Science &Technology

4 wednesday, february 22, 2012

Lasers create 3D maps of earthquake faults 3D data used in projection room to analyze topographic changes

The california aggie

topsies, so be careful when eating. The Ancestor’s Tale by Richard Dawkins: The unfortunate fact about Richard Dawkins is that he is, to say Amy the least, a polarizing figure. Stewart What a lot of people forget is that though he is loudly critical of religion, he is actually an evolutionary biologist at heart. This book is thick, but don’t let that intimidate you; the book is a beautifully written travel back in evolutionary time, from humans to the most common ancestor of all living things. It isn’t just a list cientists have a loveof evolutionary relationships, hate relationship with however. Each ancestor rescience books meant for the general public. On the veals something about our own history and about life in one hand, making science reachable to the general pub- general. Microcosm by Carl lic is a great goal; on the othZimmer: This book is about er hand, this can sometimes E. coli — not the nauseating mean oversimplifying research or being less accurate. illness, but about the bacteria itself. Microcosm is writ It’s a delicate balancing act that not every author can ten to clear the name of this much-maligned species; deaccomplish. If a book is too technical, it will only appeal spite its reputation, its use in research has probably saved to the researchers in that many more field. I’ve lives than it read sev... this book can be a bit gruesome has sickened. eral books that seem at times when discussing autopsies, Zimmer explores why it’s promisso be careful when eating such a good ing when model organI read the ism and what summary but soon devolve into sen- we’ve learned from it. Bonk by Mary Roach: sationalism, or even worse, Although Roach is better pseudoscience. known for her best-sellers With this in mind, I’d like Stiff and Packing for Mars, to introduce a few of my favorite popular science books her book Bonk is also a pageturner. Roach explores sex in from a few different fields. a funny yet frank way. What These books serve as good happens during an orgasm? introductions for those who Why did a couple have sex don’t know much about the inside of a medical scangiven topics. If you need a ner? Has there ever been zegood nonfiction book that ro-gravity lovemaking in you don’t need for class, give space? Roach’s ability to disthese a try. cuss sometimes uncomfort Origins by Neil DeGrasse able topics with both science Tyson: Neil DeGrasse Tyson and humor is a rare talent in is probably one of the more both researchers and writers, well-known modern astronso this is a book to read when omers, from his appearancyou want a not-so-serious es on “The Colbert Report” science book. Remember not to his willingness to answer to skip the footnotes! questions from the public 50 Great Myths of Popular on websites such as Reddit. His book Origins explores the Psychology by Scott Lilienfeld: Sometimes, it can seem start of the universe and its current state with his unique like psychology is nothing more than common sense. combination of a sense of humor and awe at the beauty Lilienfeld combats this perception by debunking comof the universe. His explanation does involve physics, but monly held beliefs about psychology. For example, did you he leaves equations for the appendices, so don’t worry if know that “letting out your you don’t have a background anger” through actions like punching a punching bag or in physics. yelling loudly is not actual The Poisoner’s Handbook ly helpful? Lilienfeld explains by Deborah Blum: Half why not. crime, half chemistry is the This is not an exhaustive best way to describe this overview of all the good scibook. Blum explores the ence books. I chose these for emergence of toxicology in their ability to introduce cosProhibition-era America. If mology, chemistry, evolution, you’re looking for detailed medicine, sexuality and psychemical explanations, this chology to those unfamiliar book isn’t it; she usually just with the topics. Put these in describes the general shape your Amazon cart (or wherof the molecules involved. However, her medical expla- ever you shop) and happy reading! nations are fairly accurate and her story-telling ability is undeniable. Warning — this Do you have other science books to suggest? book can be a bit gruesome AMY STEWART can be reached at science@ at times when discussing au- theaggie.org.

Popular science

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Fault line across Paso Superior, Mexico.

By HUDSON LOFCHIE Aggie Science Writer

Geologists at UC Davis have a tool at their fingertips that puts everyday laser rangefinders to shame. Their technology allows them to take 100,000 range samples per second. The system is called Light Distance and Ranging, or LiDAR for short, and is being used to create hyperaccurate topography maps of post-earthquake regions. The juiced-up rangefinder is loaded on an airplane and is then flown over a region to create a three dimensional image of the land below. It is operated by a team from the National Center for Airborne Laser Mapping. “We learn a lot about earthquake faults by studying fresh quake ruptures,” said Ken Hudnut, a geophysicist with the United States Geological

courtesy of KeckCAVES

Survey (USGS). “The record of [ground] displacement is useful for assessing the hazard presented by faults.” LiDAR has been in use for nearly a decade, but up until recently, it had only been used to document a region after an earthquake. Now, it is being used to map areas both before and after an earthquake to measure exactly what changed in the topography with down-to-the-inch resolution. The system uses a series of tools to maintain accuracy even when flying 10,000 feet above an area. First, the ground coordinates are mapped with GPS, and then those same coordinates are programmed in the plane’s GPS to keep it on track. In addition, the LiDAR system itself has a gyroscope and accelerometer to correct for the plane’s pitch and roll. The LiDAR system collects a huge

amount of data, over 100 gigabytes over just a few acres, so researchers require tools that will allow them to efficiently visualize all of that data. This is when UC Davis geologists use KeckCAVES to analyze the vast amounts of data. Donated by the Keck foundation, the CAVES, or Center for Active Visualization in the Earth Sciences, is a three dimensional projection room built to explore the data collected by the LiDAR system. “There are three walls and a floor with stereoscopic displays,” said Michael Oskin, a geology professor at UC Davis. “Users wear 3D glasses and CAVES allows you to walk around inside of your data.” The system provides a far more immersive environment for analyzing data and is far superior to looking at

