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Category: Biology Page 29 of 32

Science Under the Stars!

By Pranali Dalvi

The 8th annual Science under the Stars, held in the lower lobby of the French Family Science Center, brought together several Duke departments, research groups, and organizations. Kids of all ages were busy participating in hands-on science activities.

Bioluminescence demo by Dr. Hendricks

 

 

 

Lab administrator Dr. Diane Hendricks had a station to illuminate the bioluminescent properties of Pyrocystis fusiformis, a marine dinoflagellate. Dinoflagellates bioluminesce when their cell wall is exposed to sheer stress, which triggers the light response. When asked why dinoflagellates glow, some kids hypothesized that dinoflagellates glow to look larger and more threatening so they can ward off predators. Scientists mistakenly thought so for a while, too. However, scientists now favor the burglar alarm hypothesis, based on the idea that the enemy of my enemy is my friend.

“Rather than trying to scare away the predators, they are actually attracting the predators of their predators,” Dr. Hendricks explained. Because the color blue is most easily seen in the ocean, many sea creatures bioluminesce blue. As a memento of Dr. Hendricks’s demo, kids were able to take home glowsticks of various colors!

The physics department showed students how to make Oobleck. Oobleck is a mixture of 2 parts corn starch and 1 part water. It displays shear thickening behavior, meaning that its viscosity – or resistance to flow – increases with shear rate. When the shear rate is low, the corn starch grains can easily move past one another and oobleck flows easily. However, under high shear stress, the corn starch grains pack tightly together and prevent the flow of grains past one another.

The process of preparing oobleck

Oobleck is an example of a non-Newtonian fluid. Non-Newtonian fluids are those whose resistance to flow changes according to the force that is applied to the fluid. One application of non-Newtonian fluids is in the soles of running shoes. The sheer thickening fluid hardens in response to the forces exerted during running or walking.

A favorite stop for the kids was CSI Durham presented by the Department of Evolutionary Anthropology and Anatomy. Students were required to perform cranial, pelvic, and femoral assessments to identify who the “missing victim” was. The skull and pelvis have distinct features in males versus females, and the femoral head and length diameter predict stature pretty accurately.

The event was sponsored by the Chemistry Department and organized by Dr. Kenneth Lyle.

Even ferns get Gaga

by Ashley Mooney

Biology professor Kathleen Pryer discussed the sex lives of ferns with a group of students Monday in the Center for LGBT Life.

“We’re trying to develop a new lifecycle (of ferns) that we hope textbooks will pick up,” Pryer said. “There are a range of ways that ferns have sex and each of these has is own evolutionary consequences and genetic outcomes.”

At the lunchtime lecture, Pryer also revealed her lab’s newly discovered fern species, Gaga germanotta, named after pop star Lady Gaga.

By naming a species after somebody outside of the world of scientific research, Pryer said she wanted to give Lady Gaga a namesake that will recall her activism efforts.

“The work that she’s done, the money that she’s put behind the Born This Way foundation, I think is incredible,” Pryer said. “She’s a real champion for justice and equality, and I wanted to do this so that she would have a scientific namesake—something that will last forever long after she’s gone.”

Lady Gaga also bears some likeness to a fern gametophyte, which is a fern early in its developmental cycle. At the 2010 Grammys, Lady Gaga wore a costume that strongly resembles a gametophyte, Pryer said.

The new species is part of a genus containing 19 species that were originally listed as cheilanthes. True cheilanthes—ones that have kept their original designation—are South American ferns that are nearly indistinguishable from Gaga ferns in appearance. Their differences, she said, are in their DNA.

“When we line up all our sequence data [of the Gaga ferns]… in a particular gene there is a string of GAGA,” she said. “The closest relatives of the genus Gaga doesn’t have that synapomorphy.”

Flowering plants—the most diverse types of plants on the planet with approximately 350,000 species—reproduce using seeds. Ferns on the other hand reproduce through spores contained on the undersides of their leaves.

Pryer noted that many people do not understand the vast diversity of ferns. There are about 12,000 species, including the typical forest ferns, aquatic ferns, desert ones and ferns that are the size of trees.  Pryer’s main focus has been on desert ferns—most of which appear similar but have different DNA patterns.

