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Learning (And Harvesting) from Extremophiles
kudyadi writes "BBC News has an article on the threat posed to extremophiles by anxious prospectors ready to exploit their unique nature. Potential discoveries include glycoprotein, which prevents Antarctic fish from freezing, and an extract from green algae for use in cosmetic skin treatment, and anti-tumour properties in a strain of yeast. This article explains the issue more lucidly, but in the end, one must consider the environmental ramifications of this biological exploitation before moving ahead full scale. So how is Tux in danger? Let me remind you of a thing called the food chain and then read this."
Extremophiles are organisms that live at the edge of the range of environments life can exist in. Essentially very hot (at boiling water temperatures), to extreme cold temperature (cell contents should be freezing but they don't), to high acidity, alkalinity, or high salt. concentrations.
They are a literal gold mine for biotech companies. Heat extremophiles are a great source of heat stable enzymes that work in almost boiling water. This makes them good for many industrial processes and also makes them easy to make and purify in a none extremophile organism (you grow it up in the bacteria, smash open the cells and cook the contents till the only thing left active is the heat stable protein).
Cold tolerant organisms have great antifreeze techniques, as well as a source of enzymes that are able to work efficiently at cold temperatures. Handy for many industrial processes and even as additives in such mundane things as laundry detergent that is designed for use in cold water. The anitfreeze may have applications in crygenic applications (more pratically for freezing tissue samples and organs rather than a whole human).
The problem with cold extremophiles is the biggest source exist in Antartica, and people are sensitive about what happens in that region of the world. The point I should make is that this research will only require sampling and identification and growth in the lab of these organisms, and is really a pratical outgrowth of the scientific research already carried out in Antartica. These organisms are not going to be "harvested" in Antartica for any commercial purpose, and I can't see further research in this area creating anymore disturbance to the ecosystem than the research already carried out in Antartica since the first explorers. If anything this increases the need to preserve the ecosystem, along the same lines as the saving rainforest for the potential undiscovered medicinal plants.
You wrote it as though "glycoprotein" is a recent discovery. Actually a glycoprotein is a class of substances, to wit:
A sugar (usually a ketose or aldose) attached to a protein. There are *many*. They've been known about for ages. Perhaps you mean that they've discovered an *interesting* glycoprotein?
way off base, in many ways..the bug is Thermus aquaticus; isolation of heat stable DNA polymerase, called Taq, was first described by a russian group, then patented by cetus for use in PCR. Many other companies have patented isolation of similar enzymes from other organisms, eg stratagene has pfu polymerase, from pyroccocus furiosis, there is alos pwo polymerase, vent, etc etc The patenting of a use for a natural product,or a method of obtaining a natural product is an intrinsic part of the patent system. It may not be fair, or right, but thems are the rules. Actually, the cost of heat stable polymerase is not that great (related to other parts of the proces, such as dNTPS, etc) it is the cost of the license for the process, such as a pcr licence, that is exspensive.
If I remember corrently, the original patent for the use of thermostable Thermophilus aquaticus DNA polymerase belongs to Roche. Before I posted this comment, I checked in espacenet for any patents by Invitrogen regarding "thermostable" or "thermophilus" or "aquaticus". I couldn't find any hits.
You are right, however, there are a number of patents regarding Taq polymerase, but they actually patent a method using this enzyme, or a laboratory-made mutation of this enzyme, mostly with the goal of improving fidelity of DNA replication. That is in accordance with established copyright laws (afaik -- ianal), they didn't simply patent something they found, but a method that uses it.
If you are a researcher at a non-commercial institution, you are if I'm correctly informed, exempt from certain patent laws, and I heard of people who have their own expression vectors for Taq polymerase, and use it to produce polymerase for their lab's use.
Also, no biotech company would go to the point of "harvesting" the polymerase from Thermophilus aquaticus, when you can have your friendly E.coli make the same protein in a much easier way.
Most molecular biology techniques which led to the knowledge you are talking about require enzymes which were discovered in extremophile bacteria.
The prime example is Taq DNA polymerase, used in almost every Polymerase Chain Reaction experiment ever. It comes from an extremely heat tolerant bacterium. With no PCR, you can't do meaningful DNA sequencing, and the entire science of genomics, and most modern molecular biology, would be dead in the water.
This even includes protein structure determination. While we could do this for abundant proteins without these enzymes, we can't do it for low abundance proteins, because they require an engineered bacterium to produce them in large enough quantities for structure determination. To do that, you need to know the DNA sequence, so you need to have sequenced the gene in question. To sequence it, you need to isolate enough of it to sequence. PCR is the method for doing that.
And besides, people have been trying purely in silico drug design for years now. I'm not aware of there being more than half a dozen or so pharmaceuticals in production that were discovered that way.
Well, if we're being idiots and just sucking up mass quantities straight out of the wild, I could see it being a problem. But these lifeforms do live in weird places, so I can't imagine that it's cheap to do that.
