Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Bug splatter on your car's windshield is a treasure trove of genomic biodiversity

09.10.2009
If you have ever taken a long road trip, the windshield of your car will inevitably be splattered with bugs by the time you arrive at your destination. Could the DNA left behind be used to estimate the diversity of insects in the region?

In a study published online in Genome Research, scientists answered this question, utilizing a novel analysis pipeline that will accelerate future studies of biodiversity.

Recent advances in DNA sequencing technology are allowing researchers to investigate genomic questions of a scale and depth not previously possible. Among the fields benefiting from these new innovations is metagenomics, an approach applying DNA-sequencing technology directly to environmental samples. Scientists can now estimate biodiversity by sequencing DNA collected nearly anywhere, from extreme environments to your own skin, and the possibilities seem limitless.

Metagenomics has traditionally been applied to microbial samples, but investigators led by Anton Nekrutenko of Penn State University believe that this tactic can be utilized in studies of biodiversity of higher organisms. However, they also understand the complex computational infrastructure needed to interpret the massive amounts of data typical of these studies in an accurate and reproducible manner. "Metagenomics is still a 'soft science,'" said Nekrutenko, "where precise identification of species abundance in complex samples is very, very challenging."

To meet this challenge, the group developed the Galaxy metagenomic pipeline, a powerful analysis approach that incorporates all steps of analysis, from handling raw sequencing data to the drawing of evolutionary trees. Nekrutenko and colleagues then put the pipeline to the test by conducting one of the first metagenomics studies of eukaryotic biodiversity.

The group set out to collect a metagenomic sample with the goal of estimating how many species of insects resides in our immediate surroundings. To gather genetic material, they utilized a simple but effective collection method – the front bumper of a moving vehicle. Two samples of bug splatter were collected, the first after driving from Pennsylvania to Connecticut, and the second after traveling from Maine to New Brunswick, Canada.

After sequencing DNA from the splatter samples, the research team used their metagenomic pipeline to address the question of how many species inhabit the regions sampled on the trips. The group accurately identified sequences corresponding to a number of insect taxa amongst other sequences, primarily matching bacteria. Furthermore, they found significant differences in diversity between the first and second trips.

The authors note that there are likely many other insect species that went undetected, as the diversity of organisms represented in sequence databases is currently limited. However, with advances in sequencing technology rapidly driving down costs, the genomic catalog of species diversity is expected to grow rapidly. Together with advanced analysis methods such as the Galaxy pipeline, comprehensive biodiversity studies of all of the life around us are within reach.

Scientists from the University of California San Diego (San Diego, CA), Penn State University (University Park, PA), and Emory University (Atlanta, GA) contributed to this study.

This work was supported by a Beckman Foundation Young Investigator Award, the National Science Foundation, Penn State University, the Huck Institute for the Life Sciences, Emory University, and the Pennsylvania Department of Health.

Media contacts: Anton Nekrutenko, Ph.D. (anton@bx.psu.edu) has agreed to be contacted for more information.

Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (calicchi@cshl.edu; +1-516-422-4012).

About the article: The manuscript will be published online ahead of print on October 9, 2009. Its full citation is as follows: Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, Nekrutenko A, The Galaxy Team. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res doi:10.1101/gr.094508.109.

About Genome Research:

Launched in 1995, Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.

About Cold Spring Harbor Laboratory Press:

Cold Spring Harbor Laboratory is a private, nonprofit institution in New York that conducts research in cancer and other life sciences and has a variety of educational programs. Its Press, originating in 1933, is the largest of the Laboratory's five education divisions and is a publisher of books, journals, and electronic media for scientists, students, and the general public.

Genome Research issues press releases to highlight significant research studies that are published in the journal.

Peggy Calicchia | EurekAlert!
Further information:
http://www.cshl.edu
http://www.genome.org

More articles from Life Sciences:

nachricht Complementing conventional antibiotics
24.05.2018 | Goethe-Universität Frankfurt am Main

nachricht Building a brain, cell by cell: Researchers make a mini neuron network (of two)
23.05.2018 | Institute of Industrial Science, The University of Tokyo

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Molecular switch will facilitate the development of pioneering electro-optical devices

A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.

The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...

Im Focus: LZH showcases laser material processing of tomorrow at the LASYS 2018

At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.

At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...

Im Focus: Self-illuminating pixels for a new display generation

There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?

At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...

Im Focus: Explanation for puzzling quantum oscillations has been found

So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics

Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...

Im Focus: Dozens of binaries from Milky Way's globular clusters could be detectable by LISA

Next-generation gravitational wave detector in space will complement LIGO on Earth

The historic first detection of gravitational waves from colliding black holes far outside our galaxy opened a new window to understanding the universe. A...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Save the date: Forum European Neuroscience – 07-11 July 2018 in Berlin, Germany

02.05.2018 | Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

 
Latest News

When corals eat plastics

24.05.2018 | Ecology, The Environment and Conservation

Surgery involving ultrasound energy found to treat high blood pressure

24.05.2018 | Medical Engineering

First chip-scale broadband optical system that can sense molecules in the mid-IR

24.05.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>