Popular Mechanics gave a “Breakthrough Award” to MIT researchers who reprogrammed a virus to instead form a tiny, tiny battery anode. The researchers, lead by Dr. Angela Belcher, used the bacteriophage M13, which is a workhorse of molecular biology to incorporate cobalt oxide and gold, forming a nanowire. M13 grows in a tight cylindrical spiral, and I suspect that the scientists exploited this property in convincing the virus to grow a nanowire. As Popular Mechanics recognized with their award, this is a very interesting development.
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The sequencing of the human genome project took ten years and cost millions and millions of dollars. It was coordinated effort of researchers around the world. But the technology used to sequence DNA developed so quickly during the project that it finished five years ahead of schedule. And the technology continues to improve.
In fact, it generally follows Moore’s Law, which states that computer processor power will double every 18-months but has been applied to many areas of technology. As price comes down and speed and accuracy increase, some in the field have projected that in ten years, a single individual will be able to have her own genome sequenced for $1000.
That day is getting closer. A recent paper in Nature (PubMed; subscription required for summary and article) demonstrates a new sequencing technology that allows a single technician to sequence 25 million bases in just four hours. By comparison, the sequencers that I used when I worked on the Human Genome Project could each produce about 10,000 bases in the same time frame. The authors of the paper assembled an entire bacterial genome in a single run.
The advent of individualized genomic medicine will be a boon to health care, provided that safeguards are put in place to protect patients’ privacy. Otherwise, it may just further corrupt our already-crippled health insurance system.
Technology like this and the Internet always remind me of my 8th grade history teacher (who was also a football coach) who told us that, unlike every previous generation of Americans, our standard of living would not increase dramatically from what our parents experienced. It makes me chuckle.
I read a lot of Wired. This month’s issue has a cover story about the exportation of tech jobs to India. I haven’t gotten to it yet, but this topic has been in the news a lot lately. It got me thinking about whether biotech jobs would ever be sent overseas to cheaper labor markets. I worry about this because since I decided to go back to school, I have fully expected and planned to get a job in the private sector rather than trying for an academic position.
Moving tech support or programmers to another location is a fairly straightforward proposition. All you need is a desk, a computer, a telephone, and then just route the calls. Moving a lab is a very different beast. In addition to the physical space, there’s a lot of specialized equipment, stocks, samples, chemicals, and chemical waste. Not to mention that the scientific community in this country is much stronger and more respected. The brain-drain historically is from India to the U.S.
However, the research climate in this country is changing. Politico-religious pressures are dampening stem cell research. The intellectual property laws are stifling innovation. We’ve already seen this situation drive prominent researchers to other countries. It seems likely that, without a major reversal in policy, this American brain-drain will continue. The United States will not be a leader in biotech.
It’s a conclusion that seems preposterous to us. The U.S. has been number one for so long that we can’t imagine being anything else. The Russians couldn’t either and certainly now are having hard a time not being a superpower. But the historical fact is that all empires fall. Maybe biotech is the beginning of the end for the U.S.
I was joking around with some classmates the other day and hypothesized that a professor had engineered his E. coli to produce crack. I thought about it a little more, what would it take for a bacteria to produce cocaine?
It’s not a protein, so you can’t just clone the gene for it. There has to be some biochemical pathway to produce it, and fortunately, that pathway already exists in cocoa plants. So could you clone the genes for the enzymes in that pathway into your bacteria of choice and get coke out of it? It’s probably not that simple. There are indubitably some peculiarities in the functioning of the enzymes that will get lost in the translation from plants to bacteria. Then there’s the matter of purifying your product.
Sure, it’s theoretically possible. But it would be wise to try the idea out on something that’s not illegal.
I started reading this article yesterday about using bacteriophages to treat infections, especially strains that are resistent to most antibiotics. The great thing about phages is that they can be built entirely from their DNA. Cellular processes depend on having a progenitor — one cell becomes two becomes four. It’s been a very long time since nothing became one cell. But a bacteriophage is described entirely by its DNA; no other part of the virus enters the host. (Many viruses of higher organisms, HIV for instance, contain enzymes within in the virus particle that are required to complete their life cycle. Thus the entire virus must enter the host cell.)
The other exciting thing about phages is that they are lytic — they destroy their host. So I started thinking about ways to hijack their lifecycles. It’s routine to clone a gene who’s protein you’re interested in, overexpress it in E. coli and then purify the protein. But it can be tricky to get the protein out of the bacteria. Wouldn’t it be simpler if the bacteria broke open once they filled up with the protein? It seems like you could clone the protein into a phage genome and let it go to town.
That’s pretty academic, though. Consider a patient who’s got a nasty bacterial infection, one that’s resistent to antibiotics. You could attack with phage and it would be all good, but what if we could get those bacteria to produce something else while they’re being destroyed by the phages. You’d have 1% of your phages actually be pseudo-phages, virus particles that contain non-viral DNA that encodes some other product. This other product could be a painkiller or perhaps a cytokine or other compund to boost the immune system.
I was reading this article yesterday in Wired (the part about “Regeneration”), and earlier in the week, I read about using nanotechnology in a similar fashion. In terms of fields of study, I am interested in tissue engineering as well as bioinformatics. One possible way to combine the two would be, for instance, if there was a motif that represented growth factors, you could search all the ORFs for similar motifs. I don’t know much of anything about growth factors, but this approach should work reasonably well for, say, 7TM receptors. It’s sort of “reverse proteomics.” Another technique might be to use proteomics to identify the genes for growth factors present in, for example, a developing liver. Or even if you had just one growth factor identified, you could search for similar promoter regions.
There are a couple of catches to these genomic searches. With a search for promoters, you’d have to be so many base pairs upstream from the start codon, and you’d have to incorporate a certain amount of “fuzziness” to the search. The motif search would be harder. You’d have to know which residues were important, what other amino acids could substitute, and then look for all the possible base combinations in an ORF. To some degree, it would help to know what the active site looked like, how the important residues related both three-dimensionally and in sequence, and so on. But this is something people are currently putting a lot of effort into, so you couldn’t expect a computer to do it very well at the present moment.
