Coming attractions

October 5, 2011

The 2011 RustBelt RNA Meeting (RRM) is just around the corner.  The venue this year is in Dayton, OH, a short hop. skip, and jump from the Bluegrass.  I’ll post a follow-up after the meeting is over, but in the meantime, I though a few links to the talks and posters might be of interest.




Everyone’s reading it!

October 5, 2011


Eukaryotic mRNA Processing 2011

August 28, 2011

The bi-annual Cold Spring Harbor Laboratory Meeting on Eukaryotic mRNA Processing is one that I try to attend on a regular basis.  The last two meetings (2009 and this year) posed special problems for me, since I am also the driver and mule for Amy’s moving trip to Juniata College.  The two institutions – CSHL and JC – don’t seem to “talk” to each other, and move-in has been coincident with the meeting (basically, 1 day apart, not enough time to drive to PA, return, and fly to NY).  This means that I have ended up driving from Lexington to Cold Spring Harbor for the past two meetings.  Load the car up with a dorm room, drive to Huntingdon PA, unload, and just continue to Long Island.

Well, it turns out that this was a pretty fortuitous choice of travel this year.  The 2011 Eukaryotic mRNA Processing Meeting was, as usual, an exciting and productive one.  But it may well be remembered as much for the bookends of the meeting – the eastern seaboard earthquake that ushered the meeting in on the 23rd, and Hurricane Irene, that necessitated some creative re-scheduling of the last day and a half of the meeting.  Many participants were busier Friday re-scheduling shuttles and flights than listening to presentations.  I was able to leave at the crack of dawn Saturday and beat the storm by about half a day.

The bookends aside, the meeting was excellent (as usual).  I won’t post specifics here (CSHL has rules about commentary and disclosure that I will give a wide berth to).  A few themes do merit mention.  One is that polyadenylation and mRNA 3′ end formation was topical this year.  This is due largely to studies such as I have discussed here and here.  More and more labs have begun to look at alternative polyadenylation in the context of gene regulation and clinical outcomes, and the number of talks and posters that touched on polyadenylation was gratifyingly large.

A second theme was one that has been developing for the better part of a decade.  It has become apparent that the various chapters in the life of an mRNA are not separated, either in time or space.  The connections between the many steps – transcription initiation, elongation, termination, capping, splicing, polyadenylation, transport, translation, etc. – are being revealed in ever more fascinating detail.  This was evident throughout the meeting.

A third theme was technical.  In a nutshell, high-throughput DNA sequencing as applied to RNA has become all the rage.  Lots of people are using variations on the themes I describe here and here to study alternative polyadenylation.  (I hope to be able to discuss additional plant studies in the near future – stay tuned.)  This in addition to other RNA-Seq applications, ChIP-Seq, CLIP-Seq, CRAC (see the brief mention near the bottom of this site), and other acronym-encoded approaches.  (I’m kicking myself for missing an opportunity to come up with my own clever term. Oh well.)  As sequencing becomes more affordable, I think that this trend will continue.

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Videos …

August 14, 2011

A while ago,  I posted about an interesting virtual meeting on the ribosome.  Somewhat belatedly, I can point to a link to videos of the talks.  Lots of good stuff.  Enjoy.

(HT to Paul Nelson.)

Following up

July 23, 2011

A short time ago, I mentioned this article.  This study was the product of a collaboration between five laboratories – two plant poly(A) labs, a seed biology lab, and two bioinformatics groups.  As the abstract indicated, this paper describes the results of a characterization of polyadenylation in plants using so-called Next Generation DNA sequencing technology; as such it is an addition to other recent studies, albeit the first (to my knowledge) that deals with plants.

I’m more than happy to answer questions about the paper in the comments.  What I will do in the essay is described one of the more perplexing findings, and “amend” the PNAS paper with a few illustrations that we couldn’t include in the paper (even the online Supplemental Files – we maxed out the print and SI page limits).

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A good day

July 11, 2011

It’s a good day for the Plant Physiology Program at the University of Kentucky, what with two new PNAS papers appearing in the Early Edition almost simultaneously.

