The Road to a Tastier Tomato

This week, I discovered that I’ve lived life deprived of a good tomato.

As a tomato-lover, I was surprised to learn from Professor Harry Klee of the University of Florida that the supermarket tomatoes I’ve enjoyed throughout my 18-year existence are all flavorless compared to the tomatoes of the past. He spoke at Duke as a guest of the University Program in Genetics and Genomics on Feb. 28.

It turns out that commercial tomato growers, by breeding more profitable (i.e. higher-yield, redder-color, larger-fruit) tomato varieties over the past 50 years, inadvertently excluded what Klee believes is the most important tomato trait of all:

Commercial tomato growers have bred larger, redder tomatoes that are less flavorful than heirloom and older varieties. Image courtesy of Harry Klee.

Flavor.

Apparently, I was one of very few people unaware of this issue. The public outcry in response to the increasing flavorlessness of commercial tomatoes began over a decade ago, when Klee first began to study tomato genetics.

From his research, Klee has drawn several important, unexpected conclusions, chief among them:

1: Flavor has more to do with smell than taste;

2: Lesser-known biochemical compounds called “volatiles” influence the flavor of tomatoes more than sugars, acids, and other well-known, larger compounds;

3: These “volatiles” are less present in modern tomato varieties than in tastier, older, and heirloom varieties;

But fear not—

4: Tomatoes can be back-bred to regain the genes that code for volatile compounds.

In other words, Klee has mapped the way back to the flavorful tomatoes of the past. His work culminated in a cover story of the Jan. 27 issue of Science. The corresponding paper describing the analysis of over 300 tomato strains to identify the chemicals associated with “good” and “bad” tomatoes.

Dr. Harry Klee and collaborators in his lab at the University of Florida. Image courtesy of Harry Klee.

To prove that modern tomatoes have less of the compounds that make them tasty, Klee and his team recruited a panel of 100 taste-testers to rank 160 representative tomato varieties. According to Klee, the team “developed statistical models to explain the chemistry of ‘liking’ [tomatoes],” then narrowed down the list of compounds that correlated with “liking” from 400 to 26. After tracing these 26 compounds to genetic loci, they used whole-genome sequencing to show that these loci are less expressed in modern tomatoes than in “cerasiforme” (i.e. old) and heirloom tomato varieties.

Further studies showed that tomato weight is inversely correlated with sugar content—in other words, “a gigantic fruit doesn’t taste as good,” Klee said.

If Klee can convince tomato growers that consumers value flavor over size, color, and quantity, then he might just single-handedly put flavorful tomatoes back on the shelves. Nevertheless—and despite the publicity surrounding his work—Klee understands it make take a while before commercial tomato growers see the light.

Klee and his team of scientists have genetically mapped the way back to the tasty tomatoes of the past. Image courtesy of Harry Klee.

“Growers get no more money if the tomato tastes good or bad; they’re paid for how many pounds of red objects they put in a box…[but] we can’t just blame the modern breeders. We’ve been selecting bigger and bigger fruit for millennia, and that has come at the cost of reducing flavor,” Klee said.

Post by Maya Iskandarani

3D-Printable Material Sets Terminator’s Eyes Aglow

Pumpkins just not cutting it for you this year?

If you want a unique, hand-made Halloween decoration – and happen to have access to a 3D printer – Duke graduate student Patrick Flowers has just the project for you: this 3D-printed Terminator head, complete with shining, blood-red eyes.

Flowers, a PhD candidate in Benjamin Wiley’s lab, is not spending his time studying early eighties action flicks or the Governator’s best break-out roles. Instead, he and his labmates are working hard to brew up highly-conductive, copper-based materials that can be 3D printed into multilayer circuits – just like the one powering this Terminator’s glowing LED eyes.

Their latest copper concoction, which they have named “Electrifi,” is about 100 times more conductive than other materials on the market. The team has a taken out a provisional patent on Electrifi and also started a company, named Multi3D, where 3D-printing aficionados can purchase the material to include in their very own devices.

Micro CT scan of the 3D Terminator head

This X-ray view of Terminator’s head, collected with Duke SMIF’s Micro CT scanner, shows the embedded 3D circuit powering his LED eyes.

Creating a conductive, 3D-printable material is a lot trickier than just throwing some copper into a printer and going to town, Flowers said.

