Duke Research Blog

Following the people and events that make up the research community at Duke.

Category: Guest Post (Page 2 of 14)

Where Some Ski, Others Do Science

For most people, Lost Trail is a ski spot located at 7,000 feet in the Rocky Mountains on the border of Idaho and Montana. Skiers and snowboarders descend down steep slopes, past forests and alpine meadows that get more than 25 feet of snow each year. But for a team of researchers led by Duke biology professor Thomas Mitchell-Olds, buried beneath the snow is a hidden population of native plants on the cusp of dividing into two new species.

Molly Rivera-Olds shovels snow at Lost Trail Pass.

Studying a spindly North American wildflower called Boechera stricta, Mitchell-Olds and colleagues suspected that a process called chromosomal inversion — in which part of a chromosome breaks off and reattaches itself upside down — plays a central role in speciation. To test the idea, they planted Boechera stricta seedlings in a mountaintop meadow near the Lost Trail resort.

To reach the meadow, the researchers carried thousands of seedlings up the mountain in specially constructed backpacks. They also lugged up nine empty garbage cans and filled them with snow to water the plants throughout the summer.

Once the seedlings matured, the researchers measured flowering time, seed production, and survival. They found that plants with the chromosomal inversion had a leg up on the steep slopes of the Rocky Mountains. Eventually, the researchers say, this can lead to plants with the inverted DNA splitting off and forming a new species.

The findings were published April 3, 2017 in the journal Nature Ecology & Evolution.

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CITATION:  “Young Inversion with Multiple Linked QTLs Under Selection in a Hybrid Zone,” Cheng-Ruei Lee, Baosheng Wang et al. Nature Ecology & Evolution, April 3, 2017. DOI:10.1038/s41559-017-0119.

Guest post by Molly Rivera-Olds

 

 

 

 

 

Durham Students Give Themselves a Hand Up

Picture this: a group of young middle schoolers are gathered trying to get a “hand” they’ve built out of drinking straws, thread and clay to grasp a small container. What could such a scene possibly have to do with encouraging kids to stay in school and pursue science? It turns out, quite a lot!

brothers keeper

Angelo Moreno (right), a graduate student in molecular genetics and microbiology, helps students with their soda straw hand.

This scene was part of an event designed just for boys from Durham schools that took place one March evening at the Durham Marriot and Convention Center. It was hosted by Made in Durham, a local non-profit focused on helping Durham’s young people graduate from high school, go to college, and ultimately be prepared for their careers, and My Brother’s Keeper Durham, the local branch of former President Obama’s mentoring initiative for young men of color.

The first evening of a convention centered on building equity in education and was geared toward career exploration. Each of the boys got to choose from a series of workshops that highlighted careers in science, technology, engineering, art, and mathematics — also known as STEAM. The workshops ranged from architectural design to building body parts, which was where they learned to build the artificial hands.

Sharlini Sankaran, the executive director of Duke’s Regeneration Next Initiative, who heard about my outreach activities from earlier this year, contacted me, and together we drummed up a group of scientists for the event.

With the help of Victor Ruthig in Cell Biology, Angelo Moreno in Molecular Genetics and Microbiology, Ashley Williams in Biomedical Engineering, and Devon Lewis, an undergraduate in the Biology program, we dove into the world of prosthetics and tissue engineering with the young men who came to our workshop.

Biology undergrad Devon Lewis (top) worked with several of the students.

After some discussion on what it takes to build an artificial body part, we let the boys try their hand at building their own. We asked them what the different parts of the hand were that allowed us to bend them and move them in certain ways, and from there, they developed ideas for how to turn our household materials into fully functioning hands. We used string as tendons and straws as finger bones, cutting notches where we wanted to create joints.

There was a lot of laughter in the room, but also a lot of collaboration between the different groups of kids. When one team figured out how to make a multi-jointed finger, they would share that knowledge with other groups. Similar knowledge sharing happened when one group figured out how to use the clay to assemble all their fingers into a hand. Seeing these young men work together, problem solve, and be creative was amazing to watch and be a part of!

According to feedback from event organizers, “ours was the most popular session!” Sharlini said. When we reached the end of our session, the kids didn’t want to leave, and instead wanted to keep tinkering with their hands to see what they could accomplish.

The boys had a lot of fun, asked a lot of good questions, and got to pick our brains for advice on staying in school and using it to propel them towards career success. I have distilled some of the best pieces of advice from that night, since they’re good for everyone to hear:

  • Don’t be afraid to ask a lot of questions.
  • Don’t be discouraged when someone tells you no. Go for it anyways.
  • Don’t be afraid of failure.
  • And don’t think you have to fit a particular mold to succeed at something.

“I left feeling really inspired about our future generation of scientists and engineers,” Sharlini said. ”It’s good to know there are so many Duke students with the genuine and selfless desire to help others.”

It was a joy to participate in this event. We all had fun, and left having learned a lot — even the parents who came with their sons!

Outreach like this is incredibly important. Being mentors for young people with a budding interest in science can make the difference between them pursuing it further or dropping it altogether. Engaging with them to show them the passion we have for our work and that we were kids just like they are allows them to see that they can do it too.

Guest Post by Ariana Eily

Mental Shortcuts, Not Emotion, May Guide Irrational Decisions

If you participate in a study in my lab, the Huettel Lab at Duke, you may be asked to play an economic game. For example, we may give you $20 in house money and offer you the following choice:

  1. Keep half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In such a scenario, most participants choose 1, preferring a sure win over the gamble.

