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

Cells Need Their Personal Space

One of the body’s first lines of defense against harmful pathogens is the skin. The constant maintenance of this epithelial cell layer which serves as a barrier to infection  is essential to fighting off disease.

Jody Rosenblatt, an Associate Professor in the Department of Oncological Sciences at the University of Utah School of Medicine, has made it her lab’s mission to study the function of epithelia as a barrier, how this barrier is maintained, and what happens when it goes awry.

Jody Rosenblatt, PhD is an investigator for the Huntsman Cancer Institute at the University of Utah School of Medicine and a Howard Hughes Medical Institute Faculty Scholar

Rosenblatt recently spoke at Duke’s Developmental & Stem Cell Biology Colloquium where she presented some extraordinary findings about how epithelia can squeeze out  both healthy and dying cells  to preserve the protective barrier.

Some c cells commit suicide via programed cell death and are forced out of the cell layer because they are no longer functional. But in the case of forcing out living cells, “cell extrusion is more like a homicide” said Rosenblatt. The fact that perfectly functional living cells are pushed out of a cell layer perplexed her group until they discovered it was happening as a response to cell overcrowding.

Rosenblatt explained that like people, cells tend to like their personal space, so when this is compromised, live cells are actively pushed out of the cell layer, restoring balanced cell numbers.

Rosenblatt’s lab took this discovery a step farther and pinpointed the pathway that likely induces the extrusion of live cells.

Piezo1, a stretch-activated calcium ion channel present in epithelial cells, senses crowding and activates sphingosine-1-phosphate (S1P), the driver of epithelial cell extrusion. When Piezo1 channels are inhibited and don’t sense stretching, cells cannot extrude.

Using zebrafish, Rosenblatt showed that when extrusion was blocked by compromising the S1P2 pathway, epidermal cells form masses that are resistant to chemotherapy drugs and signals for programmed cell death.

Rosenblatt explains the importance of regulating cell extrusion in the epithelium to maintain the tissue’s function as a protective barrier for our organs. Misregulation of this function can result in diseases such as metastatic cancers.

This finding lead them to examine samples of human pancreatic, lung, colon, and breast tumors. They found that in all of these cancers, S1P2 is significantly reduced. But if they restored S1P2 activity in cell lines of these cancers, the extrusion pathway was rescued and tumor size and metastases were greatly decreased!

Rosenblatt and her colleagues have shown that the importance of cell extrusion cannot be overstated. If extrusion is compromised, cells can begin to pile up and move beneath the cell layer, which can lead to invasion of the tissues beneath the epithelium and metastasis to other sites in the body.

Now that we are uncovering more of the pathways involved in tumor formation and metastasis, we can develop new drugs that may be the key to fighting these devastating diseases.

Guest Post by Amanda Cox, PhD candidate in biology

 

Young Scientists, Making the Rounds

“Can you make a photosynthetic human?!” an 8th grader enthusiastically asks me while staring at a tiny fern in a jar.

He’s not the only one who asked me that either — another student asked if Superman was a plant, since he gets his power from the sun.

These aren’t the normal questions I get about my research as a Biology PhD candidate studying how plants get nutrients, but they were perfect for the day’s activity –A science round robin with Durham eighth-graders.

Biology grad student Leslie Slota showing Durham 8th graders some fun science.

After seeing a post under #scicomm on Twitter describing a public engagement activity for scientists, I put together a group of Duke graduate scientists to visit local middle schools and share our science with kids. We had students from biomedical engineering, physics, developmental biology, statistics, and many others — a pretty diverse range of sciences.

With help from David Stein at the Duke-Durham Neighborhood Partnership, we made connections with science teachers at the Durham School of the Arts and Lakewood Montessori school, and the event was in motion!

The outreach activity we developed works like speed dating, where people pair up, talk for 3-5 mins, and then rotate. We started out calling it “Science Speed Dating,” but for a middle school audience, we thought “Science Round-Robin” was more appropriate. Typically, a round-robin is a tournament where every team plays each of the other teams. So, every middle schooler got to meet each of us graduate students and talk to us about what we do.

The topics ranged from growing back limbs and mapping the brain, to using math to choose medicines and manipulating the different states of matter.

The kids were really excited for our visit, and kept asking their teachers for the inside scoop on what we did.

After much anticipation, and a little training and practice with Jory Weintraub from the Science & Society Initiative, two groups of 7-12 graduate students armed themselves with photos, animals, plants, and activities related to our work and went to visit these science classes full of eager students.

First-year MGM grad student Tulika Singh (top right) brought cardboard props to show students how antibodies match up with cell receptors.

