Category Archives: Research

Quantum Theory Fails Reality Checks

Reality just got a one-two punch. A new experiment has tried to suss out which of two counterintuitive ingredients is more basic to quantum theory, only to find that they go hand in hand.

Einstein was famously bugged by what are now well-established facts of quantum theory: the randomness of a particle’s choices and the possibility of instantaneous linkages between far-flung light or matter. Experimenters now conclude that Einstein cannot even pick his poison, because allowing for instant links kills any simple notion of reality, too.

$600 Million for Basic Biomedical Research

Howard Hughes Medical Institute (HHMI) will hold a national competition for investigators that will result in an investment of at least $600 million in basic biomedical research. Up to 50 new researchers will be selected by spring 2008. HHMI Announces New Open Competition:

HHMI seeks applications from outstanding scientists studying biomedical problems in a broad array of disciplines, including not only biology and medicine, but related areas of chemistry, physics, engineering and computational biology. This competition is open to early career stage scientists at approximately 200 eligible institutions.
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HHMI values innovation and encourages its investigators to extend the boundaries of science. By appointing scientists as Hughes investigators — rather than awarding research grants — HHMI is guided by the principle of “people, not projects.” HHMI investigators have the freedom to explore and, if necessary, to change direction in their research. Moreover, they have support to follow their ideas through to fruition — even if that process takes many years.
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This new competition represents the first time that HHMI has opened up a general competition to the direct application process. In the past, faculty members had to be nominated by their institutions for HHMI investigator positions.

More details and apply via: 2008 HHMI Investigator Competition.

T-rex Treasure

T. rex remains yield new treasure

Already, the breakthrough has yielded a payoff. Schweitzer and the Harvard scientists found molecular similarities between the Tyrannosaurus rex and modern chickens. They say the finding strengthens a growing case that birds are living relatives of dinosaurs. More tests are needed to see whether the bits of dinosaur proteins match those in other living creatures — including alligators and crocodiles, which, by outward appearances, seem closely related to the ancient species. Molecular maps of proteins in those reptiles are not yet available.
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The very existence of the molecular relics had been unimaginable. Until now, scientists thought such soft stuff survived no more than a million years in animal remains. Usually, tissue degrades and bone gets replaced by mineral, yielding fossils molded precisely like the originals. Although the fossils enable scientists to piece together a skeletal sketch of ancient life forms, they tell only so much.

The discovery of the protein fragments, detailed in the journal Science today, suggests that new molecular clues may be buried in other well-preserved fossils around the world. And those clues could help explain the biology of dinosaurs and other extinct animals. The newly discovered microscopic fragments are not DNA — the inherited code stored in billions of cells that defines every living creature. As a result, no one should expect any Jurassic Park-like replicas of dinosaurs to result from Schweitzer’s finding.

Universal Blood

Universal Blood by Katherine Bourzac:

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.

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.

CERN Pressure Test Failure

photo of Femilab inner triplet quadrupole at CERN

On March 27th a high-pressure test at CERN of a Fermilab-built ‘inner-triplet’ series of three quadrupole magnets in the tunnel of the Large Hadron Collider failed. Fermilab Director on the test failure:

We test the complex features we design thoroughly. In this case we are dumbfounded that we missed some very simple balance of forces. Not only was it missed in the engineering design but also in the four engineering reviews carried out between 1998 and 2002 before launching the construction of the magnets. Furthermore even though every magnet was thoroughly tested individually, they were never tested with the exact configuration that they would have when installed at CERN–thus missing the opportunity to discover the problem sooner.

We need and want to make sure that we find the root causes of the problem and from the lessons learned build a stronger institution. Beyond that, there is no substitute for the commitment each of us makes to excellence, to critical thinking and to sweating every detail.

In a Fermilab Update on Inner Triplet Magnets at LHC they state: “The goal at CERN and Fermilab is now to redesign and repair the inner triplet magnets and, if necessary, the DFBX without affecting the LHC start-up schedule. Teams at CERN and Fermilab have identified potential repairs that could be carried out expeditiously without removing undamaged triplet magnets from the tunnel.”

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.

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.