One study deals with terpene metabolism in a eukaryotic microorganism:

Niehaus TD, Okada S, Devarrene TP, Watt DS, Sviripa V, Chappell JC.  2011. Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Published online before print July 11, 2011, doi: 10.1073/pnas.1106222108

The abstract:

Botryococcene biosynthesis is thought to resemble that of squalene, a metabolite essential for sterol metabolism in all eukaryotes. Squalene arises from an initial condensation of two molecules of farnesyl diphosphate (FPP) to form presqualene diphosphate (PSPP), which then undergoes a reductive rearrangement to form squalene. In principle, botryococcene could arise from an alternative rearrangement of the presqualene intermediate. Because of these proposed similarities, we predicted that a botryococcene synthase would resemble squalene synthase and hence isolated squalene synthase-like genes from Botryococcus braunii race B. While B. braunii does harbor at least one typical squalene synthase, none of the other three squalene synthase-like (SSL) genes encodes for botryococcene biosynthesis directly. SSL-1 catalyzes the biosynthesis of PSPP and SSL-2 the biosynthesis of bisfarnesyl ether, while SSL-3 does not appear able to directly utilize FPP as a substrate. However, when combinations of the synthase-like enzymes were mixed together, in vivo and in vitro, robust botryococcene (SSL-1+SSL-3) or squalene biosynthesis (SSL1+SSL-2) was observed. These findings were unexpected because squalene synthase, an ancient and likely progenitor to the other Botryococcus triterpene synthases, catalyzes a two-step reaction within a single enzyme unit without intermediate release, yet in B. braunii, these activities appear to have separated and evolved interdependently for specialized triterpene oil production greater than 500 MYA. Coexpression of the SSL-1 and SSL-3 genes in different configurations, as independent genes, as gene fusions, or targeted to intracellular membranes, also demonstrate the potential for engineering even greater efficiencies of botryococcene biosynthesis.

The second paper, on a totally different subject:

Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ, Hunt AG. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Published online before print July 11, 2011, doi: 10.1073/pnas.1019732108

The abstract:

Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3′UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.

I’ll have more to say about the second paper in another essay.  In the meantime, I’m happy to answer questions about it.

(No, Joe and I did not conspire to have these come out on the same day …)


July 11, 2011

It’s been awhile since I’ve done an ID post.  Thomas Cudworth on UD goads me thusly:

From June 17 to June 21, 2011, at the University of Oklahoma (Norman) campus, the conference “Evolution 2011” was in session.  It was co-sponsored by three scientific societies – The Society for the Study of Evolution, The Society of Systematic Biologists, and the American Society of Naturalists.  It was billed by its promoters as “the premier annual international conference of evolutionary biologists on the planet.”

It is interesting to make a mental list of the Darwin-defenders who have been most active in the culture wars, whether by publishing popular books defending Darwin, by appearing as witnesses against school boards in court cases, by working for the NCSE, by running pro-Darwinian blog sites, or by attacking Darwin critics throughout cyberspace, and to see which of them either read papers or at least contributed to the research and writing of papers for this premier conference.

Among those who have not attacked religious belief, but have violently bashed ID and/or passionately upheld neo-Darwinian theory, Paul Gross (co-author of Creationism’s Trojan Horse) and plant scientist Arthur Hunt (who has debated ID people live and on the internet) were not listed as contributors to any of the papers.

The theme of my column is qualifications. The question is: are most of the Darwinian preachers in the culture-wars competent to discuss the latest developments in evolutionary biology? If they are not competent, shouldn’t the public know this?

What I’m trying to do here is to give everyone a chance to say whether these people are or are not qualified. And I invite any of the named people — Falk, Venema, Moran, Miller, etc. — to write in here, listing their publications and conference papers in the field of evolutionary biology, and explaining why we should prefer their account of evolution to those of Darwin-critical specialists in evolutionary theory such as Lynn Margulis, Stuart Newman, Richard Sternberg, etc.

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July 3, 2011

Qingshun Li named 2011 Sigma Xi Researcher of the Year .

News of the success of former students is always welcome.  This award is most deserving, to say the least.

From the release:

Qingshun Quinn Li, professor of botany, has been named Miami University’s Sigma Xi Researcher of the Year for 2011. Li’s research focuses on the molecular mechanism of gene expression in plants through messenger RNA processing.


Li joined Miami in 2001. He has taught courses including introductory biology, genetics, biotechnology, development and advanced molecular biology. He is assistant chair of the department of botany and the director of the cell, molecular and structural biology graduate program. He is also the president of the Dayton Association of Chinese Americans.



June 16, 2011

A short vacation built around a trip to pick up Amy returning from a semester in The Gambia.

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It’s about time

June 15, 2011