Category Archives: Life Science

Universal Blood

Red blood cells have complex sugars on their surfaces; it is these sugars that determine whether the blood is type A, B, O, or both A and B. People with type A red blood cells carry antibodies against type B blood cells. If they are given a transfusion of type B red blood cells, their body will attack and kill the cells. Similarly, people with type B blood will mount an immune attack against a transfusion of type A blood.

Researchers led by Henrik Clausen of the University of Copenhagen have discovered two enzymes that efficiently chop the A and B sugars off of red blood cells, making them universal. The company ZymeQuest, based in Beverly, MA, has licensed the enzymes and developed a machine that can simultaneously treat eight units of blood with the enzymes in 90 minutes.

ScienceMatters@Berkeley April 2007

As usually the latest issue of ScienceMatters@Berkeley includes several intersting articles including, The Protein Machine by Kathleen M. Wong

A large percentage of known antibiotics target bacterial ribosomes, including tetracycline, erythromycin, and streptomycin. Many of these antibiotics have been isolated from microbes themselves. “It’s a byproduct of the chemical warfare that’s been going on among bacteria for hundreds of millions of years,” Cate says. “We want to understand how these natural products inhibit translation. Then, based on what we understand about the ribosome mechanism, we should be able to come up with new ways to stop bacterial translation based on the old compounds.”

Self-Tuning Genes:

Researchers such as UC Berkeley’s Adam Arkin have found that regulatory feedback is associated with chance fluctuations in mRNA or protein levels—a phenomenon called expression noise. “Even though they’re all genetically identical, and grown under the same conditions, yeast clones don’t express certain proteins at exactly the same level,” Brem says. “Some genes are noisier than others. That makes people think the cell is actively tuning the distribution around an expression level set by the regulatory network.” Noise may ensure that a few individuals can handle abrupt changes in their environment. In other words, if a colony is suddenly assaulted by toxic chemicals or high heat, a few individuals will already have expression levels suited to those conditions.

Math and Nature

Can’t Knock It Down:

Give mathematicians such a toy, and they’re liable to turn it into a math problem.

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Next, the pair began to investigate whether all three-dimensional shapes have at least two stable and two unstable balance points. They tried to generalize their two-dimensional proof to higher dimensions, but it didn’t hold up. Therefore, it seemed possible that a self-righting three-dimensional object could exist. Such a shape would have only one stable and one unstable balance point.
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Once the pair had built their Once the pair had built their self-righting object, they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back., they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back.
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The mathematicians still face an unanswered question. The self-righting objects they’ve found have been smooth and curvy. They wonder if it’s possible to create a self-righting polyhedral object, which would have flat sides. They think it is probably possible, but they haven’t yet managed to find such an object. So, they are offering a prize to the first person to find one: $10,000, divided by the number of sides of the polyhedron.

Changing the Circadian Clock with the Seasons

Changing the Circadian Clock with the Seasons:

The findings – gleaned from work on the fruit fly Drosophila – have broad implications for understanding how innate behaviors such as mating, migrating, and hibernating are stimulated by environmental cues. Dan Stoleru, the lead author of the Cell paper and a postdoctoral fellow in Rosbash’s laboratory at Brandeis University, adds that the study reveals insights into possible causes of seasonal depression as well as other forms of mood disorders that respond to light therapy.
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Rosbash is a leader in the field of circadian research. For the past 25 years he has been defining the machinery that underlies the nearly universal pattern of circadian rhythms in insects, animals, and humans. He employs the tools of Drosophila genetics to understand how the circadian clock ticks and which master neural circuits underlie circadian activity patterns.

Bedbugs Are Back

Bedbugs bounce back: Outbreaks in all 50 states by Meredith May:

Pest control companies nationwide reported a 71 percent increase in bedbug calls between 2000 and 2005. Left alone, a few bedbugs can create a colony of thousands within weeks. “We never treated bedbugs until 2002. Now we have a dedicated bedbug crew working on this every day,” said Luis Agurto, president of Pestec in San Francisco.

Agurto’s arsenal includes a vacuum, steam heat to cook the bedbug eggs and targeted spraying of insecticides. It takes three, eight-hour visits and about $500 to $750 to exterminate one room. A whole house would cost closer to $5,000.
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Nearly all exterminators use pyrethroids, which are a synthetic version of pyrethrum, the substance found in chrysanthemum flowers. But last fall, at the University of Kentucky, some of the nation’s best bedbug researchers delivered some sobering news — while they could kill bedbugs born in the lab with pyrethroids, four groups of adult bedbugs brought in from the outside were unaffected.