“The kids really enjoyed it!” said Alex LeMay, middle- and high-school science teacher at the Durham School of the Arts. “They also mentioned that the grad students were really good at explaining ideas in a simple way, while still not talking down to them.”

That’s the ultimate trick with science communication: simplifying what we do, but not talking to people like they’re stupid.

I’m sure you’ve heard the old saying, “dumb it down.” But it really doesn’t work that way. These kids were bright, and often we found them asking questions we’re actively researching in our work. We don’t need to talk down to them, we just need to talk to them without all of the exclusive trappings of science. That was one thing the grad students picked up on too.

“It’s really useful to take a step back from the minutia of our projects and look at the big picture,” said Shannon McNulty, a PhD candidate in Molecular Genetics and Microbiology.

The kids also loved the enthusiasm we showed for our work! That made a big difference in whether they were interested in learning more and asking questions. Take note, fellow scientists: share your enthusiasm for what you do, it’s contagious!

Another thing that worked really well was connecting with the students in a personal way. According to Ms. LeMay, “if the person seemed to like them, they wanted to learn more.” Several of the grad students would ask each student their names and what they were passionate about, or even talk about their own passions outside of their research, and these simple questions allowed the students to connect as people.

There was one girl who shared with me that she didn’t know what she wanted to do when she grew up, and I told her that’s exactly where I was when I was in 8th grade too. We then bonded over our mutual love of baking, and through that interaction she saw herself reflected in me a little bit; making a career in science seem like a possibility, which is especially important for a young girl with a growing interest in science.

Making the rounds in these science classrooms, we learned just as much from the students we spoke to as they did from us. Our lesson being: science outreach is a really rewarding way to spend our time, and who knows, maybe we’ll even spark someone who loves Superman to figure out how to make the first photosynthesizing super-person!

Guest post by Ariana Eily , PhD Candidate in Biology, shown sharing her floating ferns at left.

 

Seeing Nano

Take pictures at more than 300,000 times magnification with electron microscopes at Duke

Sewer gnat head

An image of a sewer gnat’s head taken through a scanning electron microscope. Courtesy of Fred Nijhout.

The sewer gnat is a common nuisance around kitchen and bathroom drains that’s no bigger than a pea. But magnified thousands of times, its compound eyes and bushy antennae resemble a first place winner in a Movember mustache contest.

Sewer gnats’ larger cousins, horseflies are known for their painful bite. Zoom in and it’s easy to see how they hold onto their furry livestock prey:  the tiny hooked hairs on their feet look like Velcro.

Students in professor Fred Nijhout’s entomology class photograph these and other specimens at more than 300,000 times magnification at Duke’s Shared Material & Instrumentation Facility (SMIF).

There the insects are dried, coated in gold and palladium, and then bombarded with a beam of electrons from a scanning electron microscope, which can resolve structures tens of thousands of times smaller than the width of a human hair.

From a ladybug’s leg to a weevil’s suit of armor, the bristly, bumpy, pitted surfaces of insects are surprisingly beautiful when viewed up close.

“The students have come to treat travels across the surface of an insect as the exploration of a different planet,” Nijhout said.

Horsefly foot

The foot of a horsefly is equipped with menacing claws and Velcro-like hairs that help them hang onto fur. Photo by Valerie Tornini.

Weevil

The hard outer skeleton of a weevil looks smooth and shiny from afar, but up close it’s covered with scales and bristles. Courtesy of Fred Nijhout.

fruit fly wing

Magnified 500 times, the rippled edges of this fruit fly wing are the result of changes in the insect’s genetic code. Courtesy of Eric Spana.

You, too, can gaze at alien worlds too small to see with the naked eye. Students and instructors across campus can use the SMIF’s high-powered microscopes and other state of the art research equipment at no charge with support from the Class-Based Explorations Program.

Biologist Eric Spana’s experimental genetics class uses the microscopes to study fruit flies that carry genetic mutations that alter the shape of their wings.

Students in professor Hadley Cocks’ mechanical engineering 415L class take lessons from objects that break. A scanning electron micrograph of a cracked cymbal once used by the Duke pep band reveals grooves and ridges consistent with the wear and tear from repeated banging.

cracked cymbal

Magnified 3000 times, the surface of this broken cymbal once used by the Duke Pep Band reveals signs of fatigue cracking. Courtesy of Hadley Cocks.

These students are among more than 200 undergraduates in eight classes who benefitted from the program last year, thanks to a grant from the Donald Alstadt Foundation.

