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 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 it on a basic computer monitor. The detailed imaging is reminiscent of the Pre-Crime department in Tom Cruise’s movie Minority Report.

According to a representative at Mechdyne, the manufacturer of the CAVES system, the four-walled projection system at UC Davis is one of the most elaborate they have set up and cost nearly a million dollars in hardware and software.

Now that LiDAR is being used to map both pre- and post-earthquake topography, there is a project underway to create accurate maps of every active fault region. This means that geologists will not have to predict where an earthquake will occur in order to get accurate pre-quake data as the data will already be on hand. LiDAR maps of the post-quake region can then be overlayed on the pre-quake data to create a difference map that will show exactly how the topography changed.

“Other methods are not as accurate,” Hudnut said. “LiDAR gives us an actual 3D representation of the pre- and post-earthquake landscape so we can look at the differences in very high detail.”

Other institutions involved in the research are Arizona State University, Centro de Investigación Científica y de Educación Superior de Ensenada in Mexico, NASA, the Jet Propulsion Laboratory and the Chinese Academy of Sciences. Funding came from the National Academy of Sciences, the USGS and the Keck Foundation.

HUDSON LOFCHIE can be reached at science@theaggie.org.

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 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 on the bacteria. These foreign proteins are noticed by a person’s immune system, which targets the bacteria for destruction. Once these antigens have been targeted, the immune system will always react to that particular protein.

In addition to antigens, bacteria and other cells produce many more proteins that are not exposed as antigens. Immune systems cannot identify proteins that are not exposed. Therefore, the trouble in identifying immune system targets lies in distinguishing between antigens and other proteins.

McSorley’s lab synthetically produced 2,700 proteins for testing that the salmonella produces naturally. These proteins were then isolated and injected into the blood of mice that had been previously infected with salmonella. These mice were then tested for a response.

Since the mice’s immune systems had previously been exposed to salmonella, any protein that was exposed in the bacteria would trigger a response. When a protein caused no response, it was shown not to be an antigen. If a protein did cause a response, that means it was an antigen.

These proteins can potentially be used in vaccines to prevent infections. Exposing someone to the protein without any actual bacteria will prepare an immunity without the danger of infection.

According to McSorley, “the vaccine won’t contain any live organisms and should be very safe for young children.”

By these methods, the lab has identified 117 proteins that were antigens. Only a handful have been tested due to labor and monetary constraints. By identifying these antigens, the hope is that researchers in McSorley’s lab and other institutions can continue testing for good vaccines.

McSorley collaborated closely with Renee Tsolis of the UC Davis Medical School due to similar interests and pertinent information.

“I worked together with Dr. McSorley on this project, because we had done some work trying to define the salmonella antigens recognized by mice,” Tsolis said. “We realized that we had a common interest and decided to share our data and work together.”

ALEX STANTON can be reached at science@theaggie.org.

Scientists have a love-hate relationship with science books meant for the general public. On the one hand, making science reachable to the general public is a great goal; on the other hand, this can sometimes mean oversimplifying research or being less accurate.

It’s a delicate balancing act that not every author can accomplish. If a book is too technical, it will only appeal to the researchers in that field. I’ve read several books that seem promising when I read the summary but soon devolve into sensationalism, or even worse, pseudoscience.

With this in mind, I’d like to introduce a few of my favorite popular science books from a few different fields. These books serve as good introductions for those who don’t know much about the given topics. If you need a good nonfiction book that you don’t need for class, give these a try.

Origins by Neil DeGrasse Tyson: Neil DeGrasse Tyson is probably one of the more well-known modern astronomers, from his appearances on “The Colbert Report” to his willingness to answer questions from the public on websites such as Reddit. His book Origins explores the start of the universe and its current state with his unique combination of a sense of humor and awe at the beauty of the universe. His explanation does involve physics, but he leaves equations for the appendices, so don’t worry if you don’t have a background in physics.

