The Berkeley Science Review: Articles

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The Littlest Life Form
The crown for smallest-living-thing-on-earth has just been passed to a microbe that makes its home in a toxic soup of arsenic and acid. The discovery of this microbe by Brett Baker, staff scientist in Jill Banfield’s group in the Earth and Planetary Sciences Department at UC Berkeley, was made while investigating the multi-hued pond scum deep in an abandoned Iron Mountain mine near Redding, CA. Reported in the December 22 issue of Science, the microbes, nicknamed ARMAN, measure only 200 nanometers in size—twice the size of a large virus like HIV and about a fifth the size of a typical bacterium. The Berkeley team found ARMAN using a technique called community genome sequencing, which can decipher bits of DNA from all the organisms in a real-world habitat such as a scoop of dirt or seawater. Baker took his scoop from slime floating in the stagnant mine water. “This is a great, great site [for research],” explains Baker, referring to an area which is so polluted that its water has the pH of battery acid. Only a few hardy species can thrive in such an extreme environment, making the jumble of DNA sequences gathered that much easier to interpret. ARMAN’s unexpected discovery is a first for community sequencing, but Baker says, “I have a feeling that it’s not the only one.”
—Charlie Emrich is a graduate of the biophysics program.

Smelling in Stereo
Having two eyes affords us depth perception, and having two ears lets us locate the source of a sound, but why do we have two nostrils? Researchers in Noam Sobel’s group in the Department of Neurobiology recently uncovered a clue: Their research demonstrates a link between asymmetry in nasal airflow (different nostrils sucking in different volumes of air) and a person’s ability to locate a scent. They asked blindfolded test subjects to crawl on all fours and follow a chocolate scent trail. Their results show that humans are surprisingly adept at tracking scents and improve with practice. Using sophisticated particle tracking equipment, the group showed that the air sampled by the human nose is naturally asymmetric, allowing for the sampling of spatially distinct regions of air with one sniff. Test subjects were fitted with a homebuilt device that forced the same airflow into both nostrils and were once again put to the task. According to Jessica Porter, the lead graduate student on the project, “they could still navigate the track when forced to use both nostrils symmetrically, but were not nearly as accurate or fast.”
—Harish Agarwal is a graduate student in physics.

Catch a Wave
High-energy physicists aren’t the only ones who get to come up with new particles; condensed-matter researchers, who study solids and liquids, can play the same game. Interactions between the particles in materials can lead to emergent phenomena that resemble new particles (all given names ending with “-on”). A phonon is a particle associated with a sound wave in a solid that makes the atoms jiggle back and forth. Similarly, a photon is a particle associated with light or electromagnetic waves. Phonons and photons can couple together to produce yet another particle: the polariton, which is light passing through a crystal as a combination of sound and electromagnetic waves. A recent experiment at Lawrence Berkeley Laboratory’s Advanced Light Source has succeeded in imaging the atomic motions of polaritons using extremely fast pulses of X-rays. This project may lead to techniques, dubbed polaritonics, to alter a crystal’s structure. Andrea Cavalleri, a scientist in the Materials Science Division at the time, and coworkers recently studied polaritons in lithium tantalate (LiTaO3), a crystal used in optical devices. They recorded the diffraction pattern as terahertz radiation (between infrared and microwaves in the electromagnetic spectrum) passed through the crystal. With the aid of simulations, they reconstructed the resulting atomic motions and made a movie showing the waves passing through the sample. Though not exactly a feature film—it would only last about a millionth of a billionth of a second in real time—the movie offers an unprecedented view into what atoms are actually doing inside a solid. Watch the movie at tinyurl.com/2k9pa6.
—David Strubbe is a graduate student in physics.

Matchmaker, Matchmaker
When sexually reproducing organisms undergo meiosis to produce sperm or eggs, it’s vital that each one of these cells receives exactly one of each chromosome. This allows the normal genetic complement—two of each chromosome—to be restored upon fertilization. When this fails to happen correctly, the result is usually an offspring that is inviable or has a genetic disease like Down syndrome. To better understand how cells divvy up their genetic material evenly, Abby Dernburg’s lab studies meiosis in the nematode worm, C. elegans. Recently, the group has identified a family of proteins, each of which binds to only one or two of C. elegans’ six chromosomes—in other words, they’re able to tell them apart. A paper published in the December 2006 issue of Developmental Cell shows that these proteins not only recognize individual chromosomes, but they help them find their matches (for example, pairing one chromosome 3 with the other chromosome 3). This step is crucial for correct separation later; the chromosomes need to pair up before they can split up into individual sperm or eggs. Though it’s still unclear exactly how these proteins work their pairing mojo, the discovery sheds some light on how cells can tell a chromosome 5 from a chromosome 2, and divide them up accordingly.
—Jacqueline Chretien is a graduate student in molecular and cell biology and a member of the Dernburg lab.

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