Beyond the variation in appearance of fern species, Pryer said the plants have multiple mating strategies, even though textbooks usually only teach one form.

Pryer describing the fern lifecycle often depicted in textbooks. Credit: Ashley Mooney.

One of the lifecycles they’re investivating involves a bisexual gametophyte, which is usually the first gametophyte in a population to mature. It forms a notch where it produces archegonia while antheridia develop on the outside. Most ferns have archegonium—the female component where eggs are located—and antheridia, which contain sperm. The gametophyte emits a pheromone that signals to all nearby developing gametophytes that they should become male.

Pryer said the diversity she found in ferns is only one type of sexual diversity in the world, and she hopes that a common interest in such differences will connect her field with the general population.

“We live in this world and we’re all interested in diversity in many different ways,” she said. “This makes a connection between what [scientists] do and human diversity and it also makes people who are Gaga fans say, ‘hey, what’s up with these botanists.’ I’m hoping that we can engage the two communities. When people talk about interdisciplinary work, I’m taking it to ‘the edge of glory.’”

YouTube Video about the naming: 19 Species of Ferns Named for Lady Gaga

Duke Today coverage: http://today.duke.edu/2012/10/gagafern

 

Student Cameron Kim, Working to Reprogram Cells

By Nonie Arora

Meet Cameron Kim – a Pratt Engineering student working on synthetic biology who also officiates for the Duke Quidditch team. Originally from Brandon, Florida, Cameron became interested in molecular biology and engineering in high school.

Kim Observing His DNA Gel Credit: Cameron Kim

“I see most people identify biomedical engineering as biomechanics, neural engineering, and electrophysiology,” he says, “but there’s really this other side growing quicker and quicker, which is using the tools of molecular biology to control how we as humans function and interact with the environment.”

In Dr. Charles Gersbach’s lab, he has been working to create artificial transcription factors. Being able to control gene expression through transcriptional factors is vital to modulate cell behavior and human functions, Kim says.

Kim drew an analogy between a transcription factor and a light switch dimmer, saying that transcription factors allow for a range when turning on and off specific genes. He says that artificial transcription factors would allow him to influence a cell’s own genome without having to add extra copies of a gene. The goal is to develop a tool to reprogram cells that his lab can use to study muscle development and to hopefully repair muscles. His lab is looking at different ways to develop therapies for Duchenne muscular dystrophy.

Kim thinks that engineering design principles that he has learned through his Pratt coursework are really important to his project. “When I explain my research to a lot of people, they think I’m just doing molecular biology,” he says, “but by knowing the parts and understanding my materials, I can design biological molecules and tools do what I want them to do.” While we may traditionally associate engineers observing factors like the terrain or landscape to build a bridge, he looks at factors like energy barriers and cell functions to apply design principles to molecular biology.

Kim Presenting at the Howard Hughes Research Symposium Credit: Cameron Kim

Research is full of challenges, and Kim’s projects have been no exception. He says it has been challenging to develop his tool. While it looks great in one test, it does not work with another one. He is still investigating whether he should be looking for other factors to control or whether the challenges are due to biological limits.

When asked what advice he would give to other undergrads excited about delving into research, Kim said to recognize that “you’re not going to know everything and even brightest minds in the field don’t know everything,” and to also “find out more about whatever you’re interested and take advantage of wide base of knowledge around you.”

His project initially came out of the Howard Hughes Research Fellows Program, which he encourages first-year students to consider. Kim says, “An immersion program in research can be a just as exciting new environment as an immersion language program in another country.”

After Duke, Kim hopes to pursue medical research. He wants to ask questions like: “How can I bridge the gap from bench to bedside? What tools can I develop to reach a clinical applications?” He feels lucky to have been mentored by excellent scientists and would like to do the same for others in the future.

Packing for Proteins

This artist's rendering shows a ribbon diagram of the protein T4 phage lysozyme. Image courtesy of Ohio State.

By Ashley Yeager

If you ask vacationers about packing, they’ll probably tell you about over-stuffed suitcases and inflatable beach toys. But if you ask Yale physicist Corey O’Hern, he’ll tell you packing is about pockets, proteins and geometry.

