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Round it goes

Cyclosporin is famous for its use in transplant surgery, where it suppresses the immune system to prevent rejection. It is made by the fungus Tolypocladium inflatum as a defensive weapon, as are many of our common antibiotics, such as penicillin.

As you can see, it gets its name from its chemical structure. It is made of eleven amino acids that form a closed loop. Short chains of amino acids are called peptides, and longer ones are called proteins.

Loops of amino acids (called cyclic peptides), have several features that make them especially interesting. Because they have no dangling ends for digestive enzymes to grab onto, they don’t degrade easily, and thus can be taken orally. They hold their shape better than non-cyclic peptides, making them more specific in their interactions, since they can’t deform to fit where they aren’t wanted (an important feature in biology). They can withstand higher temperatures and acidity, since they don’t break down as easily. Proteins usually denature when heated, changing their structure dramatically, as in egg white when it is cooked. Cyclic peptides and proteins are much more stable.

The stability of cyclic proteins can be further increased by linking the amino acids inside the loop together, forming ladder-like stuctures, webs, and knots.

The stability and specificity of cyclic proteins makes them especially useful to organisms, as they can remain active in many environments, are difficult for a pathogen to degrade, and can target their activity to reduce side effects.

One cyclic protein of interest is rhesus theta-defensin-1. It is a protein found in some primates which gives them a defense against HIV. Cyclic proteins have not yet been found in humans, but a genetic sequence similar to rhesus theta-defensin-1 has been found, with a small mutation (a premature stop codon) that prevents it from forming the full protein. Analyzing this sequence in a range of different primates shows that the mutation occurred seven to ten million years ago. If it had not been for this mutation, humans might have retained a defense against HIV to this day.

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Categories: Biology, Chemistry, Genetics, Health.

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By sfield
— October 8, 2009 at 10:08 am

Star shade for alien planets

As budget cuts have limited some grand schemes for detecting Earth-like planets around distant stars, an new scheme to do it on the cheap has been proposed to NASA.

Called the New World Observer, the plan is to place a flower-shaped disk in front of the James Webb Space Telescope (the proposed successor to the Hubble Space Telescope). The 40 meter (131 foot) disk will be placed 30,000 kilometers (18,641 miles) in front of the telescope, to shield the telescope from the bright starlight, allowing the faint planets around it to be seen. The project is the brain-child of Webster Cash, director of the Center for Astrophysics and Space Astronomy in Colorado.

The strange shape of the disk, with flower-like petals on the edges, prevents diffracted light from reaching the telescope. The petals cause the diffracted light from the edges of the disk to destructively interfere with one another.

The star shade should allow the telescope to see planets around stars as far away as 35 light years from Earth.

The disk does not need to be made with extreme precision — a few millimeters here or there will not make much difference from 20 miles away. And the disk can be a few meters out of alignment and still block the light from the star. The cost of the project is thus small enough to qualify for one of NASA’s least expensive missions, the “Discovery-class”, which has a cost ceiling of $425 million.

But Webster Cash is not stopping there. His New World Imager proposal calls for two telescopes and two star shades, orbiting a thousand miles apart, forming an interferometer.

With such a telescope, he expects to be able to image features on the remote planets, such as oceans and continents, and search for “biomarkers” such as oxygen and ozone, that would indicate life exists on the planet.

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Categories: Astronomy.

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By sfield
— September 28, 2009 at 10:10 am

Don’t take photosynthesis for granite

Minik Rosing thinks he has found the oldest evidence of photosynthesis yet, in rocks 3.7 billion years old. He had already reported fossil plankton from that era in sedimentary rocks from Greenland and presented radiologic evidence of enrichment by living organisms in earlier papers.

He also thinks photosynthesis may be responsible for the creation of all the continents on earth.

Photosynthesis makes three times as much energy available for geochemical activity as all of the energy that comes from the molten interior. The new date for photosynthesis puts it in a time when there were no continents on earth. Continents are formed from granite, which is less dense than the basalt from which it is made, and on which it floats. Basalt is weathered into clays, and those clays form granite when they are melted.