You don’t have to be a scientist, either. Historians and art conservators have used scanning electron microscopes to study the surfaces of Bronze Age pottery, the composition of ancient paints and even dust from Egyptian mummies and the Shroud of Turin.

Instructors and undergraduates are invited to find out how they could use the microscopes and other nanotech equipement in the SMIF in their teaching and research. Queries should be directed to Dr. Mark Walters, Director of SMIF, via email at mark.walters@duke.edu.

Located on Duke’s West Campus in the Fitzpatrick Building, the SMIF is a shared use facility available to Duke researchers and educators as well as external users from other universities, government laboratories or industry through a partnership called the Research Triangle Nanotechnology Network. For more info visit http://smif.pratt.duke.edu/.

Scanning electron microscope

This scanning electron microscope could easily be mistaken for equipment from a dentist’s office.

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Post by Robin Smith

Totally Tubular! Fluid forces that affect the development of biological tubes

Have you ever wondered how something as simple as fluid can impact the development of a large organism? How about the way tubes form in relation to each other? Or maybe you’ve wondered how it is possible for something as rigid as a spine to be formed from fluid?

Zebrafish embryos are relatively transparent, making them easier to study.

Zebrafish embryos are relatively transparent, making them easier to study.

Dr. Michel Bagnat and his lab work to analyze each of these questions and more in their research about how biological tubes are formed and how pressure exerted by these fluids affects the formation of these tubes.

Dr. Bagnat, an associate professor of cell biology, uses ‘forward genetics,’ a process by which genes are modified in order to see the effect and function of each gene in the organism. The technique enables them to identify and analyze the role of fluid secretion in zebrafish. Fluid secretion also plays a role in many human diseases, including cystic fibrosis and polycystic kidney disease.

The void in a blood vessel is called the lumen. Bagnat studies the cells lining the lumen.

The void in a blood vessel is called the lumen. Bagnat studies the cells lining the lumen.

One of the most interesting aspects of tubal formation is that biological tubes often form in relation to each other. Dr. Bagnat and his lab study this type of tubal formation through studying the lumen, or the thin membrane lining the intestinal tubes of zebrafish. There are many cellular mechanisms that can affect the formation of the lumen, and extensive research is conducted in order to better understand these mechanisms.

These same sorts of forces can even help build a structure as complex as the spine. Dr. Bagnat’s research covers this specific field. The notochord of zebrafish, or the scaffold which will develop into a spine, is heavily affected by the growth of vacuoles, or fluid-filled sacs in the cell. Dr. Bagnat’s research explores the deeper mechanisms behind the filling of these fluid vacuoles in cells and how each cell’s vacuole stops and starts filling with fluid.

This image of fluid-filled sacs forming a fish notochord was on the cover of a journal.

This image of fluid-filled sacs forming a fish notochord was on the cover of a journal.

Overall, Dr. Bagnat’s research holds strong implications for how we understand the development and formation of biological tubes not just in zebrafish but in our own human bodies.

Guest Post by Vaishnavi Siripurapu, North Carolina School of Math and Science, Class of 2018

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Life Lessons from a Neuroscientist

I recently had the privilege of sitting down with Dr. Anne Buckley, a professor and  neuropathologist working in Dr. Chay Kuo’s cell biology lab at Duke. I got a first-hand account of her research on neuron development and function in mice. But just as fascinating to me were the life lessons she had learned during her time as a researcher.

Anne Buckley, M.D. Ph.D., is an assistant professor of pathology

Anne Buckley, M.D. Ph.D., is an assistant professor of pathology

Buckley’s research looks at brain tumors in mice. She recently found that some of the mice developed the tumors in an area full of neurons, the roof of the fourth ventricle, which is of particular interest because humans have developed tumors in the same location. This discovery could show how neurological pathways affect tumor formation and progression.

Buckley also gave me some critical words of advice, cautioning me that research isn’t for everyone.

“Research is not glamorous, and not always rewarding,” she warned me. When she first started research, Buckley learned a hard lesson: work doesn’t necessarily lead to results. “For every question I went after, I found ten more unresolved,” she said. “To be a researcher, it takes a lot of perseverance and resilience. A lot of long nights.”

But that’s also the beauty of research. Buckley says that she’s learned to find happiness in the small successes, and that she “enjoys the process, enjoys the challenge.”

And when discoveries happen?

“When I look at data, and I see something unexpected, I get really excited,” she says. “I know something that no one else knows. Tomorrow, everyone will know. But tonight, I’m the only person in the world who knows.”

kendra_zhong_headshotGuest Post by Kendra Zhong, North Carolina School of Science and Math, Class of 2017