“You may not believe it or may not have heard about it, but I’m going to argue that just geometry is important for understanding protein structure,” and “that makes protein structure look like a packing problem,” O’Hern said at a Sept. 26 physics colloquium. The protein packing problem and solving it could have implications for drug design.

O’Hern first learned about packing problems in physics as an undergraduate at Duke in the early 1990s. Working with Duke physicist Bob Behringer, he tried to explain how corn and coffee beans get jammed in their dispensers. O’Hern continued this type of work as a graduate student at the University of Pennsylvania and then earned a faculty post as a theorist in Yale’s engineering and applied science department.

“I didn’t believe in fate until I went to Yale and learned about Fred Richards. Now I do,” O’Hern said, explaining that the Yale biophysicist was interested in the structure of proteins and the “interior packing,” or arrangement, of their amino acids. O’Hern said Richards thought of proteins as a jigsaw puzzle and tried to figure out how the weird pieces fit together.

To better understand a protein’s geometry, Richards would trace water molecules over the surface of its amino acids. He thought that the inner folds of proteins were “well-packed” because the strong attractions of the atoms in those areas. “I don’t completely believe Richards’ results,” but the work “made me feel destined to get in on the research,” O’Hern said.

He now looks at how tightly animo acid molecules fit together in certain regions of the protein, T4 phage lysozyme. To study its packing properties, O’Hern simulates the energy and entropy in the pockets, or cavities, of the lysozyme’s inner folds. His early results suggest that the most stable forms of the protein have the most entropy, or randomness, among the amino acids in the pockets.

That way of packing is definitely counter-intuitive, O’Hern said. He’s still working on how the results are possible and, in a broader sense, how they could affect packing and folding of drugs to improve their effectiveness.

Lemurs Most Threatened Mammals on the Planet

By Karl Leif Bates

Things seem to be going from bad to worse for the lemurs of Madagascar.

A report issued two weeks ago by a working group in Antananarivo, Madagascar’s capital, concludes that these prosimian primate cousins of ours are THE most endangered mammals on the planet with 91 percent of all lemurs on the Red List of threatened status.

Google Earth image

The 5,000-acre Betampona Nature Reserve in the eastern rainforest region is the smallest and oldest of Madagascar's officially protected areas. It looks like a green island surrounded by damaged forests and subsistence farming. The reserve is jointly managed by the Madagascar Fauna Group, of which the Duke Lemur Center is a founding partner, and was the site of first reintroduction of lemurs which had been bred in captivity at DLC.

In a poor and poorly governed country, humans are steadily chewing away at lemur habitat and at the lemurs themselves.

One species, the northern sportive lemur, is down to just 18 individuals on a tiny speck of habitat at the extreme northern end of the island. There are none in captivity.

“When these species disappear from Madagascar, they are lost forever,” Lemur Center Director Anne Yoder said. Captive breeding programs, like the one at the Duke Lemur Center, are a poor substitute for the protection lemurs really need.

The warning is unfortunately all too familiar to the faculty, staff and volunteers of the DLC, and it casts their work in conservation, education and research as even more critical.

In addition to its crucial work in Durham, DLC has been working on the ground in Madagascar for more than 20 years to preserve habitat and build a corps of conservation-minded citizens. Post-doctoral researcher Erik Patel  participated in the Antananarivo workshop and reported on the meeting last week.

Learn More:

Anne Yoder and Charlie Welch on Duke Lemur Center blog.

Russ Mittermeier, chairman of the Madagascar Primate Specialist Group and President of Conservation International in the Huffington Post.

Infographic from Duke Lemur Center

The Duke Lemur Center's breeding population becomes ever more important as wild lemurs disappear.

Hands-On Lab Experience Helps Student Set Goals

Story and Photos by Gabriel Aikens, NCCU Summer intern

The bubbling of reactions and the sight of stern-looking, goggle-wearing scientists with lab coats on the verge of discovering the next big cure is what goes on in Duke’s biology labs, right? No, not at all.

Besides seeing lab coats and a variety of beakers, one might be surprised to also find people in hoodies or khaki shorts and sneakers listening to their favorite songs and joking with each other.

