Chemistry Center ignites celebration of science

“Why do I have a garbage can full of liquid nitrogen? Because I’m a chemist,” Doug Mulford, director of undergraduate education for Emory’s Department of Chemistry, told a crowd of enthralled children and adults.

Decked out in safety glasses and a red lab coat printed with flames, Mulford conducted a ribbon immolation ceremony on Saturday, to officially open Emory’s Sanford S. Atwood Chemistry Center addition. The crowd gasped and cheered in the courtyard as Mulford ignited a thermite reaction, a pyrotechnic mixture of aluminum and iron oxide. The reaction shot off sparks and smoking-hot globules of molten iron to sever the ceremonial ribbon.

Rain did not dampen anyone’s enthusiasm for the grand opening, which included fun science demonstrations by students from chemistry, biology and physics.

In fact, chemists love water droplets and clouds. Graduate students from Emory’s Pi Alpha Chemical Society showed how to make both, using liquid nitrogen.

“We’re pouring really hot water into really cold liquid nitrogen, causing it to expand into a plume of air that comes up as a cloud,” explained Daniel Collins-Wildman, who braved nature’s drizzle in the courtyard along with fellow graduate student Amanda Dermer.

In fact, Collins-Wildman said, the liquid nitrogen is so cold (77 Kelvin) that ice particles form in the cloud, creating what is known as a nucleation site where water drops can form.

“I conducted an experiment with this by accident once, when I was making macaroni and cheese,” he said. He brought the water to a roiling boil. As usual, bubbles formed along the sides of the pot, where the temperature is higher and the pot’s irregular surface creates the potential for nucleation. Then the power went out. The bubbles on the sides of the pot disappeared. The water was still hot when he turned the heat back on. Without the small bubbles acting as nucleation sites the water boiled violently, a phenomenon known in chemistry as "bumping."

"I heard this weird sound," Collins-Wildman said. "All those little bubbles that had formed slowly before, this time formed immediately as one huge bubble that came to the surface with a BLURP!”

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Leaping molecules! How a frog evolved violet vision

The story of the evolution of color vision in the African clawed frog, above, "is full of mysterious twists and turns," says evolutionary biologist Shozo Yokoyama. Photo by Brian Gratwicke.

By Carol Clark

The African clawed frog is tongue-less, has long, curvy toes and eyes that are perched on top of its head, but that’s not all that’s odd about it. This species of frog also took a strange evolutionary path to change from ultraviolet to violet vision: Some of its visual pigment molecules kept trying to leap ahead, but other molecules shut them down and kept the process moving at a crawl. 

Science Advances published the complete molecular interactions involved in the pathway, as detailed in a study led by Shozo Yokoyama, a biologist at Emory University who specializes in adaptive evolution of vision.

“It’s the most bizarre, and sophisticated, case of color vision evolution that I’ve ever encountered,” says Yokoyama, who previously headed up efforts to construct the most extensive evolutionary tree for vision, including 500 species of animals, from eels to humans.

“This frog had these quirks for rapid molecular change, but it also had something to control these quirks,” he says. “In fact, it had triple protection.”

Five classes of opsin genes encode visual pigments for dim-light and color vision. Bits and pieces of the opsin genes change and vision adapts as the environment of a species changes.

Ultraviolet (UV) vision gives a bi-chromatic, high-contrast view of the world that can be useful for many basic behaviors. Mice, for instance, are mainly nocturnal and mark their territory with urine and feces that reflects UV light for other mice. Unfortunately for mice, however, many of their predators are also UV sensitive so they, too, can spot these signs of mice more easily.

Violet vision, or the ability to see blue light, provides better resolution and detail for colors in a scene. Among the possible reasons that frogs evolved from UV to violet sensitivity may have been to give them a better view of potential mates. It may also have improved their ability to pick out predators – such as a green snake amid green leaves.

In other recent research, Shozo Yokoyama, above, finished the first detailed and complete picture of the evolution of human vision. Photo by Bryan Meltz, Emory Photo/Video.

In previous research on the African clawed frog (Xenopus laevis), Yokoyama and collaborators had identified some of the genetic mutations involved in the process of the frog’s switch from UV vision to its current function of violet vision. They also noticed that amino acid site 113 on this pigment of the African clawed frog had changed from glutamic acid to aspartic acid.

“Out of all the species in the animal kingdom that have been studied, site 113 is made up of glutamic acid, but this frog had changed site 113 to aspartic acid,” Yokoyama says. “Why did it do that? This question was very mysterious and interesting to me. What is so special about this frog?”

Yokoyama studies ancestral molecules to tease out secrets of adaptive evolution. The lengthy process involves teams of collaborators to first estimate and synthesize ancestral proteins and pigments of a species, then conduct experiments on them. The technique combines microbiology with theoretical computation, biophysics, quantum chemistry and genetic engineering.

For the current paper, he and his co-authors found that 12 mutations were involved in the frog’s vision shift. These 12 molecular changes could have 500 million possible combinations of pathways that connect the ancestral UV vision and the frog’s violet vision. The researchers narrowed the problem down and focused on changes in the six layers of transmembranes where the 12 molecules in the process are located. That focus reduced the number of possible evolutionary pathways to 720.

They then assembled molecular “chimeras” between the ancestral and frog pigments for all of these pathways. They tested how the molecules functioned in all the different combinations, to hone in on the right pathway.

The results showed that the mutations that occurred on transmembranes four, five and six happened early during the evolutionary process. It was not until eons later, however, that these mutations came into play.

The mutations occurring on transmembrane two caused small shifts in the range of the light spectrum that the pigment detected. The mutations occurring early in evolution on transmembrane three, however, where site 113 resides, caused a big jump in the light-wave range – from 400 nanometers to 600 nanometers. 

“Rapid change is not convenient evolutionarily,” Yokoyama says. “In fact, it can be a disaster.” 

He uses the example of emerging from a darkened movie theater on a sunny day, and being temporarily blinded until your eyes adjust to the new environment.

Three times, molecules on transmembrane three mutated to cause a big jump toward violet sensitivity. The first time it happened, transmembrane five came into play, shrinking the molecular structure of the pigment and making it non-functional.

The second time that transmembrane three mutated, launching another jump, transmembrane six sprang into action, again shrinking the molecular structure.

The third time transmembrane three tried to make the evolutionary leap, number four shut it down by destroying a critical chemical structure of the pigment.

The frog pigment essentially put on the brakes early during the evolutionary process for the mutations from glutamic acid to aspartic acid at site 113. Only towards the end of the process did the pigment accept the site 113 shifts. By then, Yokoyama explains, the changes to the frog’s light spectrum were no longer a big jump. Instead, they were just 15 nanometers.

“The human process for evolving from UV to violet vision was far more simple and straight-forward,” Yokoyama says. “The story of this frog is full of mysterious twists and turns. A series of strange coincidences happened at the right time, at the right spot, for the right species.”

Yokoyama’s co-authors for the current paper include Emory biologists Huiyong Jia, Takashi Koyama, Davide Faggionato and Yang Liu; and Ahmet Altun of Faith University in Istanbul and William Starmer of Syracuse University.

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A clear, molecular view of the evolution of human color vision

In U.S. politics, does narcissism trump all?

Donald Trump at a recent campaign rally. Photo by Michael Vadon.

Emory psychologist Scott Lilienfeld and his graduate student Ashley Watts recently co-authored an opinion piece for the New York Times entitled "The Narcissist in Chief." Below is an excerpt:

"The political rise of Donald J. Trump has drawn attention to one personality trait in particular: narcissism. Although narcissism does not lend itself to a precise definition, most psychologists agree that it comprises self-centeredness, boastfulness, feelings of entitlement and a need for admiration. We have never met Mr. Trump, let alone examined him, so it would be inappropriate of us to offer a formal assessment of his level of narcissism. And in all fairness, today’s constant media attention makes a sizable ego a virtual job requirement for public office. Still, the Trump phenomenon raises the question of what kinds of leaders narcissists make. Fortunately, a recent body of research has suggested some answers.

"In a 2013 article in Psychological Science, we and our colleagues approached this question by studying the 42 United States presidents up to and including George W. Bush. ...

"We found that narcissism, specifically 'grandiose narcissism' — an amalgam of flamboyance, immodesty and dominance — was associated with greater overall presidential success. (This relation was small to moderate in magnitude.) The two highest scorers on grandiose narcissism were Lyndon B. Johnson and Theodore Roosevelt, the two lowest James Monroe and Millard Fillmore."

Read the whole article in the New York Times.

If you'd like to hear more on the topic, Ashley Watts will be giving a talk titled "Should We Worry about a Narcissist in the Oval Office?" on Thursday, September 17, as part of this month's Nerd Nite Atlanta. The line-up of three speakers starts at 8 pm at Manuel's Tavern.

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Geneticist studies how plants cope with drought

 

By Carol Clark

California produces two-thirds of the fresh fruits and vegetables consumed in the U.S. As the worst drought in the state’s history continues, it is turning into a testing ground for how the world will cope with the clash of growing populations, dwindling water resources and a changing climate.

“California has all of these water-intensive crops growing in a drought-stricken area where the groundwater is also drying up,” says Roger Deal, a geneticist at Emory University who researches the ways plants build and adapt their bodies. “At the same time, the climate is changing. Obviously, something has got to give.”

Deal is among a consortium of scientists, funded by the National Science Foundation’s Plant Genome Research program, who are doing collaborative studies on how plants cope with weather extremes.

“If you look across a range of different plant species they have very different levels of tolerance to drought,” Deal says. “There is clearly something genetic and physiological about those differences. We’re trying to understand the mechanisms at play for how plants deal with the stresses of weather extremes, and how they succeed or don’t succeed.”

Medicago truncatula

One group in the consortium is looking at strains of rice, while another is focused on two different species of tomatoes: One wild and one domestic. The Deal lab is researching Medicago truncatula, a close relative of alfalfa.

Alfalfa is an important forage crop for livestock around the world and is also part of the legume family, so it serves as a model for an entire group of plants that are agriculturally relevant to humans.

The last common ancestor between rice and alfalfa goes back at least 300 million years. The consortium is looking at plants that cover this huge evolutionary span of time to see similarities and differences in the type of stress responses in different cell types in roots – the first line of a plant’s defense.

“Plants can actually remember when they’ve been exposed to drought,” Deal says. “If you restrict the amount of water an alfalfa plant receives, it’s going to begin to wilt. Then, if you water it and bring it back to life, it’s basically more resistant to drought. We’re trying to learn the basis of this remembrance. Plants don’t have a brain, but somehow their cells remember when they’ve been exposed to drought so they can be ready when it happens again.”

Research into plant genetics is only one aspect of what we may need to do to cope in a world where weather extremes are becoming more common. The geography of agriculture may also have to change, along with people’s eating habits.

“We’ve gotten into this situation where we’re completely cut off from where our food comes from,” Deal says. “When we go to the grocery story, we expect to have a huge variety of fresh fruits and vegetables available, no matter the season. Maybe we should only be getting fresh peaches in the summer.”

Image of Medicago truncatula via ninjatacoshell/Wikipedia

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