Now imagine this choice, again starting with $20 in house money:

  1. Lose half of the $20 for sure
  2. Flip a coin: heads you keep all $20; tails you lose all $20

In this scenario, most participants prefer the gamble over a sure loss.

If you were paying close attention, you’ll note that both examples are actually numerically identical – keeping half of $20 is the same as losing half of $20 – but changing whether the sure option is framed as a gain or a loss results in different decisions to play it safe or take a risk. This phenomenon is known as the Framing Effect. The behavior that it elicits is weird, or as psychologists and economists would say, “irrational”, so we think it’s worth investigating!

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

Brain activity when people make choices consistent with (hot colors) or against (cool colors) the Framing Effect.

In a study published March 29 in the Journal of Neuroscience, my lab used brain imaging data to test two competing theories for what causes the Framing Effect.

One theory is that framing is caused by emotion, perhaps because the prospect of accepting a guaranteed win feels good while accepting a guaranteed loss feels scary or bad. Another theory is that the Framing Effect results from a decision-making shortcut. It may be that a strategy of accepting sure gains and avoiding sure losses tends to work well, and adopting this blanket strategy saves us from having to spend time and mental effort fully reasoning through every single decision and all of its possibilities.

Using functional magnetic resonance imaging (fMRI), we measured brain activity in 143 participants as they each made over a hundred choices between various gambles and sure gains or sure losses. Then we compared our participants’ choice-related brain activity to brain activity maps drawn from Neurosynth, an analysis tool that combines data from over 8,000 published fMRI studies to generate neural maps representing brain activity associated with different terms, just as “emotions,” “resting,” or “working.”

As a group, when our participants made choices consistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental disengagement (i.e. “resting” or “default”). When they made choices inconsistent with the Framing Effect, their average brain activity was most similar to the brain maps representing mental engagement (i.e. “working” or task”). These results supported the theory that the Framing Effect results from a lack of mental effort, or using a decision-making shortcut, and that spending more mental effort can counteract the Framing Effect.

Then we tested whether we could use individual participants’ brain activity to predict participants’ choices on each trial. We found that the degree to which each trial’s brain activity resembled the brain maps associated with mental disengagement predicted whether that trial’s choice would be consistent with the Framing Effect. The degree to which each trial’s brain activity resembled brain maps associated with emotion, however, was not predictive of choices.

Our findings support the theory that the biased decision-making seen in the Framing Effect is due to a lack of mental effort rather than due to emotions.

This suggests potential strategies for prompting people to make better decisions. Instead of trying to appeal to people’s emotions – likely a difficult task requiring tailoring to different individuals – we would be better off taking the easier and more generalizable approach of making good decisions quick and easy for everyone to make.

Guest post by Rosa Li

Venturing Out of the Lab to Defend Science

It’s 6 p.m. on a Wednesday and the grad students aren’t at their lab benches. IM softball doesn’t start till next week, what gives?

We’ve snuck out of our labs a bit early to take in a dose of U.S. policy for the evening.

Politics fall far outside our normal areas of expertise. I’m a biology Ph.D. student studying plants — even with my liberal arts education, politics isn’t my bread and butter.

Buz Waitzkin of Science & Society (blue shirt) gave grad students a highly accelerated intro to matters of science policy.

But the current political climate in the U.S. has many scientists taking a more careful look into politics. Being scholars who have a sense of the world around us has become more important than ever.

“Agency regulation, funding, it’s all decided by our branches of government,” says Ceri Weber, a 3rd year Ph.D. candidate in Cell Biology.

Weber, a budding “sci-pol” enthusiast and the general programming chair for the student group INSPIRE, feels passionately about getting scientists informed about policy.

So she organized this event for graduate scientists to talk with the deputy director of Duke Science & Society, Buz Waitzkin, who previously served as special counsel to President Bill Clinton, and now teaches science policy classes cross-listed between Duke’s Biomedical Science programs and the Law School.

Seated with food and drinks—the way to any grad student’s heart—we found ourselves settling in for an open discussion about the current administration and the impact its policies could have on science.

We covered a lot of ground in our 2-hour discussion, though there was plenty more we would love to continue learning.

We discussed: lobbying, executive orders, the balances of power, historical context, tradition, and civil actions, to name a few.

There were a lot of questions, and a lot of things we didn’t know.

Even things as simple as “what exactly is a regulation?” needed to be cleared up. We’ve got our own definition in a biological context, but regulation takes on a whole new meaning in a political one. It was neat having the chance to approach this topic from the place of a beginner.

We were floored by some of the things we learned, and puzzled by others. Importantly, we found some interesting places of kinship between science and policy.

When we discussed the Congressional Review Act, which impacts regulations—the main way science policy is implemented—we learned there is ambiguity in law just like there is in science.

One area on all of our minds was how we fit into the picture. Where can our efforts and knowledge as scientists and students can make a difference?

I was shocked to learn of the lack of scientists in government: only five ever in Congress, and three in the Cabinet.

But luckily, there is space for us as science advisors in different affiliations with the government. There are even Duke graduate students working on a grant to develop science policy fellowships in the NC state legislature.

At the end of the night, we were all eager to learn more and encouraged to participate in politics in the ways that we can. We want to be well-versed in policy and take on an active role to bring about change in our communities and beyond.

Hopefully, as the years go on, we’ll have more opportunities to deepen our knowledge outside of science in the world around us. Hopefully, we’ll have more scientists who dare to step out of the lab.

Guest Post by Graduate Student Ariana Eily

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

 

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

bagnatselfie

 

 

 

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