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.