A paper published today in PLoS One reports on research that shows the feasibility of taking a gene or genomic region from an extinct species and inserting it into the genome of an extant species and resurrect the extinct species DNA function in the transgenic mice. The extinct species was the Tasmanian tiger or Thylacine (that links to the wikipedia page, anyone want to become the curator for the EOL page which is pretty minimal at this point?) and the ‘surrogate’ species was Mus musculus.
And, as the abstract says,
While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.
That is what Platypus do, even as mammals :). Two days ago the Platypus genome was published in Nature. So if you haven’t already read it, might be worth a skim at least. So, they aren’t model organisms and not a medically or agriculturally important animals (unless someone starts figuring out how to cook platypus omelets), but platypus (platypi?) do hold a fascinating place in evolutionary history having mammalian (milk, fur) and reptilian (eggs, venom) characteristics. Their genome obviously holds clues to some of this unique history.
For example, the eggs and fertilization genes can tell us a bit of how that evolved…
Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open access’ and ‘free online access’ journals) and is asking if anyone knows of any others. He hasn’t asked for it yet, but I’ve got some ideas for open source/access phylogeny analysis programs and/or databases. I’ll post a few of those in the coming week or so, but for now here is a link to a list of such programs (some on this list I’m not sure are open source, I’ll cull these later too).
In 1993 I remember discovering the web. It wasn’t much longer after that I discovered the “Tree of Life (ToL).” I was studying for my Ph.D. in evolutionary biology and heard about it by word of mouth. Sometime in 1996 I found it on the web and was intrigued. It has grown since then, though still has a way to go. It’s goal? “… to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct.”
Today saw the unveiling of the “Encyclopedia of Life (EOL),” which is “an ambitious… project to organize and make available via the Internet virtually all information about life present on Earth.” Carl Zimmer reports on the EOL on his blog and in a NYTimes article.
Those goals overlap a lot it would seem. So I did some checking of the ToL and the EOL for two things that are most interesting to me: genomic information and evolutionary information. A short critique below (with the caveat that EOL is VERY slow today because of the launch):
Today’s tip looks at one example of how to view the same genomic data across several databases simply by browsing. You can download the data from analysis tools and databases in several formats and use that in others, and someday we’ll do a tip on that. But today’s tips shows you that many databases link out between them allowing you to view data in one context and then another simply by clicking a link. We are going to start by looking at comparative genomic data in VISTA , there’s much more in depth tutorial on VISTA here (free), then link out to the UCSC Genome Browser (free tutorial) to view the data there and then off to Ensembl (tutorial, subscription).
I just finished reading this paper out this month in PNAS, “Specific expression of long noncoding RNAS.” From the looks of it, the paper has conjured up an interesting discussion in the science blogosphere surrounding the paper and the term “Junk DNA.” Before I get to that discussion, let me give a brief synopsis of and thoughts on the paper (and a link to a ncRNA database at the end). Continue reading →