DNAi DVD 1 DNAi DVD Transcripts Selecting genes to patent Mark Adams a private company's approach to patenting genes It was never our intention to patent all the genes, all the genes aren't patentable, and the Patent Office has made that very clear, in fact, that they have stringent rules for what's patentable and what's not, and that neither the entire genome nor the entire set of genes would be patentable. So we've taken the same very selective approach to doing that, that is common in the biotechnology, pharmaceutical industries, as well as in academic universities and the NIH [National Institutes of Health]. After all, the NIH holds more gene patents than any other organization. It's sort of a bundle, the gene sequence and the protein and antibodies made from that protein are all typically part of a patent application, depending on what the commercial plan rationale is for it. Billions of bases Mark Adams there are 2.9 billion letters in the human genome In the human genome there are 2.9 billion As, Cs, Gs, and Ts. If you wanted to readout the genome sequence and could do that at ten bases a second, ACGT, ACGT, ACGT, it would take eleven years to read the genome sequence. It's a tremendous amount of information and if you print it up on a big wall poster, a tiny fraction of it, it's all As, Cs, Gs, and Ts. Mutations & cancer Bruce Ames cancer is caused by an accumulation of mutations So I think cancer is a disease of DNA. Each cell is programmed when to grow and when not to grow, everything's… there are all these circuits, and if you mutate some gene and upset one of these circuits, then the cell grows when it's not supposed to, and you end up getting a tumor cell. And people have worked out there's several steps along the way, it isn't just one hit. Cancer’s several different genes you have to mutate in sequence. That’s why cancer goes up with the fourth or fifth power of age. There’s very little cancer in young people and that's usually because you inherit a mutant gene from your mother or your father, but other than that it goes just up with age because it's several hits. Weeding out disease Bruce Ames predictions for gene testing If you have a choice of children and some of them are smarter or some of them aren't going to die at thirty or aren't going to die in infancy, of course people will choose the embryo, the fertilized embryo to use that has better prospects. It'll start with weeding out horrible genetic diseases that people DNAi DVD 2 know are in their family, and then there'll be, already, my daughter lives in London and she's expecting a baby, you have an amniocentesis or something where they test for a few, Down syndrome and a few other genetic diseases. I mean that's going to become more and more, easier and easier and it'll slowly creep in and we'll have to decide what, and people I'm sure will discuss this at great length, what's the right thing to do and what isn't and all of that. Lab safety Emmett Barkley demonstrating the P4 lab containment suit he developed for working with high risk substances The most extreme form of containment was called P4. Researchers had to wear protective suits with self-contained air supplies, they entered the lab through an airlock, it was like working in space. The guidelines may have been draconian but at least they were clear and this gave the science a stamp of approval. Cloning DNA in bacteria Paul Berg importance of being able to clone DNA using bacteria You could take a colony and put it into a hundred-gallon vat and the bacteria would grow up and fill up the vat, and every cell in that vat would contain the piece of DNA that the original bacterium picked up when you mixed them with the DNA. So that showed you could clone DNA, and I think that experiment is what galvanized the scientific community. It is in fact the experiment that motivated the moratorium letter, because it became clear you could put any kind of DNA into that plasmid and get it into a bacterium, and so you could put toxin genes, you could put drug-resistant genes, any kind of DNA you had access to could be put into a plasmid, put into a bacterium and cloned. First recombinant DNA Paul Berg describing the first experiment with recombinant DNA The first recombinant DNA made by using enzyme-created sticky ends, cohesion ends, cohesive ends, was actually done by my student, Janet Mertz. She took two different DNAs, each of them had distinguishable properties, mixed them or cut them with the enzyme, mixed them, added an enzyme that could join ends to ends, and then showed she had created a molecule that now shared the properties of the two starting materials. And the basic idea is that it's a very, very simple device based on really simple and very robust and ancient technology ofthe fountain pen. And the idea is that the robot has a set of fountain pens that it dips into these microwells where each of these wells represents a different human gene. The robot dips its fountain pens into these micro-wells and then moves over to a microscope slide and prints the tiny little drops of DNA. The grid you can see in this microarray slide is actually composed of 30,000 individual DNA dots, each targeted to match a specific human gene. DNAi DVD 3 Cohesive ends & recombination Paul Berg using cohesive ends to make recombinant DNA molecules Cohesive end in this particular context means that if you take two DNAs that have single strands protruding from their ends, and if these single strands are able to pair with each other by the same rules that DNA strands are held together, then these two molecules could come together. And what Janet showed was that if two DNAs were cut with this particular enzyme, called EcoRI, then they could be joined and fused together to make recombinant DNAs. Now that was a hugely important discovery, because it bypassed the need for the complicated procedures that we had developed in order to bring two molecules together. Computing power Ewan Birney computational power of a processing farm So we call this set-up a farm, there are 400 processors here and there are 400 computers and they're all absolutely identically set up. The only thing that's different is their name -everything else is completely the same. So there's 400 processors, it's a very powerful processor chip: Alpha, Compaq Alpha chips. And quite a lot of memory, a gig's worth of memory in each box. So this is actually a massive amount of compute behind me. And what we do is we split our problem just into, say, 20,000 pieces, and then each piece we send to one of these sort of worker bee nodes. And they do their work and then they give it back and then they say "I'm ready!", and they get another piece, and they're just endlessly being driven by a master computer which is actually set somewhere else, that drives them, as you can see. Reading the genome Ewan Birney interpreting the completed human genome sequence All of human biology somehow connects back to the genome, and so anything that you can talk about in terms of human biology you can find some line that gets you back to some region of the genome. So just scanning over it is sort of wonderful. I was trained as a biochemist and as a molecular biologist, and you just see, you know, thousands upon thousands of little stories about how your eyes work or how your bones get put together or how the liver works and what happens here with this particular disease where, when this gene has a defect then this disease happens. And it's just a rich, massive story in some sense. Impact of the genome projects Ewan Birney the increased speed of gene searching It used to take about, I don't know, eight to ten years to find a gene, say in the case of Huntington, there's this rather complicated process where they had to track many different families. And then DNAi DVD 4 there was this very annoying, painstaking process of them getting all the regions in test tubes, all the bits that they were looking at, and then carefully, experimentally checking each one. And it was eight to ten years, and a real pain in the arse. And these days you still have to gather all the families, but you do not have to do this end-game. Now it's not five years or six years, it's three months or something like that. So the question now is not can I find the gene for Huntington, but why is it that a defect in Huntington gives you what we see, this disease? Why, what is going wrong, and, perhaps more importantly what is this gene actually doing when it's going right? 'Cause that's the way we understand why in some cases, why it's going wrong. And so that's really what we've got the next hundred years’ worth of molecular biology to do, is understanding the why, not the what any more.