste of the meeting.  (One aside – the abstracts are not “open access” and attendees are asked in the abstract book to not cite anything without authors’ consent.  This means that I won’t be very explicit about the individual talks or posters.  However, in a few instances, I will provide links to related papers.)

A year (almost) of hockey

And quite a year it’s been.

From an unbelievable NCAA D1 finals.

To a scintillating Stanley Cup Finals.

To a glorious afternoon in Fenway Park.

To this afternoon’s climactic Gold Medal Game.

Not bad.  Not bad at all.

UK2K!

Daddy’s stories – the Berlin Wall

The hoopla (much deserved – it’s one of the most interesting and singular moments of our time, the fall of the Berlin Wall) over the anniversary of the fall of the Wall brings to my mind one of those stories that I have told my kids (over and over, I am afraid).

When my girls were in school, they did the time-honored show and tell bit.  One of the things they took was some crumbling remains of the Berlin Wall.  Not the Wall that fell in 1989 but rather pieces of the first “wall” that was hastily put up in 1961 and was re-built by the East Germans in the mid-1960′s.

If I had known of this in August!

The title of a recent paper that is available at the Genome Research web site:  “Windshield splatter analysis with the Galaxy metagenomic pipeline”

I could have provided a kilogram or more of sample from my recent move-in trip.

The abstract of this paper:

How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number of required tools and considerable computational infrastructure. In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article.

The citation:

Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; The Galaxy Team. Windshield splatter analysis with the Galaxy metagenomic pipeline.  Genome Res., Published in Advance October 9, 2009, doi: 10.1101/gr.094508.109.