Category: Tools and Techniques

Helium: An Abundant History and a Shortage Threatening Scientific Tools

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Most of us know helium as the gas that makes balloons float, but the second element on the periodic table does much more than that. Helium pressurizes the fuel tanks in rockets, helps test space suits for leaks, and is important in producing components of electronic devices. Magnetic resonance imaging (MRI) machines that take images of our internal organs can’t function without helium. And neither can nuclear magnetic resonance (NMR) spectrometers that researchers use to determine the structures of proteins—information that’s important in the development of medications and other uses.

A square showing helium’s abbreviation, atomic number, and atomic weight connected by lines to illustrations of a scuba diver, a car, and a person in an MRI machine. Helium’s many uses include helping deep sea divers breathe underwater, airbags in cars to inflate, and magnets in MRI scanners to work properly. Credit: Compound Interest.
CC BY-NC-ND 4.0 Link to external web site. Click to enlarge
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Scientist Interview: Exploring the Promise of RNA Switches with Christina Dawn Smolke

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Whether animals are looking for food or mates, or avoiding pathogens and predators, they rely on biosensors—molecules that allow them to sense and respond to their environments. Christina Dawn Smolke, Ph.D. Link to external web site, a professor of bioengineering at Stanford University in California, focuses her research on creating new kinds of biosensors to receive, process, and transmit molecular information. Her lab has built RNA molecules, or switches, that can alter gene expression based on biochemical changes they detect.

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The Science of Infectious Disease Modeling

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What Is Computer Modeling and How Does It Work?

Recent news headlines are awash in references to “modeling the spread” and “flattening the curve.” You may have wondered what exactly this means and how it applies to the COVID-19 pandemic. Infectious disease modeling is part of the larger field of computer modeling. This type of research uses computers to simulate and study the behavior of complex systems using mathematics, physics, and computer science. Each model contains many variables that characterize the system being studied. Simulation is done by adjusting each of the variables, alone or in combination, to see how the changes affect the outcomes. Computer modeling is used in a wide array of applications, from weather forecasting, airplane flight simulation, and drug development to infectious disease spread and containment.

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Cool Images: The Hidden Beauty Inside Plants

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Spring brings with it a wide array of beautiful flowers, but the interior structures of plants can be just as stunning. Using powerful microscopes, researchers can peek into the many molecular bits and pieces that make up plants. Check out these cool plant images from our Image and Video Gallery that NIGMS-funded scientists created while doing their research.

Several round structures that are yellow at the center and pink and purple around the edges and have honeycomb-like interiors. Credit: Arun Sampathkumar and Elliot Meyerowitz, California Institute of Technology.

In plants and animals, stem cells can transform into a variety of different cell types. The stem cells at the growing tip of this Arabidopsis plant will soon become flowers. Cellular and molecular biologists frequently study Arabidopsis because it grows rapidly (its entire life cycle is only 6 weeks), produces lots of seeds, and has a genome that’s easy to manipulate.

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Crowdsourcing Science: Using Competition to Drive Creativity

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Six student researchers sitting around a table and collaborating on a project. Credit: iStock.

Historically, crowdsourcing has played an important role in certain fields of scientific research. Wildlife biologists often rely on members of the public to monitor animal populations. Using backyard telescopes, amateur astronomers provide images and measurements that lead to important discoveries about the universe. And many meteorologists use data collected by citizen scientists to study weather conditions and patterns.

Now, thanks largely to advances in computing, researchers in computational biology and data science are harnessing the power of the masses and making discoveries that provide valuable insights into human health.

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Advances in 3D Printing of Replacement Tissue

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A bioprint of the small air sac in the lungs with red blood cells moving through a vessel network supplying oxygen to living cells. Credit: Rice University. A bioprint of the small air sac in the lungs with red blood cells moving through a vessel network supplying oxygen to living cells. Credit: Rice University.

A team of bioengineers, funded in part by NIGMS, has devised a way to use 3D bioprinting technology to construct the small air sacs in the lungs and intricate blood vessels. Continue reading “Advances in 3D Printing of Replacement Tissue”

Interview With a Scientist – Rommie Amaro: Computational and Theoretical Model Builder

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Many researchers who search for anti-cancer drugs have labs filled with chemicals and tissue samples. Not Rommie Amaro. Her work uses computers to analyze the shape and behavior of a protein called p53. Defective versions of p53 are associated with more human cancers than any other malfunctioning protein.

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Teens Explore Science and Health through Game Design

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Educators often struggle to teach teens about sexual and reproductive health. Hexacago Health Academy (HHA) Link to external web site, an education program from the University of Chicago, leverages the fun activity of gameplay to impart these lessons to young people from Chicago’s South Side community. Funded by the Student Education Partnership Award (SEPA), part of the National Institute of General Medical Sciences (NIGMS), in 2015, HHA assists teachers in their goal of helping teen students gain awareness and control over their health and also learn about careers in STEM Link to external web site and health fields.

