GPS on the shovel when digging for gold?
[See full posting at http://www.junkdna.com/new_citations.html ]
Genomics study highlights the importance of "junk" DNA in higher eukaryotes
A landmark comparative genomics study appears online today in the journal Genome Research. Led by Adam Siepel, graduate student in Dr. David Haussler's laboratory at the University of California, Santa Cruz, the study describes the most comprehensive comparison of conserved DNA sequences in the genomes of vertebrates, insects, worms, and yeast to date. One of their major findings was that as organism complexity increases, so too does the proportion of conserved bases in the non-protein-coding (or "junk") DNA sequences. This underscores the importance of gene regulation in more complex species. The manuscript also reports exciting biological findings regarding highly conserved DNA elements and the development of a new computational tool for comparing several whole-genome sequences. .... Such approaches are particularly useful for analyzing non-protein-coding sequences - sometimes called "junk" DNA. Although "junk" DNA is poorly understood, the increasing availability of whole-genome sequences is rapidly enhancing the ability of scientists to ascertain the biological significance of these non-protein-coding regions. ...The vertebrates included human, mouse, rat, chicken, and pufferfish, and the insects included three species of fruit fly and one species of mosquito. .. the researchers developed a new computational tool called phastCons. ...The scientists also observed that the proportion of conserved sequences located outside of protein-coding regions tended to increase with genome length and with the species' general biological complexity.
Most strikingly, the researchers discovered that two-thirds or more of the conserved DNA sequences in vertebrate and insect species were located outside the exons of protein-coding genes, while non-protein-coding sequences accounted for only about 40% and 15% of the conserved elements in the genomes of worms and yeast, respectively. ... "These findings support the hypothesis that increased biological complexity in vertebrates and insects derives more from elaborate forms of regulation than from a larger number of protein-coding genes." ... Some of the strongest sequence conservation in vertebrates was observed in the 3' untranslated regions (3'UTRs) of genes, which indicates that post-transcriptional regulation may be a widespread and important phenomenon in more complex species. .."There really does seem to be a lot more going on at the RNA level than people would have guessed a few years ago," commented Siepel. ... some of the conserved elements may function as long-range transcriptional regulatory elements. ... Not only will the new bioinformatics tool phastCons help researchers identify evolutionarily conserved DNA elements, the reported conserved elements are represented as conservation tracks in the widely used UCSC Genome Browser. "With phastCons and with the conservation tracks in the browser," says Siepel, "we're trying to make it as easy as possible for researchers to home in on functionally important DNA sequences."
posted by Dr. Andras J. Pellionisz at 8:27 PM
1 Comments:
Well, it did not take long since yesterday's comment on "California Gold Rush selling shovels". Today, essentially the first "shovel" for digging for "JunkDNA" is out ! There are two business problems, however. The first is, that publicly supported genome data centers (University of California, USA govenment institutions, etc) not only don't run business as a tight ship, but are not designed to make any profit . (Nor do they respond, therefore, to "customers' supply and demand dynamics"). Worse, "public money" (governments) are traditionally helpful mostly in the early (not profitable) stages of R&D (say, NASA - but even aerospace flight is sliding now into the private sector...) . For the "Internet boom", it took a Jim Clark to snatch Marc Andresson from University and ignite the private domain hyper-escalation of a brand new Industry.
The second problem has already been proven outright devastating. Internet "tools" can be incredibly helpful - but those who run the servers can (and usually do) monitor every single search in their databank. If you look up the showtime in the movie theater nearby, you might not mind revealing what you are looking for. However - as some of the Genome Database companies listed in the July 13th posting can testify - many went bankrupt because the user of a "super-tool" better not give away by Internet service*where* is he/she looking. You would not buy a shovel when going for the gold, if you knew that there is a GPS on it, telling the seller the exact location where you searched AND FOUND the biggest golden nuggets, would you???
Therefore, while the "JunkDNA tools" are already on the march (actually, since March...) the Business Model is clearly *not* the sale of data over the Internet -nobody is buying raw data, the market needs knowledge, not information- nor is it providing tools for the use over the Internet. Indeed, Big Pharma, or Nanotechnology would be crazy to "officially leak" where they are looking.
If "the party is over" for both "free rides", where is the Business Model of Regulatory DNA? - Commentator Dr. A. Pellionisz has agreed to be contacted by e-mail (businessmodel@helixometry.com) or by phone (+1-408-732-9319) for further information. July 14th, 2005.
P.S. Oh, yes. There is also the "algorithm challenge". When dealing with "JunkDNA", some mathematical postulates, processes and platfroms for its interpretation might help (such as FractoGene, the experimentally supported fractal geometrical generalization of the "gene concept"). Drs. A. Pellionisz and M. Simons are looking into the merits of such a venue, and the fractal approach to DNA was endorsed by Mandelbrot by his Keynote Lecture at Stanford, 2004 Aug., and in 2004 December by Rothemund, Papadakis and Winfree at Caltech, bringing in further endorsements of John Hopfield (Neural Networks, Genomics Institute at Princeton), Ned Seeman (author of "Nanotechnology and the Double Helix", Scientific American 2004), Len Adleman (proponent of DNA-based infotech)
8:36 PM
Post a Comment
<< Home