Morgan Morrison has been working with the plant Arabidopsis thaliana in the lab of Xinnian Dong in Duke Biology.

Don’t be fooled by the relaxed environment however. These graduate and undergraduate students are  hard at work, including intern Morgan Morrison, a North Carolina Central University senior from Charlotte interning at Duke’s Institute of Genome Sciences & Policy (IGSP) Summer Fellowship Program.  Morrison and her colleagues spend their days transferring samples into geno-grinders (machines that grind plant tissue), carefully extracting chemicals with pipettes, and handling subzero nitrogen which sizzles and hisses  loudly as samples are lowered into it..

Morrison was accepted into other summer internships but chose Duke’s because of her interest in genomics and her attraction to the university.

This internship is offered to a select few students from around the nation to take on various projects. Morrison is undergoing two projects, observing plant-microbe interactions and cloning plants to study their transcription of genes.

“I’m observing the microbes (microscopic organisms) to find useful plant-derived compounds for combatting infections,” says Morrison. “I’m cloning plants to see how resistant they are to a given disease.”

Morrison is doing molecular cloning, which is different from making genetically identical copies like cloning in the movies. Molecular cloning is the engineering of transgenic plants, which are plants containing genes transferred from another species. The plant she works with is  Arabidopsis, a small flowering plant that’s a member of the mustard family.

To perform molecular cloning, she first identifies a protein of interest (POI) that might confer resistance to the Arabidopsis and then through a series of steps inserts the DNA coding sequence  of that POI into the DNA of Arabidopsis. Then she conducts experiments test whether the new protein conferred resistance.

Morrison developed a fascination with scientific research after an AP Biology II course where she worked with Drosophila (fruit flies).

Learning lab skills will help Morgan decide on a career path.

“At the time, I didn’t know which field of science would be best for me, but I especially wanted to be involved in chemistry.”

She’s pursuing a B.S. in Pharmaceutical Science at NC Central University with a concentration in Chemistry, followed by going into a Ph.D program. “Right now, my purpose here at this Duke internship is to determine if I want to do research, and if so, what I’d like to research,” she says.

So far, she finds the internship beneficial and plans to combine her new knowledge with her future plans, which includes going to pharmacy school or becoming a patent lawyer. “As a scientist, I feel that it is good to be well-rounded in every aspect of science, via biology, chemistry, or desk work because basic skills and information are always relevant wherever you go,” she says.

Congo native Musoki Mwimba is mentoring Morrison during the internship. He’s an N.C Central University alumnus and graduate student in Duke’s Department of Biology. His interest is pharmaceutical science and part of his training and pursuit of a doctorate is mentoring newcomers. He says this requirement helps “improve his communication skills with others.”

“Though I like working by myself, working with the mentees is great because I’m learning from them,” Mwimba says. “As I see what their aspirations are, I try to help them reach them.”

As she works alongside Mwimba, Morrison wants to absorb as much as she can from this experience. “I hope to gain better understanding of what people do in this lab and master the projects I’m working on,” she says. “I’m happy I chose to come here.”

Trinity Junior in Phoenix for Summer, Doing Real Research

By: Nonie Arora

Sonya Jooma, Trinity '14, provided by Steve Yozwiak

Rising Trinity Junior Sonya Jooma is in Phoenix, Arizona this summer working at the Translational Genomics Research Institute (TGen) as an intern in the TGen-Duke Biomedical Futures Program. This is the first year TGen and Duke have partnered to offer a funded biomedical research internship exclusively for Duke students. Jooma and a second Duke undergrad, Geoff Houtz, are the first two students to participate in this pilot program.

The TGen-Duke Biomedical Futures Program joins the growing list of Duke programs for students excited about genomics, such as the Genome FOCUS program and the Institute for Genome Sciences & Policy Summer Fellowship. In fact, the Genome FOCUS spurred Jooma’s enthusiasm for genomics research. Last year, she worked in the John Willis lab researching plant genetics as part of the Howard Hughes Research Fellows Program.