See LIDAR, page 6

Protein plays DNA matchmaker role UC Davis postdoctoral fellow makes important discovery

By BRIAN RILEY Aggie Science Writer

Researchers have directly observed an essential three dimensional DNA damage repair process using a special microscopy technique. Anthony L. Forget, who now works at MIT in Cambridge, Massachusetts, worked as a postdoctoral fellow with Stephen Kowalczykowski in the department of microbiology and the department of molecular and cellular biology at UC Davis to make the discovery. Single-molecule microscopy is an exciting technique created by “the merging of two scientific disciplines, physics and biology,” Forget said. “A laser beam is manipulated to form molecular tweezers that hold a single piece of DNA in place

Protein RecA wrapped around DNA.

courtesy

under a microscope.” Forget and Kowalczykowski used microscopic fluorescent tags to view the cellular machinery one molecule

at a time. Forget used the technique to study DNA repair using a key protein from the E. coli bacteria called RecA. “The E. coli RecA protein is fairly easily purified,” said Kendall Knight, Forget’s former graduate advisor who is a professor at the University of Massachusetts Medical School. Knight was not involved in the current study. “It’s a well characterized protein that is ideal for these types of singlemolecule studies,” Knight said. Certain types of repair processes involve searching segments of DNA in order to find matches between two strands, Knight said . For E. coli, the RecA protein is involved in this type of repair.

See PROTEIN, page 2

Keeping babies cool

Researchers at UC Davis make progress in salmonella vaccine

Infants with brain damage benefit By ERIC C. LIPSKY Aggie Science writer

Doctors at the UC Davis Medical Center have been using a technique for helping children born with brain damage. In a deviation from past standards, infants are being cared for with cooling. Instead of being placed in the typical blankets infants are placed in after birth, they are being cooled so as to prevent further brain damage from occurring. The founder of the infant cooling program, called “Cool Babies,” is Ian Griffin, associate professor in the department of neonatology at UC Davis. “We look for babies that are depressed at birth; babies that are not interactive and don’t move much at birth,” Griffin said. Griffin said that the one of the most important effects of the cooling program is that it helps prevent the second wave of brain damage that occurs after birth. “The cooling slows down the processes of the brain,” Griffin said. “It slows the metabolism, meaning we can calm down the second wave of damage that occurs.” According to Griffin, the second wave of damage is propelled by the residual effects of the first wave of damage. The first wave of cells die due to lack of oxygen and build up of waste material; in the second wave, other cells die as a result of toxic compounds released from the cells that died in the first wave. “With the cooling, it’s just like how icing an injury helps prevent swelling,” Griffin said. In terms of how soon infants need to be cooled, Griffin said that infants need to be put in the cooling program within six hours of birth, but as soon as possible is best. “The infants are put on a cooling mattress that actively cools their temperature,”

Collaboration between UC Davis and UC Irvine identifies targets on bacteria By ALEX STANTON Aggie Science Writer

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Premature babies often face daunting health problems.

Griffin said. “They stay cooled for 72 hours in temperatures ranging from 33 to 37 degrees Centigrade [91.4 to 98.6 degrees Fahrenheit], and are then re-warmed over a period of 12 hours.” Griffin said that the infants typically spend 14 to 16 days in the hospital, where doctors keep following their neurological exams. “The results are good. Maybe half of the babies will survive without significant handicap with cooling,” Griffin said. “Without the cooling, about one-third of the babies will survive without significant handicap.” Griffin said that the program is important

See BABIES, page 6

A team of researchers at UC Davis led by Stephen McSorley, in conjunction with collaborators at UC Irvine, identified antigens on salmonella bacteria. This new discovery could lead to salmonella prevention. Salmonella is a bacterial infection that is carried through food. According to the Centers for Disease Control and Prevention, 400,000 cases of salmonella are reported in the United States alone. Most salmonella infections are mild. Diarrhea, fever and cramps develop within three days of initial infection. These symptoms courtesy typically persist for around a week and abate without need for medical aid. However, there do exist more severe cases of salmonella in less fortunate individuals in which the infection spreads to the blood, which is often fatal. In this regard, McSorley’s lab has been

trying to identify targets for immune attack in salmonella in hopes of being able to vaccinate. “There has been a lot of progress over the years in identification in other infectious diseases, but for some reason salmonella research seemed to be left behind,” McSorley said, “Which is terrible since many young children die of salmonella infections every year in Africa and Asia.” Currently, there exist no vaccinations for the salmonella bacterial infection. Patients whose condition necessitates medical action are treated with antiobiotics. Those who are young, elderly, have compromised immune systems, and especially those without adequate medical facilities are less likely to benefit from this treatment. Logical targets for vaccines are called antigens, which are proteins that are exposed

See VACCINE, page 6