Woman in a black buisness suit with arms crossed standing against a wall and smiling
Melissa Gilliam, founder of Ci3. Credit: Anna Knott, Chicago Magazine.

Genesis of HHA

HHA was cofounded by Melissa Gilliam Link to external web site, a University of Chicago professor of Obstetrics/Gynecology and Pediatrics and founder of the Center for Interdisciplinary Inquiry & Innovation in Sexual and Reproductive Health (Ci3) Link to external web site. During a 2013 summer program with high school students, Gilliam and Patrick Jagoda Link to external web site, associate professor of English and Cinema & Media Studies, and cofounder of Ci3’s Game Changer Chicago Design Lab Link to external web site, introduced the students to their STEM-based alternate reality game called The Source Link to external web site, in which a young woman crowdsources player help to solve a mystery that her father has created for her.

From their experience with The Source, Gilliam and Jagoda quickly learned that students not only wanted to play games but to design them too. What followed was the Game Changer Lab’s creation of the Hexacago game board, as well as the launch of HHA, a SEPA-funded project that the lab oversees.

Hexacago Game Board

At the core of HHA is the Hexacago game board Link to external web site, which displays the city of Chicago, along with Lake Michigan, a train line running through the city, and neighborhoods gridded into a hexagonal pattern.

HHA students not only play games designed from the Hexacago board template, but also design their own games from it that are intended to inspire behavior change in health-related situations and improve academic performance.

High school students seated at a table with a glossy, laminate test model of the Hexacago game and game pieces on top of it
Credit: Ci3 at the University of Chicago.

In this way, HHA is much more than just game design and play. “Students have no idea that what they’re doing is learning. In their minds, they’re really focused on designing games,” says Gilliam. “That’s the idea behind Hexacago Health Academy: helping people acquire deep knowledge of science and health issues by putting on the hat of a game designer.” Moreover, through the process of gameplay and design, students practice all the rich skills that result from teamwork, including collaborative learning, leadership, and communication.

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Computational Geneticist Discusses Genetics of Storytelling at Sundance Film Festival

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About 10 years ago, University of Utah geneticist Mark Yandell developed a software platform called VAAST (Variant Annotation, Analysis & Search Tool) to identify rare genes. VAAST, which was funded by NHGRI, was instrumental in pinpointing the genetic cause of a mystery disease that killed four boys across two generations in an Ogden, UT family.

NIGMS has been supporting Yandell’s creation of the next generation of his software, called VAAST 2, for the past few years. The new version incorporates models of how genetic sequences are conserved among different species to improve accuracy with which benign genetic sequences can be differentiated from disease-causing variations. These improvements can help identify novel disease-causing genes responsible for both rare and common diseases.

Yandell and his colleagues in the Utah Genome Project recently took part in a panel at the Sundance Film Festival called the “Genetics of Storytelling” to discuss film’s ability to convey the power of science and medicine. Yandell told the audience his story about his efforts to use VAAST to trace the Ogden boys’ genetic variation back to their great-great-great-great-great grandmother.

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What Zombie Ants Are Teaching Us About Fungal Infections: Q & A with Entomologists David Hughes and Maridel Fredericksen

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I can still remember that giddy feeling I had seven years ago, when I first read about the “zombie ant.” The story was gruesome and fascinating, and it was everywhere. Even friends and family who aren’t so interested in science knew the basics: in a tropical forest somewhere there’s a fungus that infects an ant and somehow takes control of the ant’s brain, forcing it to leave its colony, crawl up a big leaf, bite down and wait for the sweet relief of death. A grotesque stalk then sprouts from the poor creature’s head, from which fungal spores rain down to infect a new batch of ants.

A fungal fruiting body erupts through the head of a carpenter ant infected by a parasitic fungus in Thailand. Credit: David Hughes, Penn State University.

The problem is, it doesn’t happen quite like that. David Hughes, the Penn State University entomologist who reported his extensive field observations of the fungus/ant interactions in BMC Ecology Exit icon, which caused much excitement back in 2011, has continued to study the fungus, Ophiocordyceps unliateralis, and its carpenter ant host, Camponotus leonardi.

In late 2017, Hughes and his colleagues published an article in PNAS Exit icon in which they used sophisticated microscopy and image-processing techniques to describe in great detail how the fungus invades various parts of the ant’s body including muscles in its legs and head.

Although Hughes’s earlier BMC Ecology paper showed fungus in the head of an ant, the new study reveals that the fungus never actually enters the brain.

To me, the new finding somehow made the fungus’ control over the ant even more baffling. What exactly was going on?

To find out, I spoke with Hughes and his graduate student Maridel Fredericksen.

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