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Wednesday, 28 January 2009

DNA in theory and in practice

Today:

  1. Reversing the conventional DNA wisdom
  2. DNA strands become fibre optic cables
  3. Human DNA may set off AIDS timebomb

Reversing the conventional DNA wisdom

(PhysOrg.com) -- The copying of DNA's master instructions into messenger molecules of RNA, a process known as DNA transcription, has always been thought to be a unidirectional process whereby a copying machine starts and moves in one direction. But in work that represents a fundamental shift in scientists' understanding of the phenomenon, MIT researchers have found evidence that two DNA copying machines frequently start from the same site and move in different directions.

MIT Institute Professor Phillip Sharp and his colleagues, who report the results in the Dec. 4 early online edition of Science, believe this new mechanism may play a role in keeping genes poised for transcription.

"People have been studying transcription for a long time and never seen this kind of transcription before," said Amy Seila, a postdoctoral associate in Sharp's lab and lead author of the paper.

DNA, which is housed within the nucleus of cells, controls cellular activity by coding for the production of enzymes and proteins. The genetic information in DNA is not directly converted into proteins, but must first be copied, i.e. transcribed, into RNA.

During normal transcription, an enzyme called RNA polymerase binds to a gene's transcription start site, and then proceeds downstream along the DNA, copying the sequence and producing messenger RNA that carries the gene's instructions.

In the new scenario, a second RNA polymerase is believed to bind near the starting point and move upstream, producing a short RNA sequence that doesn't code for any proteins.

The researchers believe that upstream and downstream RNA polymerases, or divergent polymerases, are "paused" on the DNA and keeping the transcription start site open, so the gene can be easily accessed and transcribed.

The MIT team postulated this divergent transcription after discovering a new class of small RNA, which they dubbed TSSa-RNA because it is associated with transcription start sites.

The researchers found from analysis of tens of millions of short RNA sequences that many of these RNAs were clustered just upstream of gene transcription start sites, suggesting that DNA transcription is occurring in the reverse direction. Many of the genes where these short RNAs were found are very active, supporting the theory that this mechanism helps promote gene transcription.

The researchers observed this phenomenon in several kinds of cells in both humans and mice, leading them to believe that it is universal. source

My comment: Isn't it surprising how much this process resembles of a CD writing for example? I don't have too much to say on the article, I just wonder why this is happening. If the second RNA is not reading instruction for the protein, what is it doing? Verifying the position of the first? It's very curious.

DNA strands become fibre optic cables

Thanks to a new technique, DNA strands can be easily converted into tiny fibre optic cables that guide light along their length. Optical fibres made this way could be important in optical computers, which use light rather than electricity to perform calculations, or in artificial photosynthesis systems that may replace today's solar panels.

Both kinds of device need small-scale light-carrying "wires" that pipe photons to where they are needed. Now Bo Albinsson and his colleagues at Chalmers University of Technology in Gothenburg, Sweden, have worked out how to make them. The wires build themselves from a mixture of DNA and molecules called chromophores that can absorb and pass on light.

The result is similar to natural photonic wires found inside organisms like algae, where they are used to transport photons to parts of a cell where their energy can be tapped. In these wires, chromophores are lined up in chains to channel photons.

Albinsson's team used a single type of chromophore called YO as their energy mediator. It has a strong affinity for DNA molecules and readily wedges itself between the "rungs" of bases that make up a DNA strand. The result is strands of DNA with YO chromophores along their length, transforming the strands into photonic wires just a few nanometres in diameter and 20 nanometres long. That's the right scale to function as interconnects in microchips, says Albinsson.

To prove this was happening, the team made DNA strands with an "input" molecule on one end to absorb light, and on the other end a molecule that emits light when it receives it from a neighbouring molecule. When the team shone UV light on a collection of the DNA strands after they had been treated with YO, the finished wires transmitted around 30% of the light received by the input molecule along to the emitting molecule.

The Gothenburg group's ready-mix approach gets comparable results, says Albinsson. Because his wires assemble themselves, he says they are better than wires made by the previous chemical method as they can self-repair: if a chromophore is damaged and falls free of the DNA strand, another will readily take its place. It should be possible to transfer information along the strands encoded in pulses of light, he told New Scientist.

However, because the wire is self-assembled, he says, it's not clear exactly where the chromophores lie along the DNA strand. They are unlikely to be spread out evenly and the variation between strands could be large.

Van Hulst agrees and is investigating whether synthetic molecules made from scratch can be more efficient than modified DNA. source

My comment: Why this is cool?Because it can very well lead to a DNA computer. Even if the efficiency for the moment isn't precisely high, and there are possible fluctuation, both problems can be solved one way or another. This is very very exciting! One day we will really have living space ships and they will use such wires!

Human DNA may set off AIDS timebomb

HOW quickly HIV explodes into AIDS might depend on an individual's DNA. Some variations in the DNA in mitochondria, the parts of cells that generate energy, seem to make AIDS develop twice as fast as others.

Stephen O'Brien from the National Cancer Institute in Frederick, Maryland, and colleagues examined data from five long-term studies tracking a total of 1833 people with HIV during the 80s and early 90s. This was before antiretroviral therapy (HAART) was commonly used, so the team could follow the disease's development without intervention.

By studying the time it took for the subjects to develop AIDS-related diseases and relating it to their genetic information, the team found that some mitochondrial DNA genotypes are associated with rapid development of AIDS. For example, subjects with specific sets of variations known as U5a1 and J haplogroups progressed to AIDS at twice the average rate of the studied population. In contrast, people with the H3 haplogroup progressed more than twice as slowly (AIDS, DOI: 10.1097/QAD.0b013e32831940bb).

This supports existing theories that mitochondria are implicated in the progression of HIV/AIDS. The virus kills immune cells by triggering cell suicide, which appears to happen more easily in cells with mitochondria that generate less energy.

That means mitochondrial DNA tests could one day give an accurate prognosis for people with HIV, although further work on other genetic and environmental influence factors would be necessary first, says Hendrickson.

The research could also determine when an individual should start HIV therapy.The findings also suggest that screening mitochondrial DNA may help doctors choose the best combination of drugs. source

My comment: Ok, this one isn't so much about DNA but it's important knowledge on HIV. Especially that the virus spread best when the cell is with lower energy. It makes some sense but it also brings some personal responsibility toward our vulnerability to HIV. It's known that when you're low in energy, you draw bad luck to you, I can even confirm it from personal experience. Of course, now we're talking about a cellular energy level, but still, if we know when we're likely to stand a better chance against HIV (or any other viral infection) then we would know what drugs to take and probably even how to live.

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