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.

10 and 11

Or, if you might, 24 and 6.

No particular reason – just stumbled across this photo and had to put it here.

Putting the polyadenylation complex together

One of the reasons for the slow pace of entries here has been the intrusion of, um, life into my life.  (Yeah, figure that one out.)  Earlier this summer, a paper from my lab was published in BMC Cell Biology.  Seeing as it’s Open Access, and since it has a bit of relevance to a theme introduced in this essay, I thought I would point it out here.

The story in a nutshell – one of the subunits of the polyadenylation complex is the so-called CPSF30 protein, or its yeast relative Yth1.  (Yth1 looms large as one of the few subunits in the Giardia complex.)  What Drs. Suryadevara Rao and Randy Dinkins did was study the places within the cell where CPSF30 goes, and what happens when one co-expresses this protein with other polyadenylation complex subunits.  They did this by attaching the various proteins to fluorescent proteins and following the fusion proteins using microscopic techniques.

The results corroborated other studies that detailed interactions between various of these proteins.  However, a rudimentary deletion analysis showed that these interactions by and large involve parts of CPSF30 that are not found in the mammalian or yeast proteins.  Since the CPSF30 interacts with the other proteins of interest in this study (the 160, 100, and 73 kD subunits of the cleavage and polyadenylation specificity factor, or CPSF) in other eukaryotes, it stands to reason that the interactions themselves must have evolved independently.  This in turn suggests a somewhat different trajectory in the evolution of the complex in different eukaryotic lineages.  It also raises the possibility that the different complexes may process and polyadenylate RNAs in subtly different ways.

Some pretty pictures and a link to a fascinating movie may be found beneath the fold.  Enjoy.

Four weeks on the road …

Well, not all on the road.  Most of one week at home packing between trips, and a few days at Cold Spring Harbor in NY.

Whew!

The past few weeks (it seems a lot longer) have been spent largely on the road.  The task has been to move my oldest daughter (Heather) to Missoula MT, where she will be attending the University of Montana.  We folded a family road trip into the move and took a few weeks to accomplish the task.  A brief photo recap is beneath the fold.  I hope to return to some of the more usual blog entries after the next road trip (moving Amy back to Juniata, wrapped around the Eukaryotic mRNA Processing meeting at the Cold Spring Harbor Laboratory).  Enjoy. (Warning – quite a few pictures, which may make for slow loading.)

One year later …

Today is the one year anniversary of the beginning of this blog.  I wasn’t sure how things would develop, and still am not.  We’ve had a few good discussions, but what I have noticed most of all is how I get a steady stream of hits on the polyadenylation background essays.  It’s enough to imagine that this blog is sort of an alternative to wikipedia for those looking for information about this process.  This is good, but this interest has not come with questions.  Either these essays are clear (not likely), or someone out there is being shy.  So, those readers who are using this blog as a vehicle to learn about the process, don’t hesitate to ask questions.  You obviously want to learn something about the subject, and the best way to learn is to ask.

Graduation week

I spent the last week traveling to two graduations.  Our oldest daughter graduated on Monday from the College of Wooster, with a BA in Geology.  Heather will be attending the University of Montana in pursuit of a Master’s Degree.

Earlier, on May 6, my sister’s oldest son (Corey) graduated from Officer Candidate’s School at the US Coast Guard Academy in New London, CT.

Ensign McPartlin.  That has a great sound.

A few photos beneath the fold.

Pretty incredible

That’s a subdued way to described last night’s NCAA Division I hockey championship game between the upstart Miami (OH) RedHawks and the Boston University Terriers.  The underdog RedHawks dominated, absolutely dominated the game, especially the first 19 minutes of the third period.  With 60 seconds to go, they held a 3-1 lead.  It looked like the school would win their first national championship in any sport.

But then …!!!  BU had been playing without a goalie since about the 3 min mark (well, except when there were face-offs outside of the MU zone).  The extra skater payed off when they scored with 59 seconds left in the game, and again with 17 seconds remaining.  Stunning, especially since they had been lethargic and totally outplayed until this point.

This set up overtime.  Sudden death overtime in hockey is the most exciting, tense, enthralling spectacle in sport (IMO, at least).  In this case, it ended 11+ minutes into OT, a slapshot deflecting off a sliding MU defender over the goalie’s shoulder ….

Read more here and here (Dan Shaughnessy already calls it the greatest college hockey game ever).  I haven’t seen that many, and I expect RedHawk fans would call it more a nightmare, but it was pretty exciting.

Rooting interests – I’m a Bostonian at heart, but my good friend and collaborator is a professor at Miami.  So I’m pretty torn by this.  In a good sort of way. (Well, except in knowing that my alma mater, UMass Lowell, lost their chance to get into the NCAA tournament by one goal to, um, BU.)

One more dig – the Frozen Four beat the heck out of the Final Four this year.

Pardon the brief interruption…

One of those weather things …