The vast amounts of energy created by photosynthesis keep the atmosphere and the oceans out of balance with the minerals that make up the earth. This increases weathering, and changes the resulting products of weathering, favoring the formation of granite.

Granite is not found on any planets in the solar system except Earth. Could this be because only Earth has life?

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Categories: Biology, Chemistry, Geology, Physics.

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By sfield
— September 3, 2009 at 10:13 am

Drinking soap for my health

My root beer contains yucca extract. It says so right on the label.

As much as 12% of extracts of the plant Yucca schidigera are soap-like compounds called saponins.

Saponins are natural detergents, or surfactants. In root beer, they make the foam. Yucca saponins have a steroid base attached to carbohydrates. This makes one end of the molecule soluble in water, and the other end soluble in fats and oils. This lets them emulsify fats and oils, so they mix with water, and helps them stabilize tiny bubbles by forming a tough film at the water/air interface.

But saponins have some other rather remarkable properties besides foam making. They are stongly attracted to cholesterol. Like some cholesterol lowering drugs, they attach to cholesterol in the intestines, and prevent it from being absorbed into the body. And since the cell membranes of many pathogens such as Giardia lamblia have cholesterol as an important component, the saponins can cause the cell membranes to rupture, killing the organism and preventing disease. They also have similar antiviral and antifungal effects, and since many cancers have more cholesterol in their cell membranes than normal cells, there appear to be anticancer benefits to yucca extract also.

The saponins are also used to aid the effectiveness of vaccines, and may have immune boosting effects.

Yucca extract contains resveratrol, the antioxidant that gives red wine its heart benefits, and antimutagenics effects.

By locking up bile acids in the intestine, yucca saponins prevent bacteria from creating cancer causing secondary bile acids and may prevent colon cancer.

Yucca extract binds to ammonia, and is used in animal feeds and kitty litter to control odors.

So drink your root beer. It’s good for you.

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Categories: Chemistry, Food, Health.

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By sfield
— August 21, 2009 at 10:16 am

Pray for me

Herbert Benson believes in the power of prayer. He has reason to — he’s been studying it scientifically for years.

In a recent study, he and co-author Charles Bethea looked at whether there were any effects that could be traced to people undergoing surgery who had others praying for their speedy recovery without complications.

The study divided 1,800 patients into three groups. Six hundred patients were told that people were praying for them. Another six hundred were prayed for in the same way, but the patients were not informed. The last six hundred were not prayed for.

The last 600 had the fewest complications from their surgery. The group who were prayed for without the knowledge of the patients had an insignificantly higher number of complications.

The group that was aware that there was a group of people praying for them had significantly more complications. Fifty nine percent of them had complications, compared to fifty one percent in the first group, and fifty two percent in the second.

An earlier study of alcoholics who knew that people were praying for them found similar results. Those who knew people were praying for their success in sobriety ended up drinking significantly more after six months than those who thought no one was praying for them.

Richard Sloan, a professor of behavioral medicine at Columbia, thinks such studies are a waste of resources that could be better spent elsewhere. But it seems to me that the $2.4 million dollar study, funded mainly by a group that supports research into spirituality, would have been spent on some other similar study if not for this one, and would probably not have found its way into HIV or cancer research anyway. The U.S. government has spent a similar amount of money on the subject, $2.3 million dollars, and come up with similar results. Demonstrating that intercessionary prayer is ineffective, and sometimes harmful, can be of benefit to people who might otherwise be told that people are praying for them. Over a significantly long period, that $4.7 million dollars might be saved by reducing the costs of complications brought about by the activity of well-wishers with the best of intentions.

So go ahead and pray for your sick friends. Just don’t let them know.

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Categories: Health.

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By sfield
— July 18, 2009 at 10:25 am
By Simon Quellen Field
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