Her project at TGen, in the lab of Dr. Lisa Baumbach-Reardon, centers on the genetic basis of Infantile Spinal Muscular Atrophy. This disease causes muscle weakness and abnormality at birth. Afflicted children often die before their second birthday. According to Jooma, there are cases of this disease for which the genetic basis is unknown. As part of her lab’s exome sequencing project, they hope to identify mutations involved in the disease.

Jooma says her TGen experience has been great so far. She finds it similar to working in a research lab at Duke because of the similar lab hierarchy. However, she appreciates that TGen has overarching specific goals that focus on translating discoveries to clinical diagnostics and therapies. Jooma also looks forward to attending professional development workshops and presenting her work at TGen’s annual intern research symposium in July.

Ultimately, Jooma’s experience at TGen will be one of many exciting research projects: she hopes to pursue a career in biology research.

Sleuths Take Over Science This Summer

Story and Photos by Gabriel Aikens, NCCU Summer Intern

Science Sleuths Lance Cook, Alex St. Bernard, and staff member Emily Milligan work together on dissecting a cow's ankle, called the fetlock.

While many teens spend their summer days playing Xbox and watching cartoons, some eighth and ninth graders are constructing catapults and dissecting cow knuckles as part of Summer Science Sleuths at Duke, a two-week program that exposes kids from across the country to science in fun and creative ways.

On a recent Thursday morning inside the Biological Sciences Building, the kids dissected cow fetlocks, which are similar to the upper knuckle joints in a human hand. There were looks of amazement, curiosity, and disgust as Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure with the fetlock.

“Feel free to take one home to barbeque,” Aguiar joked. Some of the kids weakly smiled, but overcame their queasy feelings the more they operated on the fetlock with their scalpels.

“It was cool,” said ninth grader Samantha Goetz from Cream Ridge, New Jersey. “The activity is similar to what I want to do when I get older, like surgery and such.”

Dean Aguiar, program director at The Hartwell Foundation, demonstrated proper procedure on the fetlock to sleuth Natalia LeMay.

The point of the dissection was to have a better understanding of joint movement, as well as identify bone cartilage, ligaments, and synovial fluid, which is a lubricating liquid inside the joint that provides nutrients to joint tissues.

On other days during the two-week camp, the Sleuths created solar ovens, built rafts, and visited the Videri Chocolate Factory in Raleigh to learn how chocolate is made. The kids were housed in dorms at Duke and had picnics and cookouts on campus, as well as dinner at the Durham Bulls Athletic Park.

To be considered for selection to participate in Summer Science Sleuths at Duke, campers completed a survey on attitudes toward science, had a parent submit an application and had a teacher complete the recommendation form.

“This is the second year of the Summer Science Sleuths at Duke program,” said Chris Adamcyzk, executive director of the Duke Center for Science Education and creator of the program. “We want to make science fun for the kids,” she says. “ We carefully design the curriculum so that they can be introduced to a breadth of science, while making connections to their real world. Although they do experiments in the lab, they also interview scientists and take field trips to connect interesting science with everyday life.”

Fetlocks are similar to human knuckles, but a whole lot larger.

Making science fun for the kids is also the goal of Frederick Dombrose, President of The Hartwell Foundation, which funds the program.

“This wasn’t designed for kids who were at the top of their science class,” he said. “We created this for bright kids who have an interest in science so we can inspire them. This is an opportunity that most of them would’ve never been exposed to, so we want them to enjoy themselves and take advantage of this.”

CSI-House teams could make better medical diagnoses

By Ashley Yeager

Comparing a child's DNA to his parents' could help with identification of hard-to-diagnose genetic diseases. Credit: Henrik Jonsson/iStockphoto

Dr. Gregory House, star of House, M.D., and the lab techs on CSI never fail at their jobs. But that’s Hollywood. In real life, diagnosing illnesses and sequencing DNA isn’t so straightforward. It doesn’t always lead to a happy ending either, especially for children who are sick but can’t be diagnosed, even by gifted, real-life doctors.

That’s exactly why geneticist David Goldstein has teamed with pediatrician Vandana Shashi to combine a little House and CSI to identify apparent genetic diseases and quickly end some families’ diagnostic odysseys.

So far, the team has provided likely genetic diagnoses in six of 12 children it has worked with, said Goldstein at a Cardiovascular Research Center Seminar Series talk on June 27.

