Sequencing at sea

Scientists overcame equipment failure, space constraints and shark-infested waters to do real-time DNA sequencing in a remote field location

2014-08-19

(Press-News.org) SAN DIEGO, Calif. (August 19, 2014) — Daylight was breaking over the central Pacific and coffee brewing aboard the MY Hanse Explorer. Between sips, about a dozen scientists strategized for the day ahead. Some would don wetsuits and slip below the surface to collect water samples around the southern Line Islands' numerous coral reefs. Others would tinker with the whirring gizmos and delicate machinery strewn throughout the 158-foot research vessel. All shared a single goal: Be the first research group to bring a DNA sequencer out into the field to do remote sequencing in real time. Against an ocean of odds, they succeeded.

This three-week, five-island expedition took place last year with a research crew including San Diego State University computer scientist Rob Edwards, biologist Forest Rohwer, postdoctoral scholar Andreas Haas and graduate student Yan Wei Lim. They were accompanied by several other researchers from the San Diego region and around the world. The researchers published an account of their trip and methods today in the journal PeerJ.

Line Island investigations

Biologists and computer scientists at SDSU have been traveling to the Line Islands for the last decade, collecting and analyzing the coral habitat to better understand what organisms live there, how they compete for resources, and what effects their presence has on the reef's ecosystem. It always bothered Edwards that they had to wait until they were back home, on the other side of the world, before they could look at their data and develop new hypotheses.

"If only we had had that data out in the field, we could have asked those questions there and then," Edwards said.

That inkling grew into an ambitious plan to somehow, some way bring out to sea a cumbersome and expensive piece of equipment designed to analyze a sample's DNA makeup and spit out detailed information about its genome.

The project initially had its doubters.

"People are a little bit hesitant to take a half-million-dollar piece of equipment into the middle of the Pacific if you're not sure it's going to be coming back," Edwards said.

Undeterred, he and his colleagues devised a protocol for how to run a DNA sequencer on a ship. Finally, the team headed to Tahiti with a sequencer provided by San Diego–based biotech company Life Technologies. As the Explorer headed south en route to an eventual rendezvous with Antarctica, it picked up the researchers and their sequencer and set course for the Line Islands.

Problems and solutions

The problems and hurdles were manifold.

First, the touch screen needed to operate the machine broke during transit. Edwards had to hack into the sequencer's software to make it operable with his laptop.

Next, they had to find room for all the various pieces of equipment. They set up the sequencer itself in the laundry room because it was the lowest point in the ship and it would sway the least as the Explorer rocked. The microbiology lab was set up on the upper aft deck. The DNA isolation station found its home in a cabin. The mess deck (or dining room, to landlubbers) hosted the PCR machine used to amplify the DNA samples into analyzable chunks.

Once everything was in place, Lim, a doctoral student, was tasked with calibrating the sequencer. Normally, this takes about 15 minutes in a lab. Due to the boat's sway, however, it took about five hours.

Then there were the sharks. Lim recalls that every time the researchers dove to the reef to collect samples, she counted between 20 and 30 curious sharks milling about.

"I wasn't afraid," she said. "They would just swim away if you got too close."

Despite the setbacks, the researchers managed to make it all work. They successfully collected samples, sequenced their DNA, and developed new research questions on the fly. In all, 26 bacterial genomes were sequenced, along with two metagenomes, which take into account all the DNA present in a given region.

Not a bad haul for a proof-of-concept voyage, but Edwards said next time they hope to collect even more data and develop and test more complex hypotheses out in the field.

"At the end of the day, we were able to come up with the data we needed," Edwards said. "But when we go back next time, we're going to be better prepared."

A YouTube video describging the research can be found here: https://www.youtube.com/watch?v=8uTbK0vCcww&feature=youtu.be INFORMATION: About San Diego State University San Diego State University is a major public research institution offering bachelor's degrees in 91 areas, master's degrees in 78 areas and doctorates in 22 areas. The university provides transformative experiences, both inside and outside of the classroom, for its 35,000 students. Students participate in research, international experiences, sustainability and entrepreneurship initiatives, and a broad range of student life and leadership opportunities. The university's rich campus life features opportunities for students to participate in, and engage with, the creative and performing arts, a Division I athletics program and the vibrant cultural life of the San Diego region. For more information, visit http://www.sdsu.edu. END

[Attachments] See images for this press release:

ELSE PRESS RELEASES FROM THIS DATE:

Physically fit kids have beefier brain white matter than their less-fit peers

2014-08-19

CHAMPAIGN, Ill. — A new study of 9- and 10-year-olds finds that those who are more aerobically fit have more fibrous and compact white-matter tracts in the brain than their peers who are less fit. "White matter" describes the bundles of axons that carry nerve signals from one brain region to another. More compact white matter is associated with faster and more efficient nerve activity. The team reports its findings in the open-access journal Frontiers in Human Neuroscience. "Previous studies suggest that children with higher levels of aerobic fitness show greater ...