University extension offices often have the soundest scientific information – try the links below for more details.

Big Atlantic Sharks Disappearing, Study Warns

Tiger Shark

Big Atlantic sharks disappearing, study warns (phb broke link so I removed it):

Humans, mainly those in countries with a craving for shark-fin soup, have devoured so many of the oceans’ top predators that it has rattled the length of the marine food chain, according to a study to be published today in the prestigious journal Science. While previous studies have calculated declines by half or more, this one argues that seven of the largest sharks along the Atlantic Coast have all but vanished because of overfishing — down as much as 99 percent for bull, dusky and smooth hammerheads over the last 35 years.
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The study’s premise: As larger sharks disappeared, smaller ones and rays, both often prey, exploded over the same period. One in particular, the cownose ray, perpetuated to the point that by 2004 it gulped down much of the scallop population in Chesapeake Bay. ”I think that’s just the tip of an iceberg,” Fordham said. “There are so many connections we don’t understand. Sharks keep the oceans in balance.”

Photo by Jim Winstead

Neuroengineers Use Light to Silence Overactive Neurons

MIT neuroengineers’ pulsing light silences overactive neurons:

The work takes advantage of a gene called halorhodopsin found in a bacterium that grows in extremely salty water, such as the Great Salt Lake in Utah. In the bacterium, Natronomas pharaonis, the gene codes for a protein that serves as a light-activated chloride pump, which helps the bacterium make energy.

When neurons are engineered to express the halorhodopsin gene, the researchers can inhibit their activity by shining yellow light on them. Light activates the chloride pumps, which drive chloride ions into the neurons, lowering their voltage and silencing their firing.
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The group also plans to use the new method to study neural circuits. Last year, Boyden devised a technique to stimulate neurons by shining blue light on them, so with blue and yellow light the researchers can now exert exquisite control over the stimulation and inhibition of individual neurons. Learning more about the neural circuits involved in epilepsy could help scientists develop devices that can predict when a seizure is about to occur, allowing treatment (either shock or light) to be administered only when necessary, Boyden said.

More on Disappearing Honeybees

Mysterious deaths of the honeybees

Beekeepers throughout the United States have been losing between 50 and 90 percent of their honeybees over the past six months, perplexing scientists, driving honey prices higher and threatening fruit and vegetable production.

At a House Agricultural Subcommittee hearing in Washington, D.C., today, members of various organizations came together to share their concerns about what they have been calling the “Colony Collapse Disorder,” or CCD. Beginning in October 2006, beekeepers from 24 states reported that hundreds of thousands of their bees were dying and their colonies were being devastated.

Virus Traps

Scientists Explore Ways to Lure Viruses to Their Death by Carl Zimmer:

Viruses invade a cell by latching onto certain proteins on its surface. Once attached, they can slip inside the cell and manipulate it into making new copies of themselves. But viruses cannot infect red blood cells. Unlike most other cells in the body, as red blood cells develop in bone marrow they lose their DNA. If a virus ends up inside a red blood cell, there are no genes it can hijack to replicate itself.

“It occurred to us that if a virus bound to a red blood cell, that was a dead end,” said Dr. Robert W. Finberg, a professor at the University of Massachusetts Medical School.
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To test the model, the scientists mixed normal bacteria with different levels of mutant traps and then infected them with viruses. After letting the viruses replicate, the scientists took a small sample to start a new colony. They discovered there was indeed a trap threshold above which the virus population could not survive. Above that threshold, the viruses disappeared by the time the scientists started the third round of colonies.

Biologists Solve B-12 Vitamin Puzzle

MIT biologists solve vitamin puzzle

B12, the most chemically complex of all vitamins, is essential for human health. Four Nobel Prizes have been awarded for research related to B12, but one fragment of the molecule remained an enigma–until now. The researchers report that a single enzyme synthesizes the fragment, and they outline a novel reaction mechanism that requires cannibalization of another vitamin.
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Vitamin B12 is produced by soil microbes that live in symbiotic relationships with plant roots.
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BluB catalyzes the formation of the B12 fragment known as DMB, which joins with another fragment, produced by a separate pathway, to form the vitamin. One of several possible reasons why it took so long to identify BluB is that some bacteria lacking the enzyme can form DMB through an alternate pathway, Walker said.

One of the most unusual aspects of BluB-catalyzed synthesis is its cannibalization of a cofactor derived from another vitamin, B2. During the reaction, the B2 cofactor is split into more than two fragments, one of which becomes DMB. Normally, the B2-derived cofactor would assist in a reaction by temporarily holding electrons and then giving them away. Such cofactors are not consumed in the reaction.