Better to figure out what makes them tick and go and have much friendlier sorts of bacteria make the things we need in places you don't need an icebreaker or a submarine to get to.
What we call folk wisdom is often no more than a kind of expedient stupidity.-Edward Abbey
Soon we will design drugs, rather than find drugs.
I hope that we will one day indeed design rather than blindly search. We're centainly on the road to it. But then again, I heard the same line about designed drugs coming soon when I started studying biology, and that was, hmm, about 10 years ago.
To be fair, rational design has made some big steps forward, but the number of drugs and drug candidates that were designed completely in silico is really small. Likewise, the combinatorial chemistry approach is useful, but hasn't kept up with the big promises that hyped this approach maybe 5 years ago. But I may be biased there, the idea of blindly throwing together molecules and then letting a high-throughput assay sort out what works and what doesn't has always rubbed me as somewhat contrary to the ideal of science. It's a bit like simply bringing in more and faster monkeys to get that shakespeare play written.
Combinatorial chemistry and rational drug design can still learn a lot from nature, and in fact the two can be combined. It is impossible (and will stay so even in the future) to examine all possible chemical structures for a desired activity. For instance, there are 10^62 different molecules of a molecular weight below 500, a typical cutoff for drug molecules. If you would synthesize one molecule of each, you'd make a ball of mass that covers the whole solar system. (quoting from a recent seminar by Prof. H. Waldmann).
We can't explore the whole chemical diversity, but we may not need to. If you compare a random molecule library to one based on substructures occurring in nature, you'll find that the "natural" library has much higher hit rates than the random one. In a way, nature has worked for us as a filter, selectively enriching substructures that are meaningful in the context of proteins and receptors. Proteins are largely composed of conserved folds, therefore the structures that bind to them are likely to have conserved structures as well. Considering the more creative solutions nature uses to overcome extreme problems will enrich this library of natural structures, and thus be beneficial to rational drug design.
Interesting article, but why write "let me remind you of something called the food chain?"
The article describes a risk from the industry that grows up around the extremophiles, with exploitation of a natural resource that should be available to all. The submitter seems to confuse this with a risk to the organisms themselves.
I'm not arguing that harming the extremophiles wouldn't have knock on effects eventually for humans, but in terms of the article, it is beside the point. Reading some of the posts above seems to show people have confused this, or haven't actually bothered to read the article.
Meine Schwester ist sehr, sehr reizvoll - Nietzsche
Well, native Taq polymerase is available from all major suppliers(Invitrogen, Stratagen, QIAGEN, etc), as well as different modified recombinant Taq derivates (NovaTaq, AmpliTaq, MasterTaq) - there's nothing remotely resembling a monopoly here. Of course, several recombinant polymerases are patented (HotStart, AccuPrime System, Platinum Taq) - but these are not as nature made them, but heavily modified and optimized systems.
This comment does not exist.
If you read the BBC article, rather than the Hemos summary, you get a very different feeling for what the "threat" is. The BBC article mostly concentrates on the problems of intellectual property and patenting that may stifle scientific research...
Economists recognize that patents are a double edged sword. Without patents, there is no incentive for companies to invest in basic research that can then be duplicated by freeriders. With patents, you slow down further scientific advances because the information isn't freely accessible.
This is where universities can (potentially) help - there is a parallel incentive system of "grants" and "ego feeding through publications and awards" that give professors the incentive to do basic research that becomes instantly publically available.
-Marcus
I work for a Biotech company. We make enzymes in 80 m^3 tanks. And we really only need one bacteria to start! Most organisms are genetically modified in order to increase yield anyway. So I don't really get the problem. One of our best selling enzymes was found in an organism less then 50 km from the factory. It doesn't always have to come from the poles.
10 ?"Hello World" life was simple then
More like they pop, as in a popping balloon. It isn't the expansion of water inside the cell which bursts it (the membrane is elastic), it is the fact that ice crystallizes and forms very sharp crystal edges which cut through the cell membrane like a knife edge.
The idea behind cryogenic flash freezing is that by freezing the tissue extremely quickly, these ice crystals don't have a chance to form and the water instead gels into a more amorphous structure where ice crystals are small, or perhaps not even present.
That being said, I don't think I would want my body frozen while there's still a chance of getting it fixed in this century :-) It's the kind of thing I might consider if I knew that I would certainly die soon anyway.
Modern cryonics uses a sophisticated combination of chemicals and rapid cooling to achieve vitrification of the brain. This is exactly what it sounds like. Water is cooled rapidly and with inhibitors to get right past the danger range where crystalization occurs and down into the nice safe ranges of a couple of hundred degrees below 0 (centigrade, fahrenheit, whatever, I'm being all approximate anyway).
They've been getting really good at this, modern methods improving the amount that can be flash-frozen at once by freezing inside and outside of your basic frozen head simultaneously.
I'm not pinning my personal hopes on cryonics, but good to know it is getting better.
-- perl -e'print pack"H*","6e656d6f406d38792e6f7267"'