Fish study links brain size to parental duties

2014-08-19

Male stickleback fish that protect their young have bigger brains than counterparts that don't care for offspring, finds a new University of British Columbia study. Stickleback fish are well known in the animal kingdom for the fact that the male of the species, rather than the female, cares for offspring. Male sticklebacks typically have bigger brains than females and researchers wanted to find out if the difference in size might relate to their role as caregivers. In the study, published recently in Ecology and Evolution, researchers compared regular male sticklebacks ...

Natural (born) killer cells battle pediatric leukemia

2014-08-19

Researchers at Children's Hospital Los Angeles have shown that a select team of immune-system cells from patients with leukemia can be multiplied in the lab, creating an army of natural killer cells that can be used to destroy the cancer cells. Results of their in vitro study, published August 19 in the journal Leukemia, could one day provide a less toxic and more effective way to battle this cancer in children. Acute lymphoblastic leukemia (ALL) is the most common cancer of childhood. This disease hinders the development of healthy blood cells while cancer cells proliferate. ...

Anesthesia professionals not sufficiently aware of risks of postoperative cognitive side effects

2014-08-19

New York, NY, August 19, 2014 – Postsurgical cognitive side effects can have major implications for the level of care, length of hospital stay, and the patient's perceived quality of care, especially in elderly and fragile patients. A nationwide survey of Swedish anesthesiologists and nurse anesthetists has found there is low awareness of the risks of cognitive side effects following surgery. Furthermore, only around half of the respondents used depth-of-anesthesia monitors. Results are published in Annals of Medicine and Surgery. Patients generally expect to make a rapid ...

What's in your gut? Certain bacteria may influence susceptibility to infection

2014-08-19

The specific composition of bacterial species in a person's gut may protect against or increase susceptibility to Campylobacter, the most common cause of human bacterial intestinal inflammation, according research published this week in mBio®, the online open-access journal of the American Society for Microbiology. The study also found that Campylobacter infection can yield lasting changes to one's gut bacteria composition. "It has been known for a long time that the microbiota, or microorganisms in the gut, can protect a person from colonization by organisms that cause ...

Daughters provide as much elderly parent care as they can, sons do as little as possible

2014-08-19

SAN FRANCISCO — Parents are better off having daughters if they want to be cared for in their old age suggests a new study, which finds that women appear to provide as much elderly parent care as they can, while men contribute as little as possible. "Whereas the amount of elderly parent care daughters provide is associated with constraints they face, such as employment or childcare, sons' caregiving is associated only with the presence or absence of other helpers, such as sisters or a parent's spouse," said study author Angelina Grigoryeva, a doctoral candidate in sociology ...

Unlike less educated people, college grads more active on weekends than weekdays

2014-08-19

SAN FRANCISCO — People's educational attainment influences their level of physical activity both during the week and on weekends, according to a study whose authors include two University of Kansas researchers. The study finds that, on average, those with a college degree are more active on Saturdays and Sundays than on a typical weekday — whereas for people without a high school degree, the opposite is true. "Educational attainment predicts physical activity differently on weekends and weekdays," said Jarron M. Saint Onge, a KU assistant professor of sociology and ...

In an already stressful workplace, Great Recession's health effects hard to find

2014-08-19

SAN FRANCISCO — The Great Recession of 2007-2009 had little direct effect on the health of workers who survived the waves of job cuts that took place during that period, according to a new University of Akron study. That's the good news. The bad news may be the reason: Increased workloads and less satisfying job duties, the highly stressful byproducts of corporate restructurings during previous economic downturns, had by 2007 become the new normal in the workplace. Because of this long-term trend, workers who remained on the job during the Great Recession were already ...

Nurses driven mainly by a desire to help others are more likely to burn out

2014-08-19

SAN FRANCISCO — Nurses who are motivated primarily by the desire to help others, rather than by enjoyment of the work itself or the lifestyle it makes possible, are more likely to burn out on the job, University of Akron researchers say. Nursing is still a female-dominated occupation, and being female is associated with being caring, nurturing, and altrustic. Therefore, the desire to help others is often assumed to be the "right" motivation for entering the field, the researchers say. However, they found that nurses who pursue their career for reasons other than or ...

Study finds increased rates of preventable deaths in the US following common urologic procedures

2014-08-19

In recent years, a shift from inpatient to outpatient surgery in the U.S. for commonly performed urologic procedures has coincided with increasing deaths following complications that were potentially recognizable or preventable. The finding, which comes from a recent study published in BJU International, indicates the importance of monitoring urologic surgery patients for potential complications. Over the last two decades, measures to improve healthcare safety and quality have expanded significantly. In the context of surgical procedures, this has lead in a decrease in ...

Sequencing at sea

ELSE PRESS RELEASES FROM THIS DATE:

LAST 30 PRESS RELEASES: