Cavalcade of Mammals

Collected references on DNA sequencing by synthesis and related next-gen sequencing technologies:

SBS history page at Harvard

• Pubmed search
• Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Guo et al. PNAS July 8, 2008 vol. 105 no. 27 9145-9150.
• Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Ju et al. PNAS December 26, 2006 vol. 103 no. 52 19635-19640.
• Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Ruparel et al. PNAS April 26, 2005 vol. 102 no. 17 5932-5937.
• Design and Synthesis of a Photocleavable Fluorescent Nucleotide 3‘-O-Allyl-dGTP-PC-Bodipy-FL-510 as a Reversible Terminator for DNA Sequencing by Synthesis. Meng et al. J. Org. Chem., 2006, 71 (8), pp 3248–3252.
• Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Seo et al. PNAS April 26, 2005 vol. 102 no. 17 5926-5931.

Turritopsis nutricula is jellyfish that can develop back into a polyp from the jellyfish form, with cells differentiating from adult cells types to polyp types. This is quite unusual, only known to occur in a few jellyfish species.

This reversion to an immature form may allow it to become effectively immortal, renewing itself by passing through the polyp stage again. The ‘effectively immortal’ aspect hasn’t been examined–no one has followed one of these jellyfish through multiple jellyfish-polyp-jellyfish cycles or observed cycling jellyfish living longer than they otherwise would. That is, the reversion to the polyp state may have this effect but it hasn’t been demonstrated yet.

Articles describing this are getting linked around, but the research was first described in 1996. And this phenomenon has now been described in a couple jellyfish, and is not unique as the articles say. This article has lots of good pictures. This link to Development Biology, 8th ed. by Scott F. Gilbert has good background info.

Scientific articles:

• Piraino et al. (1996) Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa).
  –The original article.
• Carla et al.., (2003). Morphological and ultrastructural analysis of Turritopsis nutricula during life cycle reversal.
  –Nice photos.
• Schmich et al., (2007). Induction of reverse development in two marine Hydrozoans.
  –Two other jellyfish that undergo reverse development. With photos.

The first paragraph of Charles Darwin’s Origin of the Species:

INTRODUCTION
WHEN on board H.M.S. Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species?–that mystery of mysteries, as it has been called by one of our greatest philosophers. On my return home, it occurred to me, in 1837, that something might perhaps be made out on this question by patiently accumulating and reflecting on all sorts of facts which could possibly have any bearing on it. After five years’ work I allowed myself to speculate on the subject, and drew up some short notes; these I enlarged in 1844 into a sketch of the conclusions, which then seemed to me probable: from that period to the present day I have steadily pursued the same object. I hope that I may be excused for entering on these personal details, as I give them to show that I have not been
hasty in coming to a decision.

I’ve never read Origin, having thought of it as mainly of historical interest and not relevant today. But it does have a wealth of examples and descriptions of animals and their niches that now seems interesting to me so I’m having a go it. The Voyage of the Beagle should have even more of this sort of thing, but I figure it makes sense to read Origin first.

It’s funny that Darwin starts his book protesting that he is not hasty. He is the least hasty scientist of which I’ve ever read.

I just read a review on cutting-edge new sequencing technology (Shendure et al., 2004). There are several approaches that were new to me. One that caught my imagination incorporates “polony technology,in which PCR is performed in situ in an acrylamide gel” for DNA amplification. A related technique using emulsion has been developed by the Volgelstein lab.

My idea of developing a method using reversibly terminating nucleotides has also occurred to many other people! Apparently finding a way to do the reversibly termination has been a roadblock. I certainly didn’t have a way to do it. They have worked out approaches to detection of incoration, the other half of the method, and also a part I didn’t develop.

Very interesting tech. According to the paper, even nanopore sequencing is close to working!

The paper talks a bit about using ULCS for personal genome sequencing (PGP, everthing gets an acronym), about the whys and what it will mean. It contain the usual throw away consideration of ethics and consequences. The papers says this “will require high levels of informed consent and security”. In practice, your personal seq info and related disease susceptibility info *will* get spread to interested parties. Just look at who calls the shots; after more than a decade of attention to genetic privacy and overwhelming public support, “no US federal laws that ban genetic discrimination for medical insurance or in the workplace”.

How I would love to seqeunce 1Gb a week!