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.

Intron-mediated enhancement of gene expression

Most genes in eukaryotes (well, at least eukaryotes that are not Saccharomyces cerevisiae) possess introns, sequences that are transcribed by RNA polymerase II and subsequently spliced out from the primary transcript.  Introns have been the subject of tremendous interest since their discovery in the 1970’s, and have provided much insight (and grist for controversy) into subjects as disparate as junk DNA, the RNA World, and mechanisms of gene expression.  Among the still-unresolved matters today has to do with the timing of splicing – is it cotranscriptional* or does it occur after polII has released the transcript.

The case for co-transcriptional splicing has been built in part through numerous studies that reveal physical connections between splicing factors and the transcriptional complex; many (most) of these involve the so-called CTD (C-Terminal Domain) of RNA polymerase II.  (This recent review summarizes this emerging field.)  The general idea is that, owing to the association of splicing factors with the CTD of polII, they are able to bind the nascent transcript and initiate splicing before polII has completed the synthesis of the primary transcript.

Alternative polyadenylation and cancer

This is a follow-up of sorts to a previous essay on the subject of alternative polyadenylation.  In the previous report, I discussed some bioinformatics studies that suggested that the 3′ UTRs of mRNAs change, in bulk, in the course of development in mammals.  The implication of these results is that poly(A) site choice in mammals is regulated, with important functional consequences.

A more recent study by Mayr and Bartel adds to this notion.  These authors studied 3′ UTR length in normal and cancer cells, and found a striking correlation between 3′ UTR length and the expression of oncogenes.  Specifically, higher expression (as is found in cancer cells) is correlated with shorter 3′ UTR.  As 3′ UTR length is determined by the position of the poly(A) site along a transcript, this implicates alternative polyadenylation as one mechanism by which oncogene expression is activated.

Norman Ernest Borlaug (March 25, 1914 – September 12, 2009)

Norman Borlaug passed away yesterday.  Dr. Borlaug was the key contributor to the so-called Green Revolution, that brought great food security to countries such as Mexico, Pakistan, and India.  He was a clever and innovative plant breeder and a great champion for the use of high-yielding crop varieties in agriculture.

He was also an outspoken proponent of biotechnology.  As he stated in this short interview:

“I have devoted my life to the global challenge of providing adequate food production for a growing world population.  Forty years ago, a Green Revolution was started using improved seed and fertilizer, helping dramatically increase the harvest while sparing forest and natural areas from the plow.  It took both the scientific advances and the changes in economic policies by leaders to allow for the adoption of the Green Revolution technologies by millions of hungry farmers.

Over the past decade, we have been witnessing the success of plant biotechnology.  This technology is helping farmers throughout the world produce higher yield, while reducing pesticide use and soil erosion.  The benefits and safety of biotechnology has been proven over the past decade in countries with more than half of the world’s population.  What we need is courage by the leaders of those countries where farmers still have no choice but to use older and less effective methods.  The Green Revolution and now plant biotechnology are helping meet the growing demand for food production, while preserving our environment for future generations.”

From his foreword to “The Frankenfood Myth: How Protest and Politics Threaten the Biotech Revolution” by Henry Miller and Greg Conko (Praeger Publishers, 2004):

“As a plant pathologist and breeder, I have seen how the skeptics and critics of the new biotechnology wish to postpone the release of improved crop varieties in the hope that another year’s, or another decade’s, worth of testing will offer more data, more familiarity, more comfort. But more than a half-century in the agricultural sciences has convinced me that we should use the best that is at hand, while recognizing its imperfections and limitations. Far more often than not, this philosophy has worked, in spite of constant pessimism and scare-mongering by critics.

I am reminded of our using the technology at hand to defeat the specter of famine in India and Pakistan in the 1950s and early 1960s. Most “experts” thought that mass starvation was inevitable, and environmentalists like Stanford’s Paul Ehrlich predicted that hundreds of millions would die in Africa and Asia within just a few years “in spite of any crash programs embarked upon.” The funders of our work were cautioned against wasting resources on a problem that was insoluble.

Nevertheless, in 1963, the Rockefeller Foundation and the Mexican government formed the International Maize and Wheat Improvement Center (known by its Spanish acronym CIMMYT) and sent my team to South Asia to teach local farmers how to cultivate high-yield wheat varieties. As a result, Pakistan became self sufficient in wheat production by 1968 and India a few years later.

As we created what became known as the “Green Revolution,” we confronted bureaucratic chaos, resistance from local seed breeders, and centuries of farmers’ customs, habits, and superstitions. We surmounted these difficult obstacles because something new had to be done. Who knows how many would have starved if we had delayed commercializing the new high-yielding cereal varieties and improved crop management practices until we could perform tests to rule out every hypothetical problem, and test for vulnerability to every conceivable type of disease and pest? How much land for nature and wildlife habitat, and topsoil would have been lost if the more traditional, lowyield practices had not been supplanted?

At the time, Forrest Frank Hill, a Ford Foundation vice president, told me, “Enjoy this now, because nothing like it will ever happen to you again. Eventually the naysayers and the bureaucrats will choke you to death, and you won’t be able to get permission for more of these efforts.” Hill was right. His prediction anticipated the gene-splicing era that would arrive decades later. As Henry Miller and Gregory Conko describe in this volume, the naysayers and bureaucrats have now come into their own. If our new varieties had been subjected to the kinds of regulatory strictures and requirements that are being inflicted upon the new biotechnology, they would never have become available.”

Dr. Borlaug had been suggested at times to be the greatest living American.  Given the scope of his accomplishments, it’s hard to argue with this.

“Where Did All the Flowers Come From?”

Carl Zimmer has a good article in the NY Times entitled “Where Did All the Flowers Come From?”   The article summarizes lots of interesting stuff, but I find the speculation regarding the evolution of the endosperm to be particularly though-provoking.  Of course, anytime one mentions genome duplication to me, visions of gene silencing and small RNAs begin dancing in my mind.  A recent article from David Baulcombe’s group merits mention in this context.  This paper describes a developmental study of RNA polymerase IV-derived small interfering RNAs (siRNAs).  The remarkable finding in this paper is the observation that the synthesis of many polIV-derived siRNAs is initated at the onset of the development of the maternal gametophyte, and that these siRNAs are in turn derived from the maternal genome(s) in the endosperm.  This has ramifications for the expression of the different genomes in the endosperm, for genome imprinting, and likely for the evolution of flowers and seed development in plants.

The abstract from the paper:

“Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different small interfering RNAs (siRNAs) transcribed from thousands of loci^{1, 2, 3, 4, 5}. The biogenesis of most of the siRNAs in Arabidopsis are dependent on RNA polymerase IV (PolIV), a homologue of DNA-dependent RNA polymerase II^{2, 3, 6}. A subset of these PolIV-dependent (p4)-siRNAs are involved in stress responses, and others are associated with epigenetic modifications to DNA or chromatin; however, the biological role is not known for most of them. Here we show that the predominant phase of p4-siRNA accumulation is initiated in the maternal gametophyte and continues during seed development. Expression of p4-siRNAs in developing endosperm is specifically from maternal chromosomes. Our results provide the first evidence for a link between genomic imprinting and RNA silencing in plants.”

The citation:

Mosher RA, Melynk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC. 2009.  Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460, 283-286 (9 July 2009) | doi:10.1038/nature08084.

10 and 11

Or, if you might, 24 and 6.

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