The Poisoner’s Handbook by Deborah Blum: Half crime, half chemistry is the best way to describe this book. Blum explores the emergence of toxicology in Prohibition-era America. If you’re looking for detailed chemical explanations, this book isn’t it; she usually just describes the general shape of the molecules involved. However, her medical explanations are fairly accurate and her story-telling ability is undeniable. Warning — this book can be a bit gruesome at times when discussing autopsies, so be careful when eating.

The Ancestor’s Tale by Richard Dawkins: The unfortunate fact about Richard Dawkins is that he is, to say the least, a polarizing figure. 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 of evolutionary relationships, however. Each ancestor reveals something about our own history and about life in general.

Microcosm by Carl Zimmer: This book is about E. coli — not the nauseating illness, but about the bacteria itself. Microcosm is written to clear the name of this much-maligned species; despite its reputation, its use in research has probably saved many more lives than it has sickened. Zimmer explores why it’s such a good model organism and what we’ve learned from it.

Bonk by Mary Roach: Although Roach is better known for her best-sellers Stiff and Packing for Mars, her book Bonk is also a page-turner. Roach explores sex in a funny yet frank way. What happens during an orgasm? Why did a couple have sex inside of a medical scanner? Has there ever been zero-gravity lovemaking in space? Roach’s ability to discuss sometimes uncomfortable topics with both science and humor is a rare talent in both researchers and writers, so this is a book to read when you want a not-so-serious science book. Remember not to skip the footnotes!

50 Great Myths of Popular Psychology by Scott Lilienfeld: Sometimes, it can seem like psychology is nothing more than common sense. Lilienfeld combats this perception by debunking commonly held beliefs about psychology. For example, did you know that “letting out your anger” through actions like punching a punching bag or yelling loudly is not actually helpful? Lilienfeld explains why not.

This is not an exhaustive overview of all the good science books. I chose these for their ability to introduce cosmology, chemistry, evolution, medicine, sexuality and psychology to those unfamiliar with the topics. Put these in your Amazon cart (or wherever you shop) and happy reading!

Do you have other science books to suggest? AMY STEWART can be reached at science@theaggie.org.

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 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 single-molecule 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.

Forget, during an important turning point in the study, noticed something unexpected while reviewing the data.

“Some of the single molecules that I usually disregarded looked interesting,” Forget said . “I noticed that these DNA molecules actually had nucleoprotein filaments (RecA/damaged DNA complexes) stuck to them. I discovered that the intact template DNA had to be ‘relaxed,’ not stretched out, for the nucleoprotein filaments to interact with it.”

Forget explained that when the target double strand DNA is relaxed, or “curled up,” in a three-dimensional way, then the nucleoprotein filaments, made up of single strand DNA and RecA, can contact it in two or more places at a time. This interaction leads to the single strand DNA finding the stretch of matching DNA on the target (template) strand onto which it can align completely to finish the repair process.

The RecA protein uses this three-dimensional search process to ensure that the correct sequences of DNA can come together — a process that is called recombination.

The RecA-protein search process is only one of a number of potential mechanisms used by DNA binding proteins.

“Other DNA binding proteins carry out searches for specific DNA sequences using a hopping mechanism, while others can ‘sit down’ and slide on the DNA,” Knight said .

“Recombination is a very important process for all living creatures,” said Ryan Jensen, an assistant professor at Yale University who was not involved in the current study. “It’s absolutely essential for life as we know it by repairing lethal DNA damage and generating genetic diversity.”

Jensen previously worked as a postdoctoral student in Kowalczykowski’s lab at UC Davis with Forget.

Forget expects that the current work with the RecA protein will lead to future studies involving the more complex process in human cells, which involves the Rad51 protein.

“This experimental design could be utilized to probe the activity of Rad51 and its various poorly understood ‘helper’ proteins to see how they contribute to making the process more efficient,” said Forget.

The current study by Forget and Kowalczykowski was published in the scientific journal Nature on Feb. 16, 2012.

BRIAN RILEY can be reached at science@theaggie.org.