“Copper is really conductive originally, but if you try to extrude it out of a hot nozzle like you have to do in order to do this 3D printing, then it quickly loses all its properties,” Flowers said. And conductive materials that can stand the heat, like silver, are too expensive to use on any sort of scale, he added.

To bring the benefits of 3D printing to the world of electric circuits, Flowers and his labmates are experimenting with mixing copper with other materials to help it stay conductive through this extrusion process.

“This lab has a long history of working with copper – copper nanowires, copper particles, copper nanoparticles – so we’ve got a lot of little tricks that we use to maintain the conductivity,” Flowers said.

The team is currently testing the limits of their new material and plans to publish their findings soon. In the meantime, Flowers is busy exploring the other capabilities of Electrifi — outside of plastic android noggins.

“The circuit inside this guy is really simple, but it does show the capabilities of the material: it is embedded, it shows that I can go down, over, up, out, and go to a couple of eyes,” Flowers said. “Now I want to expand on that and show that you can make these really complicated embedded structures that have multiple layers and multiple components, other than just LEDs.”

adding_battery

Kara J. Manke, PhD

Post by Kara Manke

Cracking a Hit-and-Run Whodunit — With Lasers

The scratch was deep, two feet long, and spattered with paint flecks. Another vehicle had clearly grazed the side of Duke graduate student Jin Yu’s silver Honda Accord.

But the culprit had left no note, no phone number, and no insurance information.

Pump-Probe-Microscope-Pigment

Duke graduate student Jin Yu used laser-based imaging to confirm the source of a large scratch on the side of her car. Paint samples from an undamaged area on her Honda Accord (top left) and a suspected vehicle (top right) gave her the unique pump-probe microscopy signatures of the pigments on each car. The damaged areas of the Honda (bottom left) and the suspected vehicle on right (bottom right) show pigment signatures from both vehicles.

The timing of the accident, the location of the scratch, and the color of the foreign paint all pointed to a likely suspect: another vehicle in her apartment complex parking lot, also sporting a fresh gash.

She had a solid lead, but Yu wasn’t quite satisfied. The chemistry student wanted to make sure her case was rock-solid.

“I wanted to show them some scientific evidence,” Yu said.

And lucky for her, she had just the tools to do that.

As a researcher in the Warren Warren lab, Yu spends her days as scientific sleuth, investigating how a laser-based tool called pump-probe microscopy can be used to differentiate between individual pigments of paint, even if they appear identical to the human eye.

The team is developing the technique as a way for art historians and conservators peer under the surface of priceless paintings, without causing damage to the artwork. But Yu thought there was no reason the technique couldn’t be used for forensics, too.

“The idea popped into my mind — car paint is made up of pigments, just like paintings,” Yu said. “So, if I can compare the pigments remaining on my car with the suspected car, and they match up, that would be a pretty nice clue for finding the suspected car.”

Using a clean set of eyebrow tweezers, Yu carefully gathered small flecks of paint from her car and from the suspected vehicle and sealed them up inside individual Ziploc bags. She collected samples both from the scratched up areas, where the paint was mixed, and from undamaged areas on both cars.

She left a note on the car, citing the preliminary evidence and stating her plan to test the paint samples. Then, back at the lab, she examined all four samples with the pump-probe microscope. Unlike a standard optical microscope, this device illuminates each sample with a precisely timed series of laser pulses; each pigment absorbs and then re-emits this laser light in a slightly different pattern depending on its chemical structure, creating a unique signature.

Optical-Microscope-and-Note

After finding the gash on her Accord (top left), Yu left a note (top right) on the car that she suspected of having caused the accident. Under an optical microscope, samples from damaged areas on the cars show evidence of the same two kinds of paint (bottom). Yu used pump-probe microscopy to confirm that the pigments in the paint samples matched.

The samples from the undamaged areas gave her the characteristic pigment signatures from both of the two vehicles.

She then looked at the paint samples taken from the scratched areas. She found clear evidence of paint pigment from the suspected car on her Honda, and clear evidence of paint pigment from her Honda on the suspected car. This was like DNA evidence, of the automotive variety.

Fortunately, the owner of the suspect vehicle contacted Yu to confess and pay to have her car fixed, without demanding the results of the paint analysis. “But it was reassuring to have some scientific evidence in case she denied the accident,” Yu said.

Yu says she had no interest in forensic science when she started the investigation, but the experience has certainly piqued her curiosity.

