Single atom required for bacterial movement

Tiny things can make a huge difference.

A new study by researchers from the University of North Carolina at Chapel Hill brings this startlingly to light. They have shown that a single calcium atom affects the ability of Pseudomonas aeruginosato to move and to infect cells.

Pseudomonas aeruginosa, a common bacteria that can

cause fatal infection, ‘walks’ along solid surfaces by extending and retracting type IV pili. The pili attach to a surface and pull the bacteria along like a grappling hook. This crawling behavior, called twitching motility, is essential for infection.

When lead investigator Matthew R. Redinbo and his team crystallized the protein component of pili (PilY1), they found that it contained the binding site of a calcium atom. Modifying the protein so that it could no longer bind calcium prevented the formation of pili. Altering PilY1 so that it could not release calcium prevented the pili from retracting.

Redinbo commented:

“We found it pretty remarkable that the binding of a single atom to a protein that is outside the cell is sufficient to tell these motors that are inside the cell to either stop pushing or stop pulling."

A single calcium atom (shown in light blue) binding to a bacterial pili protein, drawn by Michael D.L. Johnson.

Things aren’t always what they seem, DNA edition

This story is cool for a number of reasons, not least of which because it involves high school students doing real science.

Brenda Tan and Matt Cost of Trinity School, Manhattan spent four months collecting DNA from every kind of sample they could think of. They tested foods, bird feathers, insects, horse manure, dog treats, you name it, and sent the samples to scientists at Rockefeller University and the American Museum of Natural History. 151 out of the 217 items they collected had useable DNA.

The DNA 'barcoding' experts sent the recovered DNA codes back to the students, who could then paste them into the Barcode of Life Database (BOLD). Over 65,000 species are currently in that database with more being added all the time.

Tan and Cost found a great deal of discrepancy between food labels and what was actually in the food.

Among their findings:

• an expensive specialty 'sheep's milk' cheese was actually made from cow's milk
• 'venison' dog treats were made of beef
• 'sturgeon caviar' was actually Mississippi paddlefish
• 'frozen Yellow catfish' was really the invasive Walking catfish
• ‘dried shredded squid' was actually jumbo flying squid (Dosidicus gigas).

They also discovered some interesting fauna, including a cockroach that may be new to science. If so, the students might get to name it.

You can follow their adventures here.

Barefoot running may be best

Things I’d rather not know about….

Specialty shoes have long been a staple of running. Lately, however, there has been a contingent of runners and doctors who insist that running barefoot is much healthier. After all, our feet and legs evolved to run barefoot, not to wear shoes. They claim that running barefoot reduces knee, ankle and foot problems. Now, a new study by D. Casey Kerrigan of the University of Virginia shows that the barefooters may be right.

The investigators used 68 volunteers (31 men, 37 women) with no history of musculoskeletal injury who normally run at least 15 miles/week in running shoes. Reflective markers were used to analyze the subjects’ motion and joint torques as they ran either with or without shoes on a specially designed treadmill.

Surprisingly, the researchers found that running in shoes increased the torque on subjects’ knees by about 35% compared with running barefoot.

The authors recommend that running shoe manufacturers strive to create a product that more closely mimics the lower joint torques of running barefoot.

In the meantime, barefoot enthusiasts suggest that people throw away their running shoes for good. Although they offer suggestions for acclimating your feet to heat, cold or gravel, I think I’ll stick to my shoes.

Mosquito attractant uncovered

Scientists led by Walter Lea from the University of California, Davis, have identified the chemical cues responsible for attracting Culex mosquitoes. These insects serve as vectors for West Nile virus and other life-threatening diseases and are responsible for over a 1000 fatalities in the US over the past decade.

Although these mosquitoes are known to be attracted to carbon dioxide, there have to be other chemical cues to specifically draw the insects to certain prey species such as humans.

To answer this question, the researchers extracted chemical odors from a variety of human subjects. They next tested the olfactory receptor neurons in the mosquitoes’ antennae to see which of the isolated chemical compounds triggered a reaction.

They discovered that a compound called nonanal, a powerful semiochemical, or message-carrying molecule, was responsible for attracting the mosquitoes. Traps baited with both nonanal and carbon dioxide drew in over 50% more mosquitoes than traps baited with carbon dioxide alone.

Could this lead to better insect repellants? That would be a boon to the thousands of people who are infected with West Nile virus each year.

Just for fun: Stellar object size

Just how big can objects in the universe get? Watch!

Thanks to Greg Laden's Blog.

Scientists recalibrate the molecular clock

Detlef Weigel, director at the Max Planck Institute for Developmental Biology and Michael Lynch of Indiana University have measured the mutation rate in Arabidopsis thaliana plants.

Genetic differences between species have been used to determine how long ago the species shared a common ancestor. To use this ‘molecular clock’, researchers sequence the genomes of species A and B, and determine how many nucleotide changes there are between them. Combined with knowledge about mutation rates, this gives a result as to how closely related the two species are.

However, the collaborators asked the question: what if there had really been many more changes, but some of those changes had reverted or been lost? For example, suppose that, over many generations, one nucleotide had changed from an A to a G, then to a C, then to a T, and then back to an A? At that position in the genome, there would appear to have been no change at all, when it fact there had been four changes.

To test this, the scientists observed five lines Arabidopsis thaliana for 30 generations, recording every nucleotide change in every plant. To be sure that their results were valid, each sequencing step was repeated 30 times. They then compared the final generation to the original plants.

Their findings? The mutation rate for each position on the genome was about one in 140 million for each generation. Because the plant has a genome of about 120 million base pairs, that’s about two changes per generation (one change in each copy of its diploid genome). If you recall that these plants can each produce thousands of seeds per generation, and that generation times are short, you can see how quickly those changes can add up.

The researchers have already used this revised molecular clock to compare Arabidopsis thaliana with a close relative, Arabidopsis lyrata. These two plants were previously thought to have diverged five million years ago, but based on the new data, the split probably occurred closer to 20 million years ago.

Top: drawing of Arabidopsis thaliana by Emmanuel Boutet, 12/5/2000

Bottom: example of DNA sequence.

This report was first seen on RichardDawkins.net.

New way to kill cancer cells

Dario C. Altieri of the University of Massachusetts Medical School may have found a novel way of fighting cancer. He and his colleagues are studying how small molecules called Gamitrinibs affect prostate cancer cell survival.

The researchers chose prostate cancer as a model, because it’s extremely common. Although largely treatable, it does result in over 30,000 deaths per year in the US.

Curing cancer is a difficult business because you must eliminate all the cancerous cells, lest they metastasize and spread to other parts of the body, while doing minimal damage to non-cancerous cells. It’s easy enough to kill every cell in the body or no cells, but tricky to kill a select subset of cells.

To make matters worse, cancer cells have mechanisms to protect them from aging and dying (apoptosis). One particular protein, tumor necrosis factor receptor-associated protein-1 (TRAP-1), a form of the heat shock protein Hsp90, appears to prevent prostate cancer cell death. Scientists found that TRAP-1 is highly expressed in cancerous human prostate tissue but not in normal prostate tissue. If TRAP-1 is overexpressed in normal prostate cells, the normal cells then become resistant to apoptosis as well.

TRAP-1 can be inhibited by treatment with Gamitrinib, a molecule first synthesized by Dr. Altieri and his colleagues. Under those conditions, prostate cancer cells die just like normal cells. In contrast, treatment with Gamitrinib did not increase the death rate of normal cells.

The researchers hope that Gamitrinib will be a useful treatment not only for prostate cancer, but also for many other types of cancer that rely on TRAP-1 to prevent apoptosis.