Junk DNA May Contain Weapon Against HIV

August 8, 2009

The Biology journal of the Public Library of Science, in its April 2009 edition, has a fascinating paper that suggests that we humans, within that part of our DNA often referred to as “junk DNA”, may have the necessary instructions to make compounds that prevent the HIV-1 retrovirus from attacking human cells.

There is a class of small anti-microbial molecules (peptides) produced by mammals, called defensins,  that are active against a broad range of pathogenic organisms.  There are three classes of these defensins in primates, based on their chemical structure:  alpha, beta, and theta.   The theta defensins are the most recently discovered, and it was originally thought that they only occurred in old-world primates, such as rhesus monkeys.  They act primarily by preventing viruses from entering the body’s cells.

The researchers found that human DNA contains the genetic encoding for these theta defensins, but they are not expressed because the genetic sequence contains a premature “stop” codon; these are called pseudo-genes. (You can think of these termination codons as being like STOP signes that indicate  the end of a gene, just as text files in ancient personal computer systems were terminated by a CTL-Z character.)   When the researchers generated a sample of human promyelocytic cells with “repaired” genes, the cells were able to produce the structures of the theta defensins.  The researchers were also able to confirm the anti-HIV activity of these compounds in vitro.

This is potentially an exciting result.  It is made even more interesting, as the researchers observe, by the fact that certain antibiotics can induce the production of these defensins:

Furthermore, we exploited the ability of aminoglycoside antibiotics to read-through the premature termination codon within retrocyclin transcripts to produce functional peptides that are active against HIV-1.

It’s also worth noting that many genetic disorders are the result of similar “premature” termination codons in the relevant genes, so a technique which can, essentially, ignore them during DNA-directed synthesis might have wide application.

It is interesting to speculate on how we humans lost the ability to make these compounds, which at least some of our close genetic relatives still have, But this discovery potentially opens up a new avenue of prevention of HIV infection.

Finding Planets

August 8, 2009

In March of this year, NASA launched a new scientific instrument, the Kepler space telescope, whose primary mission is to search for so-called exo-planets, planets orbiting stars other than our Sun.  In particular, the hope is that it may be able to identify planets that might be able to sustain life.   Roughly speaking, this means planets whose temperatures and other conditions would allow the presence of liquid water.

Launched March 6, 2009, from Cape Canaveral Air Force Station in Florida, Kepler will spend the next three-and-a-half years searching for planets as small as Earth, including those that orbit stars in a warm “Goldilocks zone” where there could be water.

In a new report of the  mission’s progress, NASA is reporting that the telescope is working well, and has managed to detect the presence of an atmosphere on a previously-known exo-planet, within the telescope’s first ten days of operation.  While this particular planet (called HAT-P-7, and located about 1,000 light-years from Earth) is not of interest as far as finding life is concerned, because it orbits quite close to its star and has a day-side temperature in excess of 4,000° F, it is a very good sign that the equipment is able to detect solid evidence of an atmosphere.

Although the quality of data now being gleaned from Kepler is better than anything before it, NASA scientists expect that the quality will be further enhanced when new analysis software is deployed:

Although this is already the highest precision ever obtained for an observation of this star, Kepler will be even more precise after analysis software being developed for the mission is completed.

Although there is an undeniable thrill to seeing human exploration of space, as the anniversary of the Apollo landings ha srecently reminded us, the automated probes that NASA has developed, such as Kepler, the Mars rovers, and the Hubble space telescope, have made a truly outstanding contribution to science.

The New Scientist also has an article on the Kepler mission.

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