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.

It’s all about ribosomes

What is all about ribosomes?  Undoubtedly, readers will quickly make the connection between the title of this short essay and the recent awarding of the 2009 Nobel Prize in Chemistry to three whose work has centered on the ribosome.  The Nobel prize announcement emphasized the links between ribosomes and antibiotics, rightly focusing attention on the fact that many antibiotics target the bacterial ribosome, different as it is from its eukaryotic (cytosolic) counterpart in important ways.  What I want to do is to ramble on about some other aspects of ribosomes that I find fascinating.  Hopefully, by turning some features of biology on their heads, readers will think differently about genomes, gene expression, and other facets of molecular biology.

The Nobel Prize in Chemistry 2009

It’s a great week for RNA biology.  Early today, it was announced that the 2009 Nobel Prize in Chemistry was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath for their work on the structure and function of ribosomes.  For the uninitiated, the ribosome is the central feature of life (moreso than even DNA!), and it is at its core a ribozyme.

As was stated in the abstract of a recent review by Steitz:

The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity.

From the press release:

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

….

An understanding of the ribosome’s innermost workings is important for a scientific understanding of life. This knowledge can be put to a practical and immediate use; many of today’s antibiotics cure various diseases by blocking the function of bacterial ribosomes. Without functional ribosomes, bacteria cannot survive. This is why ribosomes are such an important target for new antibiotics.

This year’s three Laureates have all generated 3D models that show how different antibiotics bind to the ribosome. These models are now used by scientists in order to develop new antibiotics, directly assisting the saving of lives and decreasing humanity’s suffering.

What a great subject – from the RNA World (at the very dawn of life!) to modern medical microbiology.

The Nobel Prize in Physiology or Medicine 2009

The announcement is here.  The award goes to Elizabeth Blackburn, Carol Greider, and Jack Szostak “for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”.  Needless to say, RNA is woven intricately into this subject.

10 and 11

Or, if you might, 24 and 6.

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

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.)

There’s more to UK …

That would be UK as in the University of Kentucky.

We’ve been splayed all over the news for the past several months, embarrassingly so.  Seems like we stole the show during and shortly after the NCAA tournament, and our new coach deliberately or inadvertently has kept us on p1 for much of the past several months.  It wouldn’t surprise to think that, to the rest of the country (and world), the University of Kentucky was the name of some sports franchise.

Well, the president of UK has ’bout had enough of this.  His editorial in today’s Lexington newspaper was refreshing in many ways – a slap in the H-L’s face, a grasping of the readership by the collar and shaking some sense into them, a rather public display of annoyance and exasperation, and yes, an implicit plea to taxpayers to support his school.  UK is more than 12 (yup, JM isn’t coming back) athletes who ply their trade for five months of the year.  It’s good to see the president remind the Commonwealth of this.

Guidelines for quantitative PCR

One of the more vexing and difficult issues in molecular biology is the use of PCR as a quantitative assay.  It is easy to find a wide range of approaches to this, and even easier to find papers that refer to “semi-quantitative” PCR.  As one might expect, there is a range of quality in the literature when it comes to these assays.  Worse, though, is the paucity of information that is often provided – things like the numbers of replicates, statistical tools used to analyze the data, and the like.  THis makes it hard to follow many studies, and to replicate the work of others.  (Needless to say, reviewing these papers is a bear.)

There has been a mini-debate of sorts in The Plant Cell over the past few years, and a recent issue has two additions to the discussion.  Follow below the fold for more.