The children were referred to Shashi for a pilot study where she would record their symptoms, or phenotypic behavior, much like House. Then, Goldstein and his team at the Center for Human Genome Variation collected DNA samples from the children and both of their biological parents.

Using next-generation genetic sequencers, as well as traditional DNA scanners, Goldstein and his team looked for genetic variations between the children’s and parents’ complete genome. Like looking at DNA to identify a criminal, Goldstein and his genetics team are scouring the sequences for genetic fingerprints of the diseases disrupting the children’s lives.

Once variations were identified, the entire team looked for known diseases with similar gene mutations and symptoms. Goldstein explained that the study not only pinpointed the undiagnosed congenital diseases in some patients but also presented new genes that could also be linked to the illnesses. The study’s success has led to the creation of the Genome Sequencing Clinic.

The clinic will begin to help the families of the 50,000 children (out of the four million) born each year in the US with difficult-to-diagnose genetic diseases. These types of studies will likely be the “earliest drivers for large-scale genetic sequencing,” Goldstein said.

But, he cautioned, “there’s a whole lot of junk,” or variation, in DNA. Every genome has the narrative potential for devastating diseases, and that means that House-CSI teams, like Shashi and Goldstein’s, need to be extremely careful when making diagnoses, especially if the results will influence treatment, he said.

Citation: Clinical application of exome sequencing in undiagnosed genetic conditions. Need, A. et. al. 2012. J. Med Genet. 49:6 353-361. doi:10.1136/jmedgenet-2012-100819

Culture shapes bird communication, too

SingingSwampSparrow_RL

A male swamp sparrow switches branches as he sings.Credit: Robert Lachlan, Duke.

Guest post by: Eugene Morton, York University

Bird song is one of the most fascinating and complex examples of animal communication, and the quest to understand its evolution and function has fueled the careers of many behavioral ecologists, psychologists and neurophysiologists.

Recently, scientists in the Departments of Biology and Neurobiology at Duke University have made incredible advances in this field. In “Songbirds learn songs least degraded by environmental transmission,” Susan Peters, Elizabeth P. Derryberry, and Stephen Nowicki show how a youngster chooses which songs to learn from the huge number they may be exposed to during their learning period.

Their simple but elegant experiment offered the birds a choice to learn songs that contained echoes versus no echoes and the birds chose to learn only those with no echoes. The rejected songs had been transmitted and re-recorded through 25 meters of habitat, and picked up reverberations and a few other changes along the way, but they were equally loud to the learned versions.

This says a great deal about how birds put to use their extraordinary ability to hear small time differences. What’s so great about hearing echoes?

Compared to our ability, where we hear only echoes from distant large objects, birds can hear echoes from tree trunks and vegetation. They use this ability to learn songs that transmit with the least amount of echoes or, more generally, degradation.

In this way, the birds themselves reject songs less well suited to their environment; cultural selection. As the birds were housed together while learning the songs it is not surprising that they came up with two that were never presented to them; they must also have learned from each other.

SingingSwampSparrow

A male swamp sparrows sings to his neighbors.Credit: Robert Lachlan, Duke.

Why is it important to understand the criteria birds use to choose songs to learn? I would answer because then we can understand how cultural and natural selection interact. Cultural selection favors birds that learn songs that will propagate for the greatest distance and remain undegraded.

These songs must function better than a random selection of songs would. The function must related to how the listeners of these songs are affected by them: are they more efficiently repelled if they are competitors and attracted if they are potential mates? Natural selection will favor the birds whose songs do this the best.

And it turns out that this interplay is helping birds cope with increasingly human-influenced environments. The traffic noise we generate can favor learning songs that are higher or lower in than the frequency of this noise. This ability is based upon the same cultural choice of songs described here for swamp sparrows.

It is hoped that this excellent study will stimulate others to assess the role of learning in adapting songs, not only to habitats, but to the social functions songs have. Songs function over distance and this study describes how song learning can strengthen this role and the importance of distance in song evolution.

Eugene S. Morton
Hemlock Hill Field Station, Pennsylvania
York University, Ontario, Canada
mortone@si.edu

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