Bug splatter study is data driven

The next time you take a road trip, think before you clean the bug splatter off your car. Those insect remains may actually be more interesting than your vacation photos.

“It turns out that your car is a sampling device for understanding the biodiversity of all the places you’ve been,” says James Taylor, a computational biologist at Emory.

Genome Research recently published a paper by Taylor and collaborators that applied advanced DNA sequencing techniques that are traditionally used on microbial samples to look at insect biodiversity. “We were curious whether these techniques would work for more complex organisms,” Taylor says.

To collect genetic material for the study they used the bumper and windshield of a moving vehicle. Two samples were collected: on a drive from Pennsylvania to Connecticut, and on a trip from Maine to New Brunswick, Canada.

“We found that there is a huge amount of insect diversity, but what was really surprising was to see the enormous amount of novel sequence,” Taylor says. “It’s indicative of how poorly we have sampled the whole tree of life in genome research so far. There’s an enormous amount of species out there.”

Road tested

Taylor is a co-developer of Galaxy, an open-source software system for analyzing genetic data. The Galaxy developers recently refined the system, creating the Galaxy metagenomic pipeline that allows a research team to integrate all of the data, analyses and workflows of a study, and then publish this material as a live online supplement.

The bug splatter paper served as the first test of the metagenomic pipeline.
“I believe that this study is one of the most transparent and reproducible bioinformatics papers ever,” Taylor says. “Anyone can go online, follow links and see every step of our analysis and exactly what parameters were used. And they can take our data and do their own analysis of other questions.”

No computational experience is required to use the free Galaxy system, Taylor says. “All of science is becoming computationally intensive, so tools like this are needed to improve transparency.”

DNA sequencing technology is getting cheaper, opening more doors for research by small investigators, and Taylor is focused on serving this niche.

“Nowadays, you can have a crazy idea like studying bug splatter and without a lot of money or work, you can go out and do it just to see what’s there,” he says.

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Icons of evolution

Nancy Lowe goes to church more often than most. All she has to do is step outdoors, where she finds the sacred in nature. During breaks from her job as a lead research specialist in biology, you might see her sketching a leaf or a bug somewhere on campus.

“I’m an artist and a naturalist,” she says. “Working as a lab technician is my day job.”

Lowe’s art is featured in the ongoing exhibit at Emory Library’s Schatten Gallery, marking the 150th anniversary of the publication of Darwin’s “On the Origin of Species.” The eclectic show includes original editions of “Origin,” panoramic “nanoscapes” captured by electron microscopes and a retrospective of how poet Ted Hughes’ work evolved.

Lowe’s contribution is a series of luminous paintings called “Species Icons.” On canvases glinting with gold leaf, a pitcher plant wears a halo and tube worms are strung with jewels.

“Medieval religious icons seem to glow with a certain power,” Lowe says. “They’re old and precious. I wanted to combine that feeling with the careful attention to detail in scientific illustration of organisms. For me, that’s what’s sacred – the amount of geological time that it has taken to evolve these species.”

The paintings also grew out of a question that Lowe says she’s pondered for years: “Now that evolution has become our primary creation story, what should we put on our stained glass windows?”

After graduating from the Art Institute of Chicago, Lowe worked in video and film before discovering her love of illustrating nature. She volunteered as an artist for a species inventory project in the Great Smoky Mountains National Park. She regularly teaches art, in addition to making her own. The name of her web site, "look at your fish", comes from 19th-century naturalist Louis Aggasiz. He would give his students a pan containing a pickled fish and leave them alone to stare at it for hours.

Careful observation is important to art, as well as science, she says. “I want my students to ask, ‘What’s this little bristle for on this bug?’ and realize that every structure is connected to some function. It all comes back to evolution.”

A microscope can distance scientists from their subjects, Lowe says. “We’re looking at things now through a molecular and a genetic lens. That is a more cerebral pursuit. I think we’ve lost something about teaching students to love the organism.”

Staring expert named 'visionary'

Two Emory faculty members were named among the “50 Visionaries Who Are Changing Your World” by the Utne Reader: His Holiness the Dalai Lama, whose vision sparked the Emory-Tibet Science Initiative, and Rosemarie Garland-Thomson, social critic and author of “Staring: How We Look.”

In the first book on the basic human interaction of the prolonged gaze, Garland-Thomson borrows from psychology, biology and imaginative culture to explain why staring is such a powerful impulse. She writes that people with disabilities, who are so often subjected to second looks, can take control by helping to change the perception of starers.

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Fish vision makes waves in natural selection

Emory researchers have identified the first fish known to have switched from ultraviolet vision to violet vision, or the ability to see blue light. The discovery is also the first example of an animal deleting a molecule to change its visual spectrum.

Their findings on scabbardfish, linking molecular evolution to functional changes and the possible environmental factors driving them, are in the current issue of the Proceedings of the National Academy of Sciences.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says evolutionary geneticist Shozo Yokoyama, who led the study. “Building on this framework will take studies of natural selection to the next level.”

The research team included Takashi Tada, a post-doctoral fellow in biology, and Ahmet Altun, a post-doctoral fellow in biology and computational chemistry.

For two decades, Yokoyama has done groundbreaking work on the adaptive evolution of vision in vertebrates. Vision serves as a good study model, since it is the simplest of the sensory systems. For example, only four genes are involved in human vision.

"It's amazing, but you can mix together this small number of genes and detect a whole color spectrum," Yokoyama says. "It's just like a painting."

The common vertebrate ancestor possessed UV vision. However, many species, including humans, have switched from UV to violet vision, or the ability to sense the blue color spectrum.


Fish provide clues for how environmental factors can lead to such vision changes, since the available light at various ocean depths is well quantified. All fish previously studied have retained UV vision, but the Emory researchers found that the scabbardfish has not. To tease out the molecular basis for this difference, they used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.

“Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted,” Yokoyama says.

“The finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” he adds. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet vision.”

Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light.

"Evolutionary biology is filled with arguments that are misleading, at best," Yokoyama says. "To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment." 

Last year, Yokoyama and collaborators completed a comprehensive project to track changes in the dim-light vision protein opsin in nine fish species, chameleons, dolphins and elephants, as the animals spread into new environments and diversified over time. The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes.

Their results provided a reference framework for further research, and helped bring to light the limitations of studies that rely on statistical analysis of gene sequences alone to identify adaptive mutations in proteins.

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Averting the next food crisis

While the United States battles an obesity epidemic, people in some areas of the globe face a daily struggle to find nutritionally adequate and safe foods. Emory anthropologists Craig Hadley and Kenneth Maes wrote an article for The Lancet, proposing a new global monitoring system for food insecurity:

"The theme of this year's World Food Day on Oct 16, 'Achieving food security in times of crisis,' reflects the tremendous interest in food insecurity raised by the 2008 food crisis. Yet, as the world confronts the links between global food insecurity and crises, we still have little systematic knowledge about who was affected by the 2008 food crisis and to what extent. The lack of timely data, and the failure to account for heterogeneity in human responses, have led to general predictions that are surely inaccurate and have prevented a nuanced understanding of the crisis. This lack of knowledge is rooted in methodological and conceptual shortcomings."

Read the whole article.

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