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Sunday, September 02, 2007

Natural Transgenesis, Adaptability, Evolution and Disease?

From Science News, more evidence of pathways for natural transfer of portions of genetic code between completely different species of organisms.

Specifically, a species of parasitic bacteria known as Wolbachia pipientis was studied. It afflicts cellular structures in 20% of the insect species (according to the text - how did they figure that out? we still haven't studied every species of insect?) and some other invertebrates. Small sections of genetic code from the bacterium was found incorporated into the DNA of several of its hosts. This bacteria has access to the eggs of it's host species and inserts portions of its code into the eggs, and these genes are then found in the offspring from those eggs. Very interesting successful adaptation!

While it is not completely new news... the essential concepts of natural transgenesis (naturally derived GMOs!) is especially interesting because now we can look beyond standard genetic selection (slow evolution using genes directly from each parent), and beyond (the rare) true mutations, to another source of genetic change that may have helped speed up select clades in the process of evolution?

Random effects of new code can result in nonfunctional gibberish, or 'junk genes' that don't seem to have a purpose. New code could result in beneficial adaptations which effectively give an increased potential of genetic diversity to help the host organism adapt to new environmental stresses. Randomness has it's potential problems as well, since genetic based disease results from code that leads to dysfunction in an organism's ability to adapt or survive - includes minor loss of function or maybe a gain that creates disease potential.

The realm of epigenetics and nutrigenetics is already mindboggling but more information about natural transgenesis may prove very interesting indeed.

Science News:
Week of Sept. 1, 2007; Vol. 172, No. 9 , p. 131

Share Alike: Genes from bacteria found in animals
by Patrick Barry

Some insects and roundworms pick up DNA from bacteria living within their cells, new research shows.

The DNA transfer occurs in the animals' egg cells, so the genetic modification passes between generations. The mechanism therefore provides an alternative to mutation of existing DNA as a way for the species to acquire new genetic traits.

Gene swapping is ubiquitous among bacteria and other single-celled organisms. Even plants and fungi are known to occasionally adopt a piece of foreign DNA. But scientists thought that multicellular animals picked up genes from bacteria only rarely.

"Our data are indicating that [DNA transfer] is going on all the time," says John H. Werren of the University of Rochester in New York, who led the research team.

The discovery challenges the prevailing view of animal evolution, in which genetic information is passed exclusively from parents to offspring. The transfer of DNA from bacteria means that an individual could acquire and pass on genes that it had not inherited.

"We're sort of on the edge of a transformation in the field" of animal evolution, comments Laura A. Katz of Smith College in Northampton, Mass. "These sorts of data allow us to redefine the field to capture this other process going on."

Werren's team looked at several species of insects and roundworms infected by a parasitic bacterium called Wolbachia pipientis, which afflicts about 20 percent of insect species as well as many other invertebrates. The bacterium lives inside the animals' cells, including their egg cells, giving it ready access to the chromosomes that are passed on to the animals' offspring.

"I think that physical access is the key to allowing this [DNA transfer] to happen," Werren says. The way in which animals' bodies insulate their eggs and sperm from foreign bacteria is the main barrier to heritable-DNA transfer in animals, he says.

The researchers compared the genetic code of the bacterium with the code of 11 other species: four roundworms, four fruit flies, and three wasps. The team found that all but three of the fruit fly species had segments of the bacterium's genetic code embedded in their DNA. The report appears online and in an upcoming Science.

Some of this transferred DNA is active in the host species' cells, the researchers found, but they didn't determine whether the genes serve a biological function in the host.

The team also scanned an archive of published genomes for 21 other invertebrate species and found bacterial genes in nine of them.

Such bacterial genetic code is routinely ignored during the sequencing of animals' genomes because most scientists have assumed that the foreign DNA is a sign of contamination, Werren says. However, the new research rules out the possibility of contamination, Katz says. "I think it's a really beautifully done, elegant study."

Julie C. Dunning Hotopp, a member of the research team and a scientist at the J. Craig Venter Institute in Rockville, Md., says that the mechanism by which DNA leaves the bacteria and becomes inserted into the host species' chromosomes remains uncertain.

While in-cell parasites such as W. pipientis are common among invertebrates, none is known to infect people or other mammals, Werren says.

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Semavi Lady woofed at @ 9/02/2007 06:41:00 PM | Permanent link | (0) Comments

Friday, August 24, 2007

"Cold Spot" Turns out to be an Enormous Hole in the Universe

This report from University of Minnesota astronomers (UofM link of press release) heralds discovery of "an enormous hole in the Universe, nearly a billion light-years across, empty of both normal matter such as stars, galaxies and gas, as well as mysterious, unseen “dark matter.” While earlier studies have shown holes, or voids, in the large-scale structure of the Universe, this new discovery dwarfs them all."

The 'bullhorn' illustration at the top is from the National Radio Astronomy Observatory website. The black 'nucleus' in the bull horn image is the big hole. The graphic gives perspective on how the information from radio waves of the earthbound VLA Sky Survey (seen in blue square above) combined with microwave energy reported (from space by) the WMAP Spacecraft (the orange square) have both, using different perspectives, helped to locate this enormous hole devoid of any dust/matter in our universe.

A Void Within the Void -- Berardelli 2007 (824): 1 -- ScienceNOW-
A team from the University of Minnesota, Twin Cities, had been studying data from the Very Large Array Sky Survey, which is mapping the entire universe with radio waves. The team members focused on one part of the survey where the temperature of the CMB is lower than normal [the blue gap on the psychedelic looking pic]. This cooling is significant because interactions with both visible and dark matter warm the CMB slightly, and so the team suspected that matter [in the cold spot] was absent.

[NOTE: CMB is Cosmic Microwave Background Radiation - source WMAP NASA site:
WMAP timeline theory
"The CMB radiation was emitted only a few hundred thousand years after the Big Bang, long before stars or galaxies ever existed. Thus, by studying the detailed physical properties of the radiation, we can learn about conditions in the universe on very large scales, since the radiation we see today has traveled over such a large distance, and at very early times."]
Further observations of the zone, located between 6 billion and 10 billion light-years away, revealed it to be not only devoid of galaxies but also about a billion light-years wide, the team will report in an upcoming issue of The Astrophysical Journal. "What we're suggesting is that there is no matter in this void, either normal or dark," says radio astronomer and co-author Lawrence Rudnick.

dark energy chart
The pie chart shows the generally accepted proportions of three components of our universe.
EDIT/added - Aug 31
- Pie chart above and previous cylindrical image are from the previously mentioned WMAP site where interesting graphics and other info can be found. Content of the Universe-WMAP data reveals that its contents include 4% atoms, the building blocks of stars and planets. Dark matter comprises 22% of the universe. This matter, different from atoms, does not emit or absorb light. It has only been detected indirectly by its gravity. 74% of the Universe, is composed of "dark energy", that acts as a sort of an anti-gravity. This energy, distinct from dark matter, is responsible for the present-day acceleration of the universal expansion.

Concluding that the zone is free of dark matter might be premature, cautions astrophysicist Harvey Tananbaum of the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts. Making that determination is difficult and will require confirmation, he says. Meanwhile, cosmologist Paul Davies of Arizona State University in Tempe says the discovery is "potentially very important" for testing theories about the very early universe. The potential deviation from the inflation model is "a tantalizing pointer to some new physics at the dawn of existence."

To read more about current study of the Universe and the BIG BANG theory as these have been modified with recent information from WMAP, go here.

A funny quote from Wired's version of this story: Retired NASA astronomer Steve Maran said of the discovery: "This is incredibly important for something where there is nothing to it." :D

Now for something a little more down to earth.
Science News
has an article on a virus that seems to have some correlation with obesity in some people.
Magdalena Pasarica of Louisiana State University in Baton Rouge, who led the new work, stresses that obesity has many causes, including genetic factors, overeating, and a sedentary lifestyle. In some people, however, adenovirus-36 may be the culprit, she says. Adenoviruses cause colds, but adenovirus-36, apparently, does more.

In a 2005 study of 502 obese and normal-weight people, researchers reported that 30 percent of the obese group showed signs of previous adenovirus-36 infection, while only 11 percent of the lean group did. ...see Science News article above
I think this has the potential to tie in very easily (so far) with issues of epigenetics/nutrigenetics. The genetic factor seems to be that when certain triggers reach a threshold in individuals, who have lost certain protective alleles (which can make them a genetic variant), various degenerative cascades have the potential to happen in that population. A very interesting article I have bookmarked from The Scientist tends to go offline occasionally, so here is cache link to --

Eat Your Way To Better DNA
Why what your grandmother ate while pregnant with your mother might affect your children's health, and other findings from the growing field of nutrigenomics. By KATE TRAVIS

incubatorAnd next this piece from The Scientist is interesting to me, has to do with certain receptors of bacteria being sensitive to light, and this factor having something to do with changes in potential virulence.

It actually makes a lot of sense since it seems many living organisms from plants and even larger complex animals have responses to various wavelengths of light in our environment.

I never gave much thought to lighting for the bugs we grew in the various incubators and our tests were pretty standardized anyway, growing critters that preferred dark places in humans. Even the few incubators with small clear panels at the door seemed minutely important to me, just a way to see how full an incubator might be, and what might be in there without opening the door and letting the warm air out. We always had the lights off in microbiology lab if no one were in there doing stuff anyway. The heat in a laboratory in general can get pretty stuffy due to all the fridges, centrifuges, incubators and analyzers, etc. You can't use a fan due to potential biohazardous aerosol. Air conditioning is nice but is not always very efficient in rooms full of machinery.

EDIT: 25 Aug - Yeegads, had lots of trouble with internet connection lately, add on Blogger/FTP has been temperamental for the past day. grrrr...

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Semavi Lady woofed at @ 8/24/2007 10:12:00 PM | Permanent link | (4) Comments

Blogger Diane sent us a woof // August 27, 2007

On a related note, have you tried Google Sky yet? It's part of the new version of Google Earth. Good for many hours of universe-browsing. Because of course that's what I should be doing with my time. :/   

Blogger Semavi Lady sent us a woof // August 28, 2007

LOL, like I need more encouragement!!   

Blogger vrtulobjeq sent us a woof // August 31, 2007

That pie chart is rather daunting, ie to think that our visible universe just totals 4&, you sure about that ?   

Blogger Semavi Lady sent us a woof // August 31, 2007

vrtulobjeq asks about the pie chart...
According to the WMAP project, this is the data they have so far. You can see images that we can all use from their project here.

I should update and post the text that goes along with that image, had connection problems that day as previously noted. Thanks for the visit and the point!
Content of the Universe

WMAP data reveals that its contents include 4% atoms, the building blocks of stars and planets. Dark matter comprises 22% of the universe. This matter, different from atoms, does not emit or absorb light. It has only been detected indirectly by its gravity. 74% of the Universe, is composed of "dark energy", that acts as a sort of an anti-gravity. This energy, distinct from dark matter, is responsible for the present-day acceleration of the universal expansion.

Thursday, July 12, 2007

GIANTmicrobes | Ulcer (Helicobacter pylori)

GIANT microbes!

This guy on the left is too cute. Know anyone that would like to have a pet Ulcer bacterium? Now they can be the person with everything and thank you for this thoughtful gift of a giant Helicobacter pylori. (site says toys are 5 to 7 inches long). That's a sizeable ulcer bug!

Your favorite hypochondriac or chosen victim (hopefully one with a great sense of humor) might also enjoy having Athlete's Foot, Mange, The Clap, a Pox (way cute!) and Heartworm too! Spread the joy with the kind of gifts that have been known for their ability to keep on giving! ;) The common cold also comes as a soap dispenser.

The giant mosquito, the fly and the little Martian may appease those with different tastes. It takes all kinds! Check out GIANT Microbes.

I don't think any of these would be Anatolian Shepherd proof for all but the youngest pups, but maybe adding a squeaker in the stuffing, reinforcing the stitches and giving some playtime supervision can bring lots of giggles. :D

Thanks to Mark for the alert!

"Support bacteria - they're the only culture some people have."
-- Dave Barry

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Semavi Lady woofed at @ 7/12/2007 10:51:00 AM | Permanent link | (0) Comments

Friday, April 13, 2007

Beatrix Potter, Peter Rabbit and the Mycologist

I had no idea she was into mycology!

I've seen some of her beautiful paintings for years and I merely thought, well she certainly likes to paint flowers, plants and rabbits!

Her interest in fungi is a fascinating dimension of her, particularly because of how self-motivated and enthusiastic she was in her study of them, despite a lack of scientific background. Apparently in her time, she just wasn't taken very seriously.

Fascinating story on her at The Scientist.

Roy Watling, of the British Mycological Society, says Mary Noble, one of his former colleagues, stumbled upon Potter's drawings close to 15 years ago while sorting through bags filled with Potter's work. "Until then nobody knew about her work with spores," he says. Potter's illustrations captured details about fungi that had eluded other scientists at the time. For example, Potter drew the first record of the fungus Tremella simplex in Britain. She painted the fruiting bodies, the basidiospores, and all other parts at all ages in the fungus life cycle. "She drew everything she saw," says Watling.

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Semavi Lady woofed at @ 4/13/2007 04:10:00 AM | Permanent link | (0) Comments