“I had never imagined that I can use pump-probe microscopy for forensic science before this car accident happened,” Yu said. “But I think it shows some interesting possibilities.”

Kara J. Manke, PhD

Post by Kara Manke

Finding other Earths: the Chemistry of Star and Planet Formation

In the last two decades, humanity has discovered thousands of extrasolar planetary systems. Recent studies of star- and planet-formation have shown that chemistry plays a pivotal role in both shaping these systems and delivering water and organic species to the surfaces of nascent terrestrial planets. Professor Geoffrey A. Blake in Chemistry at the California Institute of Technology talked to Duke faculty and students over late-afternoon pizza in the Physics building on the role of chemistry in star and planet formation and finding other Earth-like planets.

milky way

The Milky Way rising above the Pacific Ocean and McKay Cove off the central California coast.

In the late 18th century, French scholar Pierre-Simon Laplace analyzed what our solar system could tell us about the formation & evolution of planetary systems. Since then, scientists have used the combination our knowledge for small bodies like asteroids, large bodies such as planets, and studies of extrasolar planetary systems to figure out how solar systems and planets are formed.

The "Astronomer's periodic table," showing the relative contents of the various elements present in stars.

The “Astronomer’s periodic table,” showing the relative contents of the various elements present in stars like the sun.

In 2015, Professor Blake and other researchers investigated more into ingredients in planets necessary for the development of life. Using the Earth and our solar system as the basis for their data, they explored the relative disposition of carbon and nitrogen in each stage of star and planet formation to learn more about core formation and atmospheric escape. Analyzing the carbon-silicon atomic ratio in planets and comets, Professor Blake discovered that rocky bodies in the solar system are generally carbon-poor. Since carbon is essential for our survival, however, Blake and his colleagues would like to determine the range of carbon content that terrestrial planets can have and still have active biosystem.

Analysis of C/Si ratios in extraterrestrial bodies revealed low carbon content in the formation of Earth-like planets.

Analysis of C/Si ratios in extraterrestrial bodies revealed low carbon content in the formation of Earth-like planets.

With the Kepler mission, scientists have detected a variety of planetary objects in the universe. How many of these star-planet systems – based on measured distributions – have ‘solar system’ like outcomes? A “solar system” like planetary system has at least one Earth-like planet at approximately 1 astronomical unit (AU) from the star – where more ideal conditions for life can develop – and at least one ice giant or gas giant like Jupiter at 3-5 AU in order to keep away comets from the Earth-like planet. In our galaxy alone, there are around 100 billion stars and at least as many planets. For those stars similar to our sun, there exist over 4 million planetary systems similar to our solar system, with the closest Earth-like planet at least 20 light years away. With the rapid improvement of scientific knowledge and technology, Professor Blake estimates that we would be able to collect evidence within next 5-6 years of planets within 40-50 light years to determine if they have a habitable atmosphere.

planet

Graph displaying the locations of Earth-like planets found at 0.01-1 AU from a star, and Jupiter-like planets at 0.01-50 AU from a star.

How does an Earth and a Jupiter form at their ideal distances from a star? Let’s take a closer look at how stars and planets are created – via the astrochemical cycle. Essentially, dense clouds of gas and dust become so opaque and cold that they collapse into a disk. The disk, rotating around a to-be star, begins to transport mass in toward the center and angular momentum outward. Then, approximately 1% of the star mass is left over from the process, which is enough to form planets. This is also why planets around stars are ubiquitous.

 

The Astrochemical Cycle: how solar systems are formed.

The Astrochemical Cycle: how solar systems are formed.

How are the planets formed? The dust grains unused by the star collide and grow, forming larger particles at specific distances from the star – called snowlines – where water vapor turns into ice and solidifies. These “dust bunnies” grow into planetesimals (~10-50 km diameter), such as asteroids and comets. If the force of gravity is large enough, the planetesimals increase further in size to form oligarchs (~0.1-10 times the mass of the Earth), that then become the large planets of the solar system.

Depiction

Depiction of the snow line for planet formation.

In our solar system, a process called dynamic reorganization is thought to have occurred that restructured the order of our planets, putting Uranus before Neptune. This means that if other solar systems did not undergo such dynamic reorganization at an early point in formation of solar system, then other Earths may have lower organic and water content than our Earth. In that case, what constraints do we need to apply to determine if a water/organic delivery mechanism exists for exo-Earths? Although we do not currently have the scientific knowledge to answer this, with ALMA and the next generation of optical/IR telescopes, we will be able image the birth of solar systems directly and better understand how our universe came to be.

To the chemistry students at Duke, Professor Blake relayed an important message: learn chemistry fundamentals very carefully while in college. Over the next 40-50 years, your interests will change gears many times. Strong fundamentals, however, will serve you well, since you are now equipped to learn in many different areas and careers.

Professor Blake and the team of former and current Caltech researchers.

Professor Blake and the team of former and current Caltech researchers.

Learn more about the Blake research group or their work.

Anika_RD_hed100_2

By Anika Radiya-Dixit.

 

Middle Schoolers Ask: What’s it Like to be a Scientist?

PostdocsWhen a group of local middle schoolers asked four Duke postdocs what it’s like to be a scientist, the answers they got surprised them.

For toxicologist Laura Maurer, it means finding out if the tiny silver particles used to keep socks and running shirts from getting smelly might be harmful to your health.

For physics researcher Andres Aragoneses, it means using lasers to stop hackers and make telecommunications more secure.

And for evolutionary anthropologist Noah Snyder-Mackler, it means handling a lot of monkey poop.

The end result is a series of short video interviews filmed and edited by 5th-8th graders in Durham, North Carolina. Read more about the project and the people behind it at http://sites.duke.edu/pdocs/, or watch the videos below:

Iridescent Beauty: Development, function and evolution of plant nanostructures that influence animal behavior

Iridescent wings of a Morpho butterfly

Iridescent wings of a Morpho butterfly

Creatures like the Morpho butterfly on the leaf above appear to be covered in shimmering blue and green metallic colors. This phenomenon is called “iridescence,” meaning that color appears to change as the angle changes, much like soap bubbles and sea shells.

Iridescent behavior of a soap bubble

Iridescent behavior of a soap bubble

In animals, the physical mechanisms and function of structural color have been studied significantly as a signal for recognition or mate choice.

On the other hand, Beverley Glover believes that such shimmering in plants can actually influence animal behavior by attracting pollinators better than their non-iridescent counterparts. Glover,Director of Cambridge University Botanic Garden,  presented her study during the Biology Seminar Series in the French Family Science Center on Monday earlier this week.

Hibiscus Trionum

Hibiscus Trionum

The metallic property of flowers like the Hibiscus Trionum above are generated by diffraction grating – similar to the way CD shines – to create color from transparent material.

In order to observe the effects of the iridescence on pollinators like bees, Glover created artificial materials with a surface structure of nanoscale ridges, similar to the microscopic view of a petal’s epidermal surface below.

Nanoscale ridges on a petal's epidermal surface.

Nanoscale ridges on a petal’s epidermal surface.

In the first set of experiments, Glover and her team marked bees with paint to follow their behavior as they set the insects to explore iridescent flowers. Some were covered in a red grating – containing a sweet solution as a reward – and others with a blue iridescent grating – containing a sour solution as deterrent. The experiment demonstrated that the bees were able to detect the iridescent signal produced by the petal’s nanoridges, and – as a result – correctly identified the rewarding flowers.

Bees pollinating iridescent "flowers"

Bees pollinating iridescent “flowers”

With the evidence that the bees were able to see iridescence, Glover set out for the second experiment: once the bees find a specific type of flower, how long does it take them to find the same flower in a different location? Using the triangular arrangement of shimmering surfaces as shown below, Glover observed that iridescence produced by a diffraction grating leads to significant increase in foraging speed as compared to non-iridescent flowers.

Triangular formation of iridescent disks used for experimentation on bees

Triangular formation of iridescent disks used for experimentation on bees

While iridescence in plants is difficult to spot by a casual stroll through the garden, pollinators such as bees definitely can see it, and scientists have recently realized that insect vision and flower colors have co-evolved.

In order to ensure that pollen is transferred between flowers of the same species, these flowers have developed a unique structure of iridescence. As scientists work on understanding which plants produce these beautiful colors and how the nanoscale structure is passed down through reproduction, we can only look at our gardens in wonder at the vast amount of nature that still remains to be explored and learned.

Wonder of nature

Wonders of nature in an everyday garden

 

 

Beverley Glover is the Director of Cambridge University Botanic Garden and is currently accepting applications for PhD students

 

 

 

 

 

Post